Errors in running code in vignettes:
when running code in ‘gWidgets.Rnw’
  ...

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


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

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

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


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

Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gWidgetsRGtk2.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gWidgetstcltk.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/h5.Rcheck/00install.out’ for details.
installed size is 107.4Mb
  sub-directories of 1Mb or more:
    libs  106.3Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  5: stop("Cannot create a RasterLayer object from this file.")
  
  trying URL 'ftp://ftp.bafg.de/pub/REFERATE/GRDC/ltdata/africa.zip'
  ftp data connection made, file length 2726292 bytes
  ==================================================
  downloaded 2.6 MB
  
  testthat results ================================================================
  OK: 59 SKIPPED: 0 FAILED: 1
  1. Error: Test TRMM function (@test-TRMM.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: ‘RODBC’

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

    filter

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

    layout

Loading required package: viridis

---------------------
Welcome to heatmaply version 0.7.0
Type ?heatmaply for the main documentation.
The github page is: https://github.com/talgalili/heatmaply/

Suggestions and bug-reports can be submitted at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>

	To suppress this message use:  suppressPackageStartupMessages(library(heatmaply))
---------------------

Quitting from lines 83-85 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hgam.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘grplasso’ ‘lattice’ ‘rgl’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HierO.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘MASS’ ‘cubature’ ‘mvtnorm’ ‘numDeriv’ ‘quantmod’ ‘robustbase’
  ‘sandwich’ ‘timeDate’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        7.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/highriskzone.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HiPLARM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hiPOD.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hoardeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/homals.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HomoPolymer.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
File ‘hSDM/libs/hSDM.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: multiple methods tables found for ‘colMeans’
  Warning: multiple methods tables found for ‘colSums’
  Warning: multiple methods tables found for ‘rowMeans’
  Warning: multiple methods tables found for ‘rowSums’
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/humarray.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HUM.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyCalculate3D: no visible global function definition for ‘persp’
CalculateHUM_Ex: no visible global function definition for ‘combn’
CalculateHUM_Plot: no visible global function definition for ‘plot’
CalculateHUM_Plot: no visible global function definition for ‘polygon’
CalculateHUM_Plot: no visible global function definition for ‘text’
CalculateHUM_Plot: no visible global function definition for ‘points’
CalculateHUM_Plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    doc    1.1Mb
    libs   4.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'unknown' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 162-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hypervolume.Rcheck/00install.out’ for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/iBUGS.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.1Mb
    libs   7.8Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/iClick.Rcheck/00install.out’ for details.
Running examples in ‘iClick-Ex.R’ failed
The error most likely occurred in:

> ### Name: iClick.ARIMA
> ### Title: iClick GUI for ARIMA
> ### Aliases: iClick.ARIMA
> 
> ### ** Examples
> 
> 
> ##External data
> #data("returnsDaily24")
> #y=returnsDaily24[,c(1,5)]
> 
> ## Simulation data
> dat=rnorm(100,5,1)
> y=ts(dat, start = c(1970, 1), frequency = 12)
> 
> iClick.ARIMA(y)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: iClick.ARIMA ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ICS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cf>
          O^^S<df>^^V?ԇ<bc><89><a4>ÄMCRhnbta<a0>d6Ƙ<94>^^Ekw<fe>]<eb><c2>tk\<c1><bf>Ѕ1q<c9>ưe^^VT^^S^^S<88>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...^S<df>^^V?ԇ<bc><89><a4>ÄMCRhnbta<a0>d6Ƙ<94>^^Ekw<fe>]<eb><c2>tk\<c1>
                                                  <bf>Ѕ1q<c9>ưe^^VT^^S^^S<88>^^S<a7><8d>A...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 <c3>^^PB\<be>
            |<f9>Ǐ^^_<86>a<80>H!D&<93>A7|^^Z<86>a<9a>&c<8c>1<b6><b9><b9>9::jYV&<93>i<e3>z^^O<e0>իWM-+++{{{<bd>X<eb>d^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 cB<88><ef><9e>^^W<c4><e3>Q<c6>^^L<c7><f9>O2^^Yk^^
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because US-Engineering-Weather-Map.Rmd appears to be an R Markdown v2 document.
Error in (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE,  : 
  there is no package called 'states2k'
Quitting from lines 24-109 (US-Engineering-Weather-Map.Rmd) 
Error: processing vignette 'US-Engineering-Weather-Map.Rmd' failed with diagnostics:
object 'states2k_map' not found
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ifa.Rcheck/00install.out’ for details.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  14.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ilc.Rcheck/00install.out’ for details.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.4Mb
    include   2.6Mb
    libs     13.2Mb
Packages suggested but not available for checking: ‘rsprng’ ‘Rmpi’
Missing link or links in documentation object 'ask.user.yn.question.Rd':
  ‘winDialog’

Missing link or links in documentation object 'check.for.updates.R.Rd':
  ‘winDialog’

Missing link or links in documentation object 'installr.Rd':
  ‘winDialog’

Missing link or links in documentation object 'os.manage.Rd':
  ‘winDialog’

Missing link or links in documentation object 'updateR.Rd':
  ‘winDialog’

See section 'Cross-references' in the 'Writing R Extensions' manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Running examples in ‘iqspr-Ex.R’ failed
The error most likely occurred in:

> ### Name: QSPRpred-class
> ### Title: QSPRpredictor class
> ### Aliases: QSPRpred QSPRpred-class
> 
> ### ** Examples
> 
> data(qspr.data)
> smis <- paste(qspr.data[,1])
> ty <- qspr.data[,c(2,5)]
> trainidx <- sample(1:nrow(qspr.data), 5000)
> testidx <- (1:nrow(qspr.data))[-trainidx][1:100]
> 
> data(qsprpred_EG_5k) 
> ## same as run => qsprpred_EG_5k <- 
> 
> #-----arguments
> #smis: SMILES string set (character vector) for training
> #y: property sets (matrix) for training  
> #v_ymin: minimum value of target properties
> #v_ymax: maximum value of target properties
> #v_descriptor: function transforming SMILES strings to feature matrix 
> #v_fpnames: character vectors indicating finger print used in the descriptor
> #w0: matrix representing prior mean of coeffients in linear regression model
> #V0_inv: matrix representing the prior variance of coeffients in linear regression model
> #a0: numeric value representing the location parameter in gamma prior 
> #b0: numeric value representing the shape parameter in gamma prior 
> #------
> 
> predictions <- qsprpred_EG_5k$qspr_predx(smis[testidx])  

get fingerprint graph from SMILES strings          
Error in .jcall("org/openscience/cdk/DefaultChemObjectBuilder", "Lorg/openscience/cdk/interfaces/IChemObjectBuilder;",  : 
  RcallMethod: cannot determine object class
Calls: <Anonymous> ... get.smiles.parser -> .get.chem.object.builder -> .jcall -> .External
Execution halted
Namespaces in Imports field not imported from:
  ‘coda’ ‘lattice’
  All declared Imports should be used.
Running examples in ‘IRATER-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
sh: admb: command not found
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
  input string 443 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 451 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 452 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 460 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'isocir.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<b6>m<cb><f6><81>^^?<c9>?<e5><cc>B^^H<<c4><ef><f0>؞p<b9><cb>~<a6>i~<f3><cd>7<bf><fc><f2><8b>i<9a><86>a\<bf>
                                                  ~]<d7>u<<b7>m<bb>P(<88>^^V<b2>٬a^^X<d8><df><f4><f4><f4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<fd><f6><db><fe><9b>xud^^Lݼy<b3>'a<d6>u]Q^^T<f9><a7>a^^X?<fd><f4><93><a2>(<f1>x\^^H
                                                  <f1><e5><97>_^<bb>vm~~~gg<e7><d7>_^^?<9d><9d><9d>5^^L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<e6>y<fe><fc>y2<99><f4></<99>L<86><a3>^^E^^L,<95>J<9f>^^?<fe><b9><e3>8<99>L<e6>,<c8><eb>^^W\p
                                                  <dd>^^[<90><d7><cf>8<96><e5>4MS<d7>u<c6><d8><c2><c2><c2><d8><d
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
l.19 ...	]<d7>^^AJ^^R<89>D<b3>ٔ<f3><ef><ef><ef>g<b3><d9>J<a5><92><cd>f^^AP8<e7><e5><b2>_(d\^^W
                                                  <97>})<f6>^^@<ca>)D<84>^^_<be><bf><f3><d3>O<8d>7ޘ<e6><fc>2...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.24 <9e>^^P<91>g}}
             ^^]<d8>^^_^^A<8d><88>^^TEY^^<ae><d5>j<e8>^^Z<db><dc><dc>l6<9b>2<b7>B
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 424 is invalid in this locale
2: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 425 is invalid in this locale
3: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 433 is invalid in this locale
4: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 434 is invalid in this locale
5: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 442 is invalid in this locale
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.1Mb
File ‘jointDiag/libs/jointDiag.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘jedi.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.
Namespaces in Imports field not imported from:
  ‘rgeos’ ‘sp’
  All declared Imports should be used.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         ".shp$"))), method = "local", what = "sp", stringsAsFactors = TRUE, encoding = "cp932")
  9: read_json(as.location(x), method, parse, what, ...)
  10: file_to_sp(x, ...)
  11: match.arg(fileext, c("shp", "kml", "geojson", "json"))
  12: stop(gettextf("'arg' should be one of %s", paste(dQuote(choices), collapse = ", ")), 
         domain = NA)
  
  testthat results ================================================================
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Error: Collect administration offices data (@test-spdf_jpn.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
Invalid MIT-MAGIC-COOKIE-1 keyStartKappa: 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.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Kernelheaping.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 238 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 244 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kernlab.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[G^^[^^?<ec>dc'U<a5>^^N-.u<ba><b2><bb>E<b8><88>e<a3>V^^P<b0>!<dd>^^F<ab><84>^ғo=<e4><a4><d0>C^^O=<e5>VBo<f9>^^C^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.17 ...<f7>}^^Lb<9a>f<9c>5<9f><b8>~<fd>zL<f2><d6><d6><d6>^^XcCCC+++^^_|<f0><c1><fa><fa>z6<9b>}
                                                  <f0><e0><c1><e8><e8><a8><e7>yO<9e><<f1><<8f><88><d2><e9><f4><da><da><da>ŋ^^W...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.17 ...O<9e><<f1><<8f><88><d2><e9><f4><da><da
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/KernSmoothIRT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kml3d.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kml.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kmlShape.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.4Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 100 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kst.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.17 b<84><bd><a5>?^^T<9a>[<c1><bf><a0>^^?Ls^<85><e2>^^_Ћ^^E<a5>$<87>6v<91>\B
                                               <a6><ea><90>[q<d9>M<e8>E^^R<bf><87>^^O>&<ab><8d>k<a2>&<b5><fb>9<88>;...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.22 ^^YIN<ac><a5>^^[\<8a>
                 sY<cc>Q<d7>'<db>a^^P^^Dggg<c9>d^^R<8a>M$^^R<f9>|<9e>u^^N<e3>D<8e><87><8d><9c>ե+_)U,^^Vi<94>^^VB5<98>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.22 ...<88>H<b7>L<a5>^^T<8b>^^A/m<8d><d0><ed>v<85>^^P<be><ef><f3>O^^W<8b>E6㩘<99>',<9a><ca>\<de>
     
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    doc            1.0Mb
    libs          10.3Mb
    testdata       1.9Mb
    vignettedata   2.0Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    dataset   1.4Mb
    include  11.7Mb
    libs      4.0Mb
File ‘leaps/libs/leaps.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
  input string 428 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 433 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'an_introduction_to_lifecontingencies_package.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Ol
           [E^^Z<ff><b0><9b><8d>_q<de><f3><90>n0i^^S<9b><d1>^^VXj^^RKO<da>C^^Q<b8>R}^^B<a9> V9<ad><c4>	<e5>Ω7đ^^^<b8>p<b4>8TB...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.15 ...<93><b6><f1><f8><bd><ba><c9>k<da><d8>{<f8>mF&<ff><9c><b4>	M<b2><fe>)zz^^?f<e6><cd><f7><e6><9b><ef><fb>}ߌ<f3>\<ab>
                                                  բ<a3>߳<ee><c0><fe><a2>+<de>aFW<bc>Ì<ae>x<87>^^Y]<f1>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...+<de>aFW<bc>Ì<ae>x<87>^^
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package which this enhances but not available for checking: ‘reactR’
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    doc        1.8Mb
    libs      18.6Mb
    testdata   1.5Mb
Error in re-building vignettes:
  ...
  input string 785 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'lmer.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Mh
           ^^TK^^P<ae><97>(q$<ee>؈!.L6^^L/($oYX^^Hx^^H<eb>!<a0>'o<de><<eb>ٓ^^A/<a2>O<f0>]ċ^^G<f5>^^]<84><e7>A...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

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

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

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.16 ...[<f8><f8>㏻~8<9d>NC^^\<cb>d2<ba><ae>^^SB><fd><f4>ӑ<91>^^Q!D&<93><f9>ꫯ<de>}
                                                  <f7><dd>vڙ<9d><9d><b5>,˲,<ce><f9><d7>_^^?=11^^Aa...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.23 ...<aa>mۚ<a6>I<bb>b<8c><fd><fa><eb><af><c8>e<99><aa><aa><c2>-If<c6>X4^^Z-<97>ˊ<a2>p<ce>UU<a5><94>z<bd>^
                                                  7<c9>^^O<91><a3><92><f3><f0><95><c1><be><bb><a7><bf><8c><e8>^^@^<a1>PP^...
! You can't use `\spacefactor' in math mode.
\@ ->\spacefactor 
                  \@m 
l.24 ...<aa><aa>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/longitudinalData.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/LOST.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyTOS2D: no visible global function definition for ‘medpolish’
countTextures: no visible global function definition for ‘medpolish’
plot.imageQT: no visible global function definition for ‘segments’
simTexture: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  medpolish rnorm segments
Consider adding
  importFrom("graphics", "segments")
  importFrom("stats", "medpolish", "rnorm")
to your NAMESPACE file.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Maeswrap.Rcheck/00install.out’ for details.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    doc    6.9Mb
    libs  15.0Mb
objc[22618]: Class GNotificationCenterDelegate is implemented in both /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/magick.Rcheck/magick/libs/magick.so and /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rsvg/libs/rsvg.so. One of the two will be used. Which one is undefined.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Error in re-building vignettes:
  ...
Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Warning in arrange_impl(.data, dots) :
  '.Random.seed' is not an integer vector but of type 'NULL', so ignored
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotcc924daff2c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotcc924daff2c.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot2004ddf08f6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot2004ddf08f6.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘MARSS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘MARSS:::is.diagonal’
  See the note in ?`:::` about the use of this operator.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   4.3Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  11.5Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.7Mb
File ‘medSTC/libs/medSTC.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘medstc/medstc.o’, ‘medstc/corpus.o’,
      ‘svmlight/svm_common.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘medstc/corpus.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:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mefa.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 <f0>F<b6>9<dc> <9d>N˗<b9>\N
                  <b6>?<<af><9c><a5>)^^EZ<f4>^^X<d2><e9>t*<95><9a><99><99><91>k<d2>u]<ae><fb><97>_~<f9><f0><c3>^^O
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 Ðmt]<c7><ca>._<be>\<ab>
                 <d5>^^Xc<8c><b1><a9><a9><a9>t:
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 ...^^L^^Yc<ba><ae><e3>^^Fs^^R<b3>w-g'S^^SӒN<a7>Og^^]OBG\^^O
                                                  <ba><ca><d9><c9>t^^Z<b8>^^G<82><a7>w<e9>ҥH$R<a9>T<e2><f1><f8>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.27 ...]<e6>^^D<cf><d9>lvhh<c8>u]<c8><c4>u<dd>۷o<ef><ec><ec><c4>b<b1>L&S<af><d7>^^]<c7><e9><ef><ef><c
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyworkspace_management : tellme: no visible global function definition
  for ‘file.edit’
workspace_management: no visible global function definition for
  ‘object.size’
Undefined global functions or variables:
  file.edit object.size
Consider adding
  importFrom("utils", "file.edit", "object.size")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MergeGUI.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.6Mb
Package required and available but unsuitable version: ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘hgu133plus2.db’ ‘hgu133a.db’ ‘hgu95av2.db’
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘doSMP’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MetSizeR.Rcheck/00install.out’ for details.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
    misc   1.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MFHD.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MicroStrategyR.Rcheck/00install.out’ for details.
File ‘MigClim/libs/MigClim.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’, ‘src_cell.o’, ‘validate.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’

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

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

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

> ### Name: slices3d
> ### Title: Interactive Image Slices of 3D or 4D Volume Data
> ### Aliases: slices3d
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   #Example 1: View of a mixture of three tri-variate normal densities
>   nmix3 <- function(x, y, z, m, s) {
+       0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) +
+       0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) +
+       0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s)
+   }
>   x<-seq(-2, 2, len=40)
>   g<-expand.grid(x = x, y = x, z = x)
>   v<-array(nmix3(g$x,g$y,g$z, .5,.5), c(40,40,40))
>   slices3d(vol1=v, main="View of a mixture of three tri-variate normals", col1=heat.colors(256))
Loading required package: tkrplot
Loading required package: tcltk
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Invalid MIT-MAGIC-COOKIE-1 keyWarning: loading Rplot failed
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: slices3d ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Package required but not available: ‘BRugs’

Package suggested but not available for checking: ‘mixAK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mlDNA.Rcheck/00install.out’ for details.
Running examples in ‘mlr-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotFilterValues
> ### Title: Plot filter values using ggplot2.
> ### Aliases: plotFilterValues
> 
> ### ** Examples
> 
> fv = generateFilterValuesData(iris.task, method = "chi.squared")
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: generateFilterValuesData ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Running the tests in ‘tests/run-base.R’ failed.
Last 13 lines of output:
  17: .jnew("weka/core/Attribute", attname[i])
  
  testthat results ================================================================
  OK: 2388 SKIPPED: 2 FAILED: 6
  1. Error: clustering performance (@test_base_clustering.R#16) 
  2. Error: clustering performance with missing clusters (@test_base_clustering.R#28) 
  3. Error: clustering resample (@test_base_clustering.R#42) 
  4. Error: clustering benchmark (@test_base_clustering.R#55) 
  5. Error: clustering tune (@test_base_clustering.R#72) 
  6. Error: check measure calculations (@test_base_measures.R#187) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
The following object is masked from 'package:mlt':

    coef<-

This is mgcv 1.8-16. For overview type 'help("mgcv-package")'.

Attaching package: 'mgcv'

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

    multinom


Re-fitting to get Hessian


Re-fitting to get Hessian


Re-fitting to get Hessian

Quitting from lines 2519-2527 (mlt.Rnw) 
Error: processing vignette 'mlt.Rnw' failed with diagnostics:
NAs are not allowed in subscripted assignments
Execution halted
Error in re-building vignettes:
  ...
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'modTempEff.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...2^^F<e2><f5>2^^F<e2><f5>2<9e>m񤔏<bd>TJ<f1><cd>t:<dd>V<ad><c3><e3><96>eI)q<ff><e0>S<b9>\<ce>
                                                  ^^?<93><ab>^^U<8b>E^^?5<a5>^^T^^Z<f1>w<e3><b1>x...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<a5>¯l^^S<d2><ff><e0><c1>^^V<b8>p<f0><92><db><d9><da>ڪxxR<b3><a8>ӹ<e7><dd><c9>	~^^RQ<b9>\<fe>
                                                  <ec><b3><cf><c0>7"<92>R~<f7><dd>w<df>|<f3><cd>G^^_}t<fd><fa>u<d3>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.18 <84>L<a7>Ӧi<82><a5>^^_~<f8><e1><b5>k<d7>r<b9><9c>a^^XB^^H"<ca>f<b3>^^W.\^^X
                                             ^^Y^^Y<d1>4
The control sequence at the end of the top line
of your error message w
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/monogeneaGM.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   6.6Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 872 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'moult.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          o<db>F^^V^^?<96>[<cb>,^^RSD<82><ae><e2>]F^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.18 ...<cd><cd>o<be><f9><a6><c7><d4><fd>s<a6><d5><d5><d5>Z<ad>vD<83>^^G^^O^^^<9c><df><e8>c<fe>(<de>^^[\^^Z
                                                  r<f1><c6><ef>ܹs<ac>^^N<b7>o߾|<f9>r.<97>^^[^^_...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.18 ..._<8f>F<a3><cb><cb>ˏ^^^=<92>eY^^P<84><c3><da>3Ʈ_<bf><9e><cd>f<af>_<bf><8e>[۶u]WUu}
                                                  }<bd>\.<a7>R)4VUUQ<94>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘mph/libs/mph.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘mph.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘mph.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  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Found the following significant warnings:
  Warning: Pointer at (1) in pointer assignment might outlive the pointer target
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mra.Rcheck/00install.out’ for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘org.Mm.eg.db’
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  
  4. check_translations() works (@test.R#73) - running msgfmt on file693cc0f0d2 failed
  
  5. check_translations() works (@test.R#73) - running msgfmt on file6934f027188 failed
  
  Failed -------------------------------------------------------------------------
  1. Failure: check_for_gettext() works (@test.R#4) ------------------------------
  check_for_gettext() isn't true.
  
  
  DONE ===========================================================================
  Error: Test failures
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/msir.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MSQC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/msr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mtk.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘MASS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyDesigner.sobol: no visible global function definition for ‘runif’
basicMonteCarlo: no visible global function definition for ‘runif’
lhs003: no visible global function definition for ‘runif’
plmm.mtk : GenereXplmm: no visible binding for global variable ‘poly’
plmm.mtk : calc.plm: no visible global function definition for ‘lm.fit’
plmm.mtk: no visible global function definition for ‘var’
plmm.mtk: no visible global function definition for ‘lm’
plmm.mtk: no visible global function definition for ‘formula’
plmm.mtk: no visible global function definition for ‘update’
plmm.mtk: no visible global function definition for ‘stepAIC’
plot.plmm: no visible global function definition for ‘par’
plot.plmm: no visible global function definition for ‘barplot’
plot.plmm: no visible global function definition for ‘segments’
plot.plmm: no visible global function definition for ‘abline’
plot.plmm: no visible global function definition for ‘title’
plot.plmm: no visible global function definition for ‘legend’
plot.regressionSI: no visible global function definition for ‘par’
plot.regressionSI: no visible global function definition for ‘title’
plot.regressionSI: no visible global function definition for ‘abline’
plot,mtkProcess: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline barplot dev.new formula legend lm lm.fit par poly runif
  segments stepAIC title update var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "par",
             "segments", "title")
  importFrom("stats", "formula", "lm", "lm.fit", "poly", "runif",
             "update", "var")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyNote: found 2 marked UTF-8 strings
Invalid MIT-MAGIC-COOKIE-1 keyNamespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Package suggested but not available for checking: ‘pgirmess’
Error in re-building vignettes:
  ...
  input string 414 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'multgee.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 "M\<cd>
         U[<a1>Ffa<89>^^]<ea><86>^^?!<a8>ˮ<ba>E<dd><f1>^^WT<ed><be>^^R<92>%<a4>f<c1><a2>^^Y<a9>1^^QT<89>^^Xն<d2>^^T<df><ca>Gc<dc>`L<89>O<...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ^^D^^B<cd>fSI|<f2>H^^?<<97>J<a5>X,<86>i<eb><f5><ba><ea>LD<b9>\n
                                      ||<9c>1<96><cd>fc<b1>^^X<b0><d0><d9>^!<a2><bd>8=<85>:<f5><b0><a6>}<e7>3wO<ff><df><e0><84>lx<cb>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.17 ...<cd>fc<b1>^^X<b0><d0><d9>^!<a2><bd>8=<85>:<f5><b0><a6>}
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    examples   1.8Mb
    libs       2.7Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
Error in re-building vignettes:
  ...
Quitting from lines 218-223 (TwoModeNetworks.Rnw) 
Error: processing vignette 'TwoModeNetworks.Rnw' failed with diagnostics:
unused argument (prsep = "")
Execution halted
Error in re-building vignettes:
  ...
  input string 305 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 306 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 307 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ch-Errata.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.34 ...<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}
                                                  Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.34 ...<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}
                                                  Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyconceptIndicesSkm: no visible global function definition for
  ‘txtProgressBar’
conceptIndicesSkm: no visible global function definition for
  ‘setTxtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘txtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘setTxtProgressBar’
mvcmb: no visible global function definition for ‘runif’
mvcmb: no visible global function definition for ‘str’
mvcsph: no visible global function definition for ‘pdf’
mvcsph: no visible global function definition for ‘heatmap’
mvcsph: no visible global function definition for ‘dev.off’
mvcsph: no visible global function definition for ‘hclust’
mvcsph: no visible global function definition for ‘dist’
mvcsph: no visible global function definition for ‘str’
Undefined global functions or variables:
  dev.off dist hclust heatmap pdf runif setTxtProgressBar str
  txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "dist", "hclust", "heatmap", "runif")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyplot.matchedwake: no visible global function definition for
  ‘filled.contour’
plot.matchedwake: no visible binding for global variable ‘gray.colors’
plot.matchedwake: no visible global function definition for ‘axis’
plot.matchedwake: no visible global function definition for ‘rect’
slideWakeMatch: no visible binding for global variable ‘lm’
slideWakeMatch: no visible global function definition for ‘as.formula’
slideWakeMatch: no visible global function definition for ‘summary.glm’
Undefined global functions or variables:
  as.formula axis filled.contour gray.colors lm rect summary.glm
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "axis", "filled.contour", "rect")
  importFrom("stats", "as.formula", "lm", "summary.glm")
to your NAMESPACE file.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nat.nblast.Rcheck/00install.out’ for details.
Running examples in ‘nat.nblast-Ex.R’ failed
The error most likely occurred in:

> ### Name: nblast
> ### Title: Calculate similarity score for neuron morphologies
> ### Aliases: nblast
> 
> ### ** Examples
> 
> # load sample Kenyon cell data from nat package
> data(kcs20, package='nat')
> # search one neuron against all neurons
> scores=nblast(kcs20[['GadMARCM-F000142_seg002']], kcs20)
> # scores from best to worst, top hit is of course same neuron
> sort(scores, decreasing = TRUE)
GadMARCM-F000142_seg002 ChaMARCM-F000586_seg002 GadMARCM-F000423_seg001 
              4043.1766               1914.8224               1772.8506 
GadMARCM-F000442_seg002 FruMARCM-M000115_seg001 FruMARCM-F000085_seg001 
              1007.4565                853.8108                713.2106 
FruMARCM-F001929_seg001 FruMARCM-F001494_seg002 GadMARCM-F000050_seg001 
               604.4071                481.4737                480.4146 
GadMARCM-F000071_seg001 FruMARCM-M001339_seg001 FruMARCM-F000188_seg001 
               448.1516                433.9340                404.0470 
GadMARCM-F000476_seg001 FruMARCM-F000270_seg001 FruMARCM-F000706_seg001 
               313.2021                254.7516                204.2116 
FruMARCM-M000842_seg002 FruMARCM-M001051_seg002 FruMARCM-M001205_seg002 
               196.4543                140.8164               -251.4999 
GadMARCM-F000122_seg001 FruMARCM-F001115_seg002 
              -262.2352               -520.2581 
> hist(scores, breaks=25, col='grey')
> abline(v=1500, col='red')
> 
> # plot query neuron
> open3d()
null 
   1 
> # plot top 3 hits (including self match with thicker lines)
> plot3d(kcs20[which(sort(scores, decreasing = TRUE)>1500)], lwd=c(3,1,1))
Error in xyz.coords(x, y, z, xlab = xlabel, ylab = ylabel, zlab = zlabel,  : 
  'x' is a list, but does not have components 'x', 'y'  and 'z'
Calls: plot3d -> plot3d.default -> xyz.coords
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because NBLAST-Clustering.Rmd appears to be an R Markdown v2 document.
Invalid MIT-MAGIC-COOKIE-1 keyQuitting from lines 56-59 (NBLAST-Clustering.Rmd) 
Error: processing vignette 'NBLAST-Clustering.Rmd' failed with diagnostics:
'x' is a list, but does not have components 'x', 'y'  and 'z'
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nat.templatebrains.Rcheck/00install.out’ for details.
Errors in running code in vignettes:
when running code in ‘test-vignette.ipynbmeta’
  ...

  When tangling ‘test-vignette.ipynbmeta’:
Error: Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'test-vignette.ipynbmeta' failed with diagnostics:
Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/NeatMap.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keydata.reduction: no visible global function definition for ‘prcomp’
data.reduction: no visible global function definition for ‘hclust’
data.reduction: no visible global function definition for ‘as.dist’
data.reduction: no visible global function definition for ‘cor’
data.reduction: no visible global function definition for ‘dist’
heatmap1: no visible global function definition for ‘sd’
lineplot: no visible global function definition for ‘sd’
normalize: no visible global function definition for ‘sd’
profileplot3d : ColorFunction: no visible global function definition
  for ‘rgb’
profileplot3d : ColorFunction: no visible global function definition
  for ‘colorRamp’
profileplot3d: no visible global function definition for ‘sd’
profileplot3d: no visible global function definition for ‘gray’
Undefined global functions or variables:
  as.dist colorRamp cor dist gray hclust prcomp rgb sd
Consider adding
  importFrom("grDevices", "colorRamp", "gray", "rgb")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd")
to your NAMESPACE file.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘KEGG.db’
Running examples in ‘netClass-Ex.R’ failed
The error most likely occurred in:

> ### Name: cv.aep
> ### Title: Cross validation for aepSVM (aepSVM)
> ### Aliases: cv.aep
> ### Keywords: aep
> 
> ### ** Examples
> 
> library(netClass)
> data(expr)
> data(ad.matrix)
> x <- expr$genes
> y <- expr$y
> 
>  library(KEGG.db)
Error in library(KEGG.db) : there is no package called ‘KEGG.db’
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.7Mb
File ‘NetSim/libs/NetSim.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘utils/Random.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘utils/Random.o’

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

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

> ### Name: read.paj
> ### Title: Read a Pajek Project or Network File and Convert to an R
> ###   'Network' Object
> ### Aliases: read.paj read.paj.simplify switchArcDirection
> ###   readAndVectorizeLine
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> require(network)
> 
> par(mfrow=c(2,2))
> 
> test.net.1 <- read.paj("http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd98/A98.net")
Warning in file(file, "rt") :
  cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd98/A98.net': HTTP status was '0 (null)'
Error in file(file, "rt") : cannot open the connection
Calls: read.paj -> file
Execution halted
Running the tests in ‘tests/read.paj_tests.R’ failed.
Last 13 lines of output:
  > 
  > 
  > 
  > # this file has character encoding issues
  > scotland<-tempfile('scotland',fileext='.zip')
  > download.file('http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip',scotland)
  trying URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip'
  Error in download.file("http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip",  : 
    cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip'
  In addition: Warning message:
  In download.file("http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip",  :
    cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip': HTTP status was '0 (null)'
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/neuroim.Rcheck/00install.out’ for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    CppCode        3.5Mb
    R              2.4Mb
    classic-bugs   1.5Mb
    include        3.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because trees_with_root_edge.Rmd appears to be an R Markdown v2 document.
Error: processing vignette 'vignette_get_nltt_values.Rmd' failed with diagnostics:
(converted from warning) It seems you should call rmarkdown::render() instead of knitr::knit2html() because vignette_get_nltt_values.Rmd appears to be an R Markdown v2 document.
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nmcdr.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘RcppOctave’ ‘doMPI’
Running examples in ‘NoiseFiltersR-Ex.R’ failed
The error most likely occurred in:

> ### Name: EF
> ### Title: Ensemble Filter
> ### Aliases: EF EF.default EF.formula
> 
> ### ** Examples
> 
> data(iris)
> # We fix a seed since there exists a random partition for the ensemble
> set.seed(1)
> out <- EF(Species~., data = iris, consensus = FALSE)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: EF ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 190-198 (NoiseFiltersR.Rnw) 
Error: processing vignette 'NoiseFiltersR.Rnw' failed with diagnostics:
java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nonlinearTseries.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/norm2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/NPCirc.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
File ‘obliclus/libs/obliclus.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘oblique.tree/libs/oblique.tree.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OceanView.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/oc.Rcheck/00install.out’ for details.
installed size is 98.0Mb
  sub-directories of 1Mb or more:
    libs  97.7Mb
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
comp.freq: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 359 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OneTwoSamples.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

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

Package suggested but not available for checking: ‘farff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 121.1Mb
  sub-directories of 1Mb or more:
    libs    113.3Mb
    models    4.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OpenRepGrid.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   2.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/optBiomarker.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyavg2Lower: no visible global function definition for ‘optimize’
classificationError.data.frame: no visible binding for global variable
  ‘na.omit’
classificationError.data.frame: no visible global function definition
  for ‘terms’
classificationError.data.frame: no visible binding for global variable
  ‘predict’
classpredict.lda: no visible global function definition for ‘predict’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
simData: no visible global function definition for ‘var’
tnormAvg: no visible global function definition for ‘dnorm’
tnormAvg: no visible global function definition for ‘pnorm’
yapprox: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘org.At.tair.db’
Error in re-building vignettes:
  ...
sh: rst2pdf: command not found
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
conversion by rst2pdf failed!
Execution halted
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Attaching package: ‘BiocGenerics’

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

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

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

    IQR, mad, xtabs

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

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

Welcome to Bioconductor

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

All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘IsoGene’
Invalid MIT-MAGIC-COOKIE-1 keygenRidge: no visible global function definition for ‘plogis’
ordGene: no visible global function definition for ‘anova’
ordGene: no visible global function definition for ‘lm’
ordSelect: no visible binding for global variable ‘sd’
ordSmooth: no visible binding for global variable ‘sd’
plot.ordPen: no visible global function definition for ‘grey’
plot.ordPen: no visible global function definition for ‘devAskNewPage’
plot.ordPen: no visible global function definition for ‘plot’
plot.ordPen: no visible global function definition for ‘lines’
predict.ordPen: no visible global function definition for ‘plogis’
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 411 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 412 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 420 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dicom.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Al
           ^^SG^^W~<b1><89><cc>V<c2><de>^^Q^^T<b6><a1>&<d6>J^^P<a4>D!<c2>B*H<91>s<f0>9<b7><dc>z<e6>^^D<87><f6>^^BG<ae>\9r<ab>P%<84>^^O<95>"...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<de>^^Q^^T<b6><a1>&<d6>J^^P<a4>D!<c2>B*H<91>s<f0>9<b7><dc>z<e6>^^D<87><f6>^^BG<ae>\9
                                                  r<ab>P%<84>^^O<95>".(>`YTj<a4>^^U<b6><eb>?-<b4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<83>/<be><f8>b^^O<8b>^^\<f0><d8><eb>61l^^W@y.<97>K<a5>R<d9>l<f6>ȑ#sss<b9>\nzz
                                                  :^^H<d9>B<88>d2^^Y<bc>Q<e5>+<df><f7><a3>Ѩi<9a>B^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 420 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'nifti.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^S[^^[^^?L<95>:P'9Ko1M^^X<90><ca>U<92>\^^FD^^DI^^W<85><ba>r#<fe>]<b9>r<a3>K<b7>ݸ^^U<bb>^^UA^^L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 x<9c><ed>\<cd>k^^S[^^[^^?L<95>:P'9Ko1M^^X<90><ca>U<92>\^^F
                                           D^^DI^^W<85><ba>r#<fe>]<b9>r<a3>K<b7>ݸ^^U<bb>^^UA^^L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...!^^Dc^^L<f7>s<b9><dc><ce><ce>N<a5>Ry<fb><f6>-c^^L<8f>8<e7><9c><f3><e1><e1>aιl"[	!\<d7>
                                                  
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 !<96><96><96><aa><d5><ea><eb>ׯ?|<f8>^^@<af>ptW<b9>\<ae>
   
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘osi-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract_id
> ### Title: Extract components from OSI metadata
> ### Aliases: extract_id extract_keywords extract_name extract_superseded
> ###   extractors
> 
> ### ** Examples
> 
> 
> #Get the names of all licenses
> all_license_metadata <- license_list()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Peer certificate cannot be authenticated with given CA certificates
Calls: license_list ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 8
  1. Error: All licenses can be retrieved (@test_connectors.R#6) 
  2. Error: Keyword retrieval works (@test_connectors.R#14) 
  3. Error: ID retrieval works (@test_connectors.R#22) 
  4. Error: Content retrieval works (@test_connectors.R#29) 
  5. Error: licenses IDs can be retrieved (@test_extractors.R#4) 
  6. Error: licenses names can be retrieved (@test_extractors.R#11) 
  7. Error: licenses superseded states can be retrieved (@test_extractors.R#18) 
  8. Error: licenses keywords can be retrieved (@test_extractors.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’ ‘Rmpi’
File ‘parmigene/libs/parmigene.so’:
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running the tests in ‘tests/regtest-party.R’ failed.
Last 13 lines of output:
  > fit <- rpart(Kyphosis ~ Age + Number + Start, data = kyphosis)
  > pfit <- as.party(fit)
  > all(predict(pfit, newdata = kyphosis, type = "node") == fit$where)
  [1] TRUE
  > 
  > ## J48: iris data
  > library("RWeka")
  > data("iris", package = "datasets")
  > itree <- J48(Species ~ ., data = iris)
  Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
    java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
  Calls: J48 ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
  Execution halted
Errors in running code in vignettes:
when running code in ‘constparty.Rnw’
  ...
       8 0.5408163 0.4591837
       9 0.0729927 0.9270073

> library("RWeka")

> (j48 <- J48(Survived ~ ., data = ttnc))

  When sourcing ‘constparty.R’:
Error: java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Execution halted
Error in re-building vignettes:
  ...
Loading required package: grid

Error: processing vignette 'constparty.Rnw' failed with diagnostics:
 chunk 10 (label = J48) 
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Execution halted
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 419 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'party.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 !8<e7>hV*<95>p]<ad>V?<ff><fc><f3><f9><f9><f9>R<a9><84>^^A<a5>^^X<ed>v<fb><f2><e5><cb>B^^H!D<b9>\<fe>
                                                <f2><cb>/?<f9><e4><93>J<a5>r<e3><c6>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.19 ...^Uc,^^H^^B<c3>0<a0><<e7><e6><e6>*<95><ca><f8><f8><f8>G^^_}<d4>^^Oϧ|<ef><8d>}<f6><d9>g}
                                                  6<c5><fb>^^SB<f8><be><df>n<b7><a1>֛<cd>f*<95><8a><e3>xcc<a3><db>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘hu6800.db’ ‘golubEsets’

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

    union

Loading required package: lpSolve

> library(golubEsets)

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

    lowess

Loading required package: igraph

Attaching package: ‘igraph’

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve

Error: processing vignette 'pathClass.rnw' failed with diagnostics:
 chunk 2 (label = loadALLpackage) 
Error in library(golubEsets) : there is no package called ‘golubEsets’
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rootSolve’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘kinship2’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘rootSolve’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyCall with DUP:
   .C("powerR", as.integer(numOffspring), as.integer(numParents), 
       as.integer(numFamilies), as.integer(additionalOffspringPhenos), 
       as.integer(ascertainment), as.integer(modelGen), as.integer(modelTest), 
       as.double(afreqMarker), as.double(penAA), as.double(penAB), 
       as.double(penBB), as.double(heritability), as.double(contsAscertainmentLower), 
       as.double(contsAscertainmentUpper), as.double(pDiseaseAlleleGivenMarkerAllele), 
       as.double(afreqDSL), as.double(qnorm(1 - alpha/2)), as.double(offset), 
       as.integer(numSim), as.integer(ITERATION_KILLER), result, 
       DUP = FALSE)
DUP is no longer supported and will be ignored.
Packages required but not available: ‘pbdMPI’ ‘pbdSLAP’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pbdPROF.Rcheck/00install.out’ for details.
Packages which this enhances but not available for checking:
  ‘pbdMPI’ ‘pbdCS’
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdRPC’
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key.win.appendLog: no visible binding for global variable ‘lines’
plotMC : panel: no visible global function definition for ‘points’
plotMC: no visible global function definition for ‘pairs’
plotMC: no visible global function definition for ‘mtext’
plotMC: no visible global function definition for ‘axis’
plotMC: no visible global function definition for ‘par’
readADpaths: no visible global function definition for ‘read.table’
readRep: no visible global function definition for ‘read.table’
saveADpaths: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  axis lines mtext pairs par points read.table write.table
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "pairs", "par",
             "points")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.3Mb
Running examples in ‘PBSmodelling-Ex.R’ failed
The error most likely occurred in:

> ### Name: PBSoptions-class
> ### Title: S4: Project Options Class
> ### Aliases: PBSoptions-class print,PBSoptions-method
> ###   show,PBSoptions-method
> ### Keywords: classes methods
> 
> ### ** Examples
> 
> local(envir=.PBSmodEnv,expr={
+   #initialize an option manager with a single logical option
+   .mypkg <- new( "PBSoptions", filename="my_pkg.txt", 
+     initial.options=list( sillyhatday=FALSE ) )
+ 
+   #retrieving an option
+   silly <- getOptions( .mypkg, "sillyhatday" )
+   cat( "today is", ifelse( silly, "silly hat day!", "monday" ), "\n" )
+ 
+   #set an option
+   setOptions( .mypkg, sillyhatday = TRUE, photos = "/shares/silly_hat_photos" )
+ 
+   #create a GUI which works with options
+   createWin( c( 
+     "check name=optionsillyhatday text=\"silly hat day\"",
+     "entry name=optionphotos width=22 mode=character label=\"photos directory\"",
+     "button func=doAction text=save action=saveOptionsGUI(.mypkg)" ), astext = TRUE )
+ 
+   #update GUI values based on values stored in .mypkg's options
+   loadOptionsGUI( .mypkg )
+   print(getOptions( .mypkg ))
+ })
today is monday 
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "tk_setPalette".
Calls: local ... eval -> eval -> createWin -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pca3d.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pcaL1.Rcheck/00install.out’ for details.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   2.1Mb
    libs   6.5Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 399 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 400 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 408 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pcse.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<cb>^^RB^^X<86><c1>^^X#<a2><a5><a5><a5><8f>^^_?r<ce>s<b9>^^\<e7>|ee<e5><fa><f5><eb><8c>1\<cd>
                                                  f<b3><85>BA<8e><8a>1v<ef>޽^^NC?<e8>E<96><97><97><8f>o0?...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<ba><ae>^^GA^^@<ad><a8><e5>gu<af>^^^O<e0><d4>4<ad>M7EQ<a4>n^^X^^AΣ<a5>\ZXW
                                                  <9a><a6><95><cb>eιi<9a><ae><eb>b<b8><8e><e3>^^DA<c0>9<c7>^^B^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...b<b8><8e><e3>^^DA<c0>9<c7>^^B^^VB^^@<ae><ae><eb>B7<c3>0<e2><f1>8<b6>^^G<d7>uGFF\<d7>
                                                  E?݌<f9><ac><c0><f9><8d>0j^^O<e0>^^D~<a8>5u<98>^^\...
The control sequence at the end of
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘pedantics/libs/pedantics.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘pedantics.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.
Packages suggested but not available for checking: ‘georob’ ‘spsurvey’
Packages unavailable to check Rd xrefs: ‘spsurvey’, ‘georob’
Running examples in ‘pedometrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: vgmICP
> ### Title: Initial covariance parameters (ICP)
> ### Aliases: vgmICP
> 
> ### ** Examples
> 
> data(meuse, package = "sp")
> icp <- vgmICP(z = log(meuse$copper), coords = meuse[, 1:2])
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error: Package(s) needed for this function to work but notinstalled: georob
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/permGPU.Rcheck/00install.out’ for details.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

infoImage: no visible global function definition for ‘quantile’
markPoisson: no visible global function definition for ‘runif’
markPoisson: no visible global function definition for ‘flush.console’
phantom : model: missing arguments not allowed in calls to ‘c’
readData: no visible global function definition for ‘read.table’
readData: no visible global function definition for ‘read.image’
readSifData: no visible global function definition for ‘flush.console’
viewData: no visible global function definition for ‘gray’
viewData: no visible global function definition for ‘dev.cur’
viewData: no visible global function definition for ‘dev.set’
viewData: no visible global function definition for ‘X11’
viewData: no visible global function definition for ‘par’
viewData: no visible global function definition for ‘image’
viewData: no visible global function definition for ‘title’
writeData: no visible global function definition for ‘write.table’
writeData: no visible global function definition for ‘make.image’
writeData: no visible global function definition for ‘write.image’
Undefined global functions or variables:
  X11 dev.cur dev.set flush.console gray image make.image par quantile
  read.image read.table runif title write.image write.table
Consider adding
  importFrom("grDevices", "X11", "dev.cur", "dev.set", "gray")
  importFrom("graphics", "image", "par", "title")
  importFrom("stats", "quantile", "runif")
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
File ‘PET/libs/PET.so’:
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
    Object: ‘misc.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘art.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘art.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 ‘pgam/libs/pgam.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘pgam.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 ‘PhaseType/libs/PhaseType.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘LJMA_arms.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 47.9Mb
  sub-directories of 1Mb or more:
    libs  47.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pi0.Rcheck/00install.out’ for details.
Package required but not available: ‘rggobi’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/playwith.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plot3Drgl.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘GSIF’ ‘gdalUtils’
Errors in running code in vignettes:
when running code in ‘jss1079.Rnw’
  ...
+ }
Loading required package: GSIF
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GSIF’
Installing package into ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plotKML.Rcheck’
(as ‘lib’ is unspecified)

  When sourcing ‘jss1079.R’:
Error: trying to use CRAN without setting a mirror
Execution halted
Error in re-building vignettes:
  ...
Loading required package: gstat
Loading required package: raster
Loading required package: sp
Loading required package: plotKML
plotKML version 0.5-6 (2016-05-02)
URL: http://plotkml.r-forge.r-project.org/
Loading required package: GSIF
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GSIF’
Installing package into ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plotKML.Rcheck’
(as ‘lib’ is unspecified)

Error: processing vignette 'jss1079.Rnw' failed with diagnostics:
 chunk 1 
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plsRcox.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         return(val)
     }, finally = options(warn = oldWarn))
  3: tryCatchList(expr, classes, parentenv, handlers)
  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5: value[[3L]](cond)
  6: private$errorHandler(req, res, e)
  
  testthat results ================================================================
  OK: 220 SKIPPED: 0 FAILED: 1
  1. Error: Includes work (@test-include.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.1Mb
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’ ‘pbdDMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda

Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pmg.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘polmineR.sampleCorpus’ ‘rcqp’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
File ‘PottsUtils/libs/PottsUtils.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘sw.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/powell.Rcheck/00install.out’ for details.
File ‘powell/libs/powell.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘powell.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'd_jss_paper.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...R,<89><ad>qI^J<a6>^^NT^^B<81>^^U6^^P<ac><f8><a5>^^O<c5>}n!<d4>^^O}
                                                  (<ec>e~h<fb>TJMa/3dx<b0>U^^O<83>b<b5>H^^Q...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.15 ...<ec><e8>ڎ<e4>V<8a>~^^Xsu<ee>9<e7><9e><ef>~<df><f9><fe><9d><ef>v^^Y<86>^^A<ed><cb><f7><bd><80><e6><a2>C^
                                                  +<a3>C^+<a3>C^+<a3><cd>ɳ5d^^VJ)<e7><bc>!S^^...
! Extra }, or forgotten $.
l.15 ...<93>MXp<c3>`B<9e>^^?[<eb>1v<ff><f8><e7><a5>^^?W6^^?q<f9>'<d7>T<d7>i<d8><d4>7<bf>]<88><ad>}
                  
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyfnfam: no visible global function definition for ‘qnorm’
fx: no visible global function definition for ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘pnorm’
normplot : <local> : replot: no visible global function definition for
  ‘plot’
normplot : <local> : replot: no visible global function definition for
  ‘dnorm’
normplot : <local> : replot: no visible global function definition for
  ‘points’
normplot : <local> : replot: no visible global function definition for
  ‘lines’
normplot : <local> : regen: no visible global function definition for
  ‘rnorm’
normplot : <local> : regen: no visible global function definition for
  ‘rexp’
nsibs: no visible global function definition for ‘qnorm’
ntdt: no visible global function definition for ‘uniroot’
plotDom: no visible global function definition for ‘plot’
plotNsibs: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘lines’
plotNtdt: no visible global function definition for ‘legend’
ptdt: no visible global function definition for ‘optimize’
ptdt: no visible global function definition for ‘uniroot’
ptdt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm legend lines optimize plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  ‘KEGG.db’ ‘org.Sc.sgd.db’ ‘org.Ag.eg.db’ ‘org.Pt.eg.db’
  ‘org.Rn.eg.db’ ‘org.Ss.eg.db’ ‘org.At.tair.db’ ‘org.Bt.eg.db’
  ‘org.Ce.eg.db’ ‘org.Cf.eg.db’ ‘org.Dm.eg.db’ ‘org.Dr.eg.db’
  ‘org.EcK12.eg.db’ ‘org.EcSakai.eg.db’ ‘org.Gg.eg.db’ ‘org.Mm.eg.db’
  ‘org.Mmu.eg.db’ ‘org.Pf.plasmo.db’ ‘org.Xl.eg.db’
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rosm’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/prim.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because PRISMA.Rmd appears to be an R Markdown v2 document.
Quitting from lines 31-43 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
    libs      1.2Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/PropClust.Rcheck/00install.out’ for details.
LastFirstDiscreteSparse: Error while checking: evaluation nested too
  deeply: infinite recursion / options(expressions=)?
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'countreg.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 <c4><eb>g^^Z<88><d7><cf>4^^P<af><9f>i <de>^^Q^^RB^^H!<8e>ޗR<aa><eb>B<a1><80>1RJ\<e0>
                                                o<b5>Z
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.18 \K
       ?<d3><f0><e7><9f>^^?~<fa><d1><d8><e5>R<ca>J<a5><b2><b3><b3><b3><b8><b8><b8><b8><b8><c8>9^^?<f8><f0><a1>m۷n<dd>::<9e>s^<ad>V766^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
                $
l.18 ...<f0><e7><9f>^^?~<fa><d1><d8><e5>R<ca>J<a5><b2><b3><b3><b3><b8><b8><b8><b8><b8><c8>9^^?<f8><f0><a1>m۷n<dd>::<9e>s^
         
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Error in re-building vignettes:
  ...
  input string 401 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 409 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 410 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 418 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'raschmix.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.19 <82>`ss3<97>˹<ae><9b>L&^^Q<85>^^PQ<b9>\<9e>
                            <99><99><b1>,+<9d>N<c3><ee><a3>?^^H<82><bd><bd>=vhRJ<c4>.<9e><e7><e5>r<b9>C<93><f3><f8>X,<86><c9>^^]ǉ^^N;rN...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 ...<b3><a8>nC!_<d7><ed><e8><be>͹<89><f7>V<e8><8c>`<ee>l<f5><b0><9b><c3>^^Z<a5><94><c2>"<a0>͡&<f6><ab>8g<e5>\<e6>
                                                  <d4>\<9e><9a><ae><fa>ꝑ<ae>y<9d><b3><8d>߃<a2>///<c7><e3>qM<d3>\...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 ...C!_<d7><ed><e8><be>͹<89><f7>V<e8><8c>`<ee>l<f5><b0><9b><c3>^^Z<a5><94><c2>"<a0>͡&<f6><ab>8g<e5>\<e6><d4>\<9e>
                                                  <9a><ae><fa>ꝑ<ae>y<9d><b3><8d>߃<a2>//
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc        3.5Mb
    examples   2.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qpcR.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyMHbi2: no visible global function definition for ‘runif’
QRLMM: no visible binding for global variable ‘D’
QRLMM: no visible global function definition for ‘par’
QRLMM: no visible global function definition for ‘plot.ts’
QRLMM: no visible global function definition for ‘abline’
QRLMM: no visible global function definition for ‘qnorm’
QRLMM: no visible global function definition for ‘plot’
QRLMM: no visible global function definition for ‘axis’
QRLMM: no visible global function definition for ‘polygon’
QRLMM: no visible global function definition for ‘lines’
QRLMM: no visible global function definition for ‘smooth.spline’
QRLMM: no visible global function definition for ‘title’
QSAEM_COM_7: no visible global function definition for ‘pnorm’
grid_example: no visible global function definition for ‘par’
grid_example: no visible global function definition for ‘smooth.spline’
grid_example: no visible global function definition for ‘plot’
grid_example: no visible global function definition for ‘axis’
grid_example: no visible global function definition for ‘polygon’
grid_example: no visible global function definition for ‘lines’
grid_example: no visible global function definition for ‘abline’
grid_example: no visible global function definition for ‘title’
rALD: no visible global function definition for ‘runif’
Undefined global functions or variables:
  D abline axis lines par plot plot.ts pnorm polygon qnorm runif
  smooth.spline title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "polygon", "title")
  importFrom("stats", "D", "plot.ts", "pnorm", "qnorm", "runif",
             "smooth.spline")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qrmtools.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyNamespace in Imports field not imported from: ‘xts’
  All declared Imports should be used.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qtbase.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qtlc.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.1Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.3Mb
    libs   5.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/QuantifQuantile.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 430 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 438 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'quantspec.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.21 ...[L=^^X^^L^^F<83>A<8e>Pض],^^V5M<b3>,<8b>]X0#<a5><c4>Z^^PQ<b9>\<b6>
                                                  ,+^^R<89>X<96><c5>^^A<8e>6<e9>E?{^^\e<e9>N^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 ...A<8e>6<e9>E?{^^\e<e9>N^^Nu^^V<8c><b0>,<8b><88>fff<d2><e9><b4>^^[c<a8>`<db>v<b9>\<8e>
                                                  D"<8c>Ir!VUU<80>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.25 <a7>ޭ^^@<89>^^H<be>ҹ<b0>^^G<ca><e5>rSSS<b9>\<8e>
                               <88><e0>^^VY<96>utt4<<^^\^^L^^F<a5><94>^<af>^^W^^F4/^^G<e4>!<f7><80>r0<ef>>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.25 ...
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.6Mb
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because Release.Rmd appears to be an R Markdown v2 document.
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because Use_case.Rmd appears to be an R Markdown v2 document.
Warning: Removed 16 rows containing missing values (geom_point).
Warning: Removed 16 rows containing missing values (geom_point).
Quitting from lines 141-142 (Use_case.Rmd) 
Error: processing vignette 'Use_case.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
File ‘QUIC/libs/QUIC.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FancyPies: no visible global function definition for ‘rainbow’
FancyPies: no visible global function definition for ‘plot’
FancyPies: no visible global function definition for ‘polygon’
Hist2GE: no visible global function definition for ‘dist’
Pies2GE: no visible global function definition for ‘rainbow’
Plots2GE: no visible global function definition for ‘aggregate’
Plots2GE: no visible global function definition for ‘x11’
Plots2GE: no visible global function definition for ‘title’
Plots2GE: no visible global function definition for ‘png’
Plots2GE: no visible global function definition for ‘dev.off’
PolyLines2GE: no visible global function definition for ‘rainbow’
Shapes2GE: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  aggregate dev.off dist plot png polygon rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow", "x11")
  importFrom("graphics", "plot", "polygon", "title")
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R2GUESS.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 231 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 232 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 240 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2OpenBUGS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\AL
           ^^[W^^S^^^^^L^^FL<8c><97><a7>^^R0N^^V̪nCq<8d><cb>V<88> ^^Q~UT<ad><9a>*<f4><92>S<a2><f6>ƥ<97><f6><94>^^^<a3>ޫ^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.18 ...Tf<92><95><d4>/<aa>^^@e<e1>p^^X9<ee><ec><ec><8c>D"<99>L<a6><b1><b1><f1><e5><97>_<ce>f<b3>O<9e><<d1>u}}
                                                  }<bd><b9><b9><b9><bf><bf>?<9f><cf>744,,,tww<af><ad><ad>577^...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.18 ...f<92><95><d4>/<aa>^^@e<e1>p^^X9<ee><ec><ec><8c>D"<99>L<a6><b1><b1><f1><e5><97>_<ce>f<b3>O<9e><<d1>u}}}
                                                  <bd><b9><b9><b9><bf><bf>?<9f><cf>744,,,tww<af><ad><ad>577^^...
I've deleted a 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R2STATS.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 231 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 232 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 240 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2WinBUGS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.17 ...^L^^L<e8><ba>N^^Hq8^^\8<ad><c7><e3>Y\\,^^V<8b><9d><9d><9d>o<bf><fd><b6>In^^O\<cb>
                                                  <b3>^^H<e3>o<^^^<a7><ba>gf^^H<f6>G,f<fe>]^^S...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<da>ڪiZOO<8f><a6>i<cb><cb><cb>^^V<8b>^^E^^@*<95>Jgg<a7><a2>(<8f>^^^=r:<9d><b9>\<ae>
                                                  V<ab><f5><f5><f5><cd><ce><ce><f6><f7><f7><ff><f6><db>o<ad><ad><ad>^^W/^^^D...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 <9d>?^^?^^^<eb>\N
                <a7>szz^^Z7^^A<ed>jqq<91><e7>yUU<91><b3>|><8f>\<86><c3>a<97>˅@^^\[^^X<86>!<84><9c>9s&<95>J<c5>b1Q^^T^^A<e0>...
The control sequence at the end of the top line
of your error message was neve
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R330.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘leaps’ ‘rgl’ ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rainbow.Rcheck/00install.out’ for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RAppArmor.Rcheck/00install.out’ for details.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.7Mb
    libs   9.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rase.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘rggobi’ ‘RODBC’
Invalid MIT-MAGIC-COOKIE-1 key
(R:2730): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keydatgen: no visible global function definition for ‘rnorm’
optimization.IC: no visible global function definition for ‘optim’
outlier.replace: no visible global function definition for ‘qnorm’
pargen: no visible global function definition for ‘runif’
rav: no visible global function definition for ‘optim’
rav2file: no visible global function definition for ‘write.table’
standardized: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  optim qnorm rnorm runif sd write.table
Consider adding
  importFrom("stats", "optim", "qnorm", "rnorm", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RBerkeley.Rcheck/00install.out’ for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   4.2Mb
Package required and available but unsuitable version: ‘mlr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rCBA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcdk.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because RClone_qmsevpops.Rmd appears to be an R Markdown v2 document.
Quitting from lines 336-337 (RClone_qmsevpops.Rmd) 
Error: processing vignette 'RClone_qmsevpops.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key.onAttach: no visible global function definition for ‘palette’
.onAttach: no visible global function definition for ‘dev.off’
helpAboutBCA: no visible global function definition for ‘help’
Undefined global functions or variables:
  dev.off help palette
Consider adding
  importFrom("grDevices", "dev.off", "palette")
  importFrom("utils", "help")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyenterTableMHTest : onOK: no visible global function definition for
  ‘na.omit’
startStop: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘depthTools’ ‘tcltk’
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keycomputeMBD : OnOutput: no visible global function definition for
  ‘tkbutton’
computeMBD: no visible global function definition for ‘tkbutton’
computeMBD : OnPlot: no visible global function definition for
  ‘tkcanvas’
computeMBD : OnPlot: no visible global function definition for
  ‘tkbutton’
computeTmean: no visible global function definition for ‘tkcanvas’
computeTmean: no visible global function definition for ‘tkbutton’
computeTmean : onOK: no visible global function definition for ‘par’
plotCentralCurves: no visible global function definition for ‘tkcanvas’
plotCentralCurves: no visible global function definition for ‘tkbutton’
plotCentralCurves : onOK: no visible global function definition for
  ‘par’
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘FrF2.catlg128’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘Rcmdr’ ‘multcomp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘tseries’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘Rcmdr’ ‘TeachingDemos’ ‘abind’ ‘forecast’ ‘tseries’ ‘xts’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘ENmisc’ ‘Hmisc’ ‘Rcmdr’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘orloca’ ‘orloca.es’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyRcmdr.new.loca.p: no visible binding for global variable ‘top’
Rcmdr.new.loca.p: no visible binding for global variable ‘buttonsFrame’
Rcmdr.orloca.norm: no visible binding for global variable ‘top’
Rcmdr.orloca.norm : onOK: no visible binding for global variable
  ‘normaVariable’
Rcmdr.orloca.norm: no visible binding for global variable ‘normaFrame’
Rcmdr.orloca.norm: no visible binding for global variable
  ‘buttonsFrame’
Rcmdr.rloca.p: no visible binding for global variable ‘top’
Rcmdr.rloca.p: no visible binding for global variable ‘buttonsFrame’
Rcmdr.zsum: no visible binding for global variable ‘top’
Rcmdr.zsum: no visible binding for global variable ‘buttonsFrame’
Rcmdr.zsummin: no visible binding for global variable ‘top’
Rcmdr.zsummin : onOK: no visible binding for global variable
  ‘algorithmVariable’
Rcmdr.zsummin : onOK: no visible binding for global variable ‘.sol’
Rcmdr.zsummin: no visible binding for global variable ‘algorithmFrame’
Rcmdr.zsummin: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  .sol algorithmFrame algorithmVariable buttonsFrame normaFrame
  normaVariable top
Invalid MIT-MAGIC-COOKIE-1 keyBOXWP: no visible binding for global variable ‘top’
BOXWP: no visible binding for global variable ‘buttonsFrame’
HIST: no visible binding for global variable ‘top’
HIST: no visible binding for global variable ‘buttonsFrame’
QQN: no visible binding for global variable ‘top’
QQN: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  buttonsFrame top
Invalid MIT-MAGIC-COOKIE-1 keyfncLRpROC: no visible global function definition for ‘palette’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘rgb’
fncPairedpROC: no visible global function definition for ‘palette’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncUnpairedpROC: no visible global function definition for ‘palette’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncvpROC: no visible global function definition for ‘palette’
fncvpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncvpROC : onOK : convert: no visible global function definition for
  ‘rgb’
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keySampleSizes: no visible global function definition for ‘xtabs’
SampleSizes: no visible global function definition for ‘weighted.mean’
SampleSizes: no visible global function definition for ‘reshape’
stage1Sample.fn: no visible global function definition for ‘runif’
stage2Sample.fn: no visible global function definition for ‘runif’
strata.options : onOK: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘Rcmdr’ ‘seeg’ ‘sgeostat’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘SLC’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘SLC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘car’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘Rcmdr’ ‘car’ ‘colorspace’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyRcmdr.steeptestDij : onOK: no visible binding for global variable
  ‘replications’
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  ‘replications’
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Packages suggested but not available for checking: ‘ROpenOffice’ ‘RODBC’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
    po    2.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rcplex.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppAPT.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    include   4.7Mb
    libs      1.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    libs     22.5Mb
Error in re-building vignettes:
  ...
  input string 420 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 428 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppEigen-Introduction.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...^?^^_Q<bd>^^Y<ec>^^^<c1><d2><d2><d2><ce><ce>N<af><b0>u<88><b3>킞<b1><87><b0><b1><b1><b1><b1><b1><81>ǹ\<8e>
                                                  ^^^۶<fd><f0><e1><c3>gϞ<9d><b4><b8>ue^^O<e1><9a><dd><d3>tv...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...<8e><8d><8d>!1<84>^^P<96>e<db><d2>܅<ee><e1><83>^^EAh-^^U<82>@<a5>HQ^^TT^^L\<83>
                                                  <be><9b>.C<b6>eY<c6>^^E<84>^^PUUQ<a9><e8><ab><d1>4<ad>V<ab>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...^^W^^@Lӌ<c7><e3><8f>^^^=<9a><9a><9a><a2><95>_|4jc<ab><c4><f6><80><bd>^^N_<c1>yl`<b9>\<ee>
                                                  <c4><dc>w^^N]^^De<f9>|<de><e7><f3>i<9a>^^V<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      21.4Mb
    libs     11.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppOctave.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    include   6.2Mb
    libs      3.1Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 379 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rcpp-introduction.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.21 ...^E}۽c<86>HgI^^[]x<bb><f7>ώ<d6>a<8b>Mӄ<87><89><ac><e3><c2><c2>^^Bclnn^^N}
                                                  p<dc><c3>^^X<83><92>@g<ce>9<ec>><bc>-<c3>0|>_<ab><d5>""<c6>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.22 ...<ba><ae><b7>Z-8=<ed>v۲,8^^@^^Hm,<cb>"<a2><95><95>^^U<9f><cf><d7>n<b7><8b><c5>b8^^\^
                                                  XX "EQЧR<a9><e8><ba>.<cb>2F&<a2>b<b1>^^X^^H...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 88.2Mb
  sub-directories of 1Mb or more:
    include   4.1Mb
    lib      52.5Mb
    libs     31.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppTOML.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcqp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcrypt.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RDieHarder.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot130762117424f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot130762117424f.png': No such file or directory
Quitting from lines 21-25 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Package required but not available: ‘Rmosek’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing link or links in documentation object 'ClassGroups.Rd':
  ‘[rebus.unicode]{UnicodeProperty}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'recexcavAAR-vignette-1.Rmd'
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because recexcavAAR-vignette-1.Rmd appears to be an R Markdown v2 document.
Loading recexcavAAR
Loading required package: kriging

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 46-61 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking: ‘RODBC’ ‘RODBCext’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.8Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  11.4Mb
Invalid MIT-MAGIC-COOKIE-1 keycook.outliers: no visible global function definition for ‘lm’
cook.outliers: no visible global function definition for
  ‘cooks.distance’
nonparRI: no visible global function definition for ‘quantile’
plot.interval: no visible global function definition for ‘par’
plot.interval: no visible global function definition for ‘plot.new’
plot.interval: no visible global function definition for ‘plot.window’
plot.interval: no visible global function definition for ‘segments’
plot.interval: no visible global function definition for ‘axis’
plot.interval: no visible global function definition for ‘title’
plot.interval: no visible global function definition for ‘legend’
plot.interval: no visible global function definition for ‘box’
plot.interval: no visible global function definition for ‘text’
robust: no visible global function definition for ‘qt’
singleRefLimit: no visible global function definition for ‘qnorm’
singleRefLimit: no visible global function definition for
  ‘shapiro.test’
singleRefLimit: no visible global function definition for ‘ks.test’
Undefined global functions or variables:
  axis box cooks.distance ks.test legend lm par plot.new plot.window
  qnorm qt quantile segments shapiro.test text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "par", "plot.new",
             "plot.window", "segments", "text", "title")
  importFrom("stats", "cooks.distance", "ks.test", "lm", "qnorm", "qt",
             "quantile", "shapiro.test")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 84 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 85 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 93 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'registry.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>[Ok^^S<dd>^^W>o<fa><ab><b5>Pf<bc> <b1>(i<ea>l*^^H5<a5> <a5>P<c6>EvBw<ee>\<fb>
                                                 1<c4>m<bf><82>[wfe<b1><b8><b0><9b><f8>'Be ^^]<82>]^^H^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<a2>J<a5>2??<af><94><9a><9e><9e><f6>}?<97><cb><d5>j5۶]<d7><c5>x!^^D^^C^^X^^Qv<b9>\<ce>
                                                  <e5>r<f8>Y<ad>V-<cb><c2><e4><fc>^^W7<c3>0<b4>,<ab><95>+0^^@...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<c7>h<b1>2O<8c><ba>u<eb>X[)^^E<ac>Ǌ<b8>ID<bb><bb><bb><90>^^V<88>ª<b0><b1>@,<cb><d0>h4\<d7>
                                                  <85>E
The control sequence at the end of the top line
of your error message was
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Error: can't see environment of caller (@test-env.R#5) 
  2. Error: reprex doesn't write into environment of caller (@test-env.R#11) 
  3. Error: I understand exactly what I'm putting in reprex env (@test-env.R#22) 
  4. Error: reprex: clipboard input works (@test-input.R#12) 
  5. Error: reprex: expression input works (@test-input.R#17) 
  6. Error: reprex: character input works (@test-input.R#23) 
  7. Error: reprex: file input works (@test-input.R#31) 
  8. Error: reprex: file input in a subdirectory works (@test-input.R#40) 
  9. Error: Circular use is detected before render (@test-input.R#47) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/reshapeGUI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/restlos.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyGUI_template : onHelp: no visible global function definition for ‘help’
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/retistruct.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 102.7Mb
  sub-directories of 1Mb or more:
    libs      100.2Mb
    pictures    1.3Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rggobi.Rcheck/00install.out’ for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc     2.0Mb
    fonts   1.5Mb
    libs    6.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rgnuplot.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key
(R:76308): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘gWidgetsRGtk2’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘RGtk2’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘RGtk2Extras-Ex.R’ failed
The error most likely occurred in:

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

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

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

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

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

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

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

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

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

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

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

Traceback:
 1: .Call(name, ..., PACKAGE = PACKAGE)
 2: .RGtkCall("S_gtk_widget_show_all", object, PACKAGE = "RGtk2")
 3: gtkWidgetShowAll(w)
 4: gtkWindowNew()
An irrecoverable exception occurred. R is aborting now ...
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.9Mb
    libs  14.7Mb
Invalid MIT-MAGIC-COOKIE-1 key.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').
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because intro_rhandsontable.Rmd appears to be an R Markdown v2 document.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rhpc.Rcheck/00install.out’ for details.
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLinit’, ‘R_RunExitFinalizers’,
    ‘R_SetParams’, ‘R_SignalHandlers’, ‘R_TempDir’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘doMC’ ‘doSNOW’ ‘e1071’ ‘fftw’ ‘foreach’ ‘jpeg’ ‘png’ ‘rggobi’
  ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘parallel’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyrite : loadHistory: no visible global function definition for
  ‘savehistory’
rite : saveGist: no visible global function definition for ‘browseURL’
rite : uploadToRPubs : processEntry: no visible global function
  definition for ‘browseURL’
rite : runCode: no visible global function definition for ‘savehistory’
rite : runCode: no visible global function definition for ‘loadhistory’
rite : knittxt: no visible global function definition for ‘Sweave’
rite : knittxt: no visible global function definition for ‘browseURL’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘packageDescription’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘na.omit’
rite : about : <anonymous>: no visible global function definition for
  ‘browseURL’
rite : <anonymous>: no visible global function definition for
  ‘capture.output’
rite : <anonymous>: no visible global function definition for
  ‘update.packages’
rite : <anonymous>: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help.search’
rite : commandCompletion: no visible global function definition for
  ‘apropos’
rite : findreplace : <anonymous>: no visible global function definition
  for ‘browseURL’
Undefined global functions or variables:
  Sweave apropos browseURL capture.output help help.search loadhistory
  na.omit packageDescription savehistory update.packages
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "Sweave", "apropos", "browseURL", "capture.output",
             "help", "help.search", "loadhistory", "packageDescription",
             "savehistory", "update.packages")
to your NAMESPACE file.
Note: information on .o files is not available
File ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required and available but unsuitable version: ‘plumber’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rLiDAR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rLindo.Rcheck/00install.out’ for details.
Mallows: no visible global function definition for ‘runif’
Mallows: no visible global function definition for ‘x11’
Mallows: no visible global function definition for ‘plot’
Mallows: no visible global function definition for ‘dev.off’
UpdateLambda: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RMark.Rcheck/00install.out’ for details.
File ‘RMC/libs/RMC.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rmgarch.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Running examples in ‘RMongo-Ex.R’ failed
The error most likely occurred in:

> ### Name: dbAggregate-methods
> ### Title: Performing a MongoDB aggregate query
> ### Aliases: dbAggregate dbAggregate-methods
> ###   dbAggregate,RMongo,character,character-method
> 
> ### ** Examples
> 
>   mongo <- mongoDbConnect("test")
>   # insert two records
>   dbInsertDocument(mongo, "test_data", '{"foo": "bar", "size": 5 }')
Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
  com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
Calls: dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck -> .Call
Execution halted
Running the tests in ‘tests/RMongo-Ex.R’ failed.
Last 13 lines of output:
  +   
  +   # print(length(output))
  +   print(as.character(output[1]))
  + 
  +   checkEquals("{ \"_id\" : \"bar\"}", as.character(output[1]))
  +   # checkEquals("bar", as.character(output[1]))
  + }
  > 
  > test.dbInsertDocument()
  Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
    com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
  Calls: test.dbInsertDocument ... dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck -> .Call
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rmosek.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rmpi.Rcheck/00install.out’ for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RnavGraph.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key.isPath: no visible global function definition for ‘tail’
.isPath: no visible global function definition for ‘head’
navGraph : <anonymous>: no visible global function definition for
  ‘tail’
navGraph : <anonymous>: no visible global function definition for ‘sd’
navGraph: no visible global function definition for ‘colors’
ng_image_array_gray : <anonymous>: no visible global function
  definition for ‘grey’
scagGraph: no visible global function definition for ‘quantile’
closeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.off’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.new’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.cur’
plot,NG_graph-ANY: no visible global function definition for ‘box’
plot,NG_graph-ANY: no visible global function definition for ‘axis’
plot,NG_graph-ANY: no visible global function definition for ‘points’
plot,NG_graph-ANY: no visible global function definition for ‘text’
plot,NG_graph-ANY: no visible global function definition for ‘segments’
updateViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.set’
Undefined global functions or variables:
  axis box colors dev.cur dev.new dev.off dev.set grey head points
  quantile sd segments tail text
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.new", "dev.off",
             "dev.set", "grey")
  importFrom("graphics", "axis", "box", "points", "segments", "text")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Running examples in ‘RnavGraph-Ex.R’ failed
The error most likely occurred in:

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

> p.digits <- digits[, sel]

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

  When sourcing ‘RnavGraph.R’:
Error: [tcl] invalid command name "image".
Execution halted
Error in re-building vignettes:
  ...
    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

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

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


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

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

Execution halted
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
installed size is 82.0Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     79.9Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R   9.9Mb
Error in re-building vignettes:
  ...
  input string 547 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 548 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 556 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RobPer_vignette.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[G^^[^^?,<bf><ae><ba>`K^^Y^^B<89>P<ea>j<bb>PhIP<9d><ee>%<84>^^V<e5><a0>R<e8>!<b7><fc>^^C<a5><e4>_p<8f>9<94>B.=<b6>Đ<d2>^^F...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...^z^^ZrՒ^^@N8<c1><ff>r<b2>m{'<88><8e><c0>9Ȕ֥<de>?<c1><8d>~<f3><cd>7s<b9>\^^T
                                                  EP<98><87>=萃<b3><bf><dd>CD<83>B<ab>՚<9e><9e><c6>'^^QE...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 <e3><d6>n<b7><d1>^^E^^?<a5>-^^C^^U^^D<c1><cc>̌<ef><fb><b9>\^^N
                                      <f5><ad>V<cd>,˂<89>c<9e>(<97><cb>e!^^D<8f>hY<96>뺨L<9c>p^^_g<cf><f7>}^^...
The control sequence at the end of the top line
of your error message was never \def'ed. I
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
File ‘robust/libs/robust.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘rb.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 examples in ‘robustX-Ex.R’ failed
The error most likely occurred in:

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

Package suggested but not available for checking: ‘RODBC’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ROracle.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rcanvec’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rotations.Rcheck/00install.out’ for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rothermel.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keybestFM: no visible global function definition for ‘data’
gaRoth: no visible global function definition for ‘data’
ros: no visible global function definition for ‘na.omit’
rosunc: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpanel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rpdb.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keycell.density.default: no visible binding for global variable
  ‘universalConstants’
conect.pdb: no visible binding for global variable ‘elements’
masses.default: no visible binding for global variable ‘elements’
toSymbols.character: no visible binding for global variable ‘elements’
toSymbols.integer: no visible binding for global variable ‘elements’
visualize.coords: no visible binding for global variable ‘elements’
visualize.coords: no visible binding for global variable ‘rgb’
Undefined global functions or variables:
  elements rgb universalConstants
Consider adding
  importFrom("grDevices", "rgb")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpg.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rpoppler.Rcheck/00install.out’ for details.
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RProtoBuf-paper.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.23 ...<a2>i^^ZVn3*<80><b0>^^X<89>^^H8<e5>ryqq<b1>^^W<d3><d2>_PV<af><d7>MӔۃ\<c9>
                                                  [<bd>^<cf>f<b3><9f>}<f6><99>i<9a><b0><ae><a0>,<93><c9>lmm<c9>w<a4>iZ...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.24 ...<af><d7>q^^T^^Yc<d3><d3><d3>D<e4><fb>>^^Q<c1>^^?<f4><de><e5>^^[<a4>r<b6><a9><d6>Q<9a><f6>"<8b>e}
                                                  X<ce>|><8f><bc><f8><d0>V^^Nc^^L6
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.25 ^^AW&<93>	^^G<96>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘RSAGA’ ‘shapefiles’
  Please remove these calls from your code.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RQuantLib.Rcheck/00install.out’ for details.
File ‘RSAgeo/libs/RSAgeo.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘RSAc.o’, ‘lib.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RSAc.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RSAP.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
-> Fetching 'http://stats.oecd.org/restsdmx/sdmx.ashx/GetData/MIG/TOT../all?startPeriod=2010&endPeriod=2011'
-> Fetching 'http://stats.oecd.org/restsdmx/sdmx.ashx/GetData/MIG/TOT../all?startPeriod=2010&endPeriod=2011'
-> DSD ref identified in dataset = 'MIG'
-> Attempt to fetch & bind DSD to dataset
-> Fetching 'http://stats.oecd.org/restsdmx/sdmx.ashx/GetDataStructure/MIG'
-> DSD fetched and associated to dataset!
-> Fetching 'http://stats.oecd.org/restsdmx/sdmx.ashx/GetData/MIG/TOT../all?startPeriod=2010&endPeriod=2011'
-> Fetching 'http://stats.oecd.org/restsdmx/sdmx.ashx/GetDataStructure/MIG'
trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Frd_e_gerdsc.sdmx.zip'
Content type 'application/octet-stream;charset=UTF-8' length 1379111 bytes (1.3 MB)
==================================================
downloaded 1.3 MB

Quitting from lines 161-164 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
HTTP request failed with status: 500 Internal Server Error
Execution halted
Note: information on .o files is not available
File ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsgcc.Rcheck/00install.out’ for details.
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  19.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsml.Rcheck/00install.out’ for details.
installed size is 47.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  45.6Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 58.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  55.5Mb
installed size is 237.6Mb
  sub-directories of 1Mb or more:
    libs  235.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File ‘Rsundials/libs/Rsundials.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Objects: ‘cvodes.o’, ‘sundials_cvodes.o’, ‘sundials_ida.o’
  Found ‘_printf’, possibly from ‘printf’ (C)
    Objects: ‘nvector_serial.o’, ‘sundials_band.o’,
      ‘sundials_smalldense.o’
  Found ‘_putchar’, possibly from ‘putchar’ (C)
    Objects: ‘nvector_serial.o’, ‘sundials_band.o’,
      ‘sundials_smalldense.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rsymphony.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rugarch.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RunuranGUI.Rcheck/00install.out’ for details.
installed size is 30.8Mb
  sub-directories of 1Mb or more:
    libs  30.2Mb
Missing or unexported object: ‘xml2::xml_find_first’
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘pixmap’ which was already attached by Depends.
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyrvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RVowpalWabbit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RVPedigree.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RWeka.Rcheck/00install.out’ for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs    8.3Mb
    yacas   1.3Mb
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘vcd’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘ggplot2’ ‘grid’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘foreign:::adQuote’
  See the note in ?`:::` about the use of this operator.
Invalid MIT-MAGIC-COOKIE-1 keycalc.hist.breaks: no visible global function definition for
  ‘nclass.Sturges’
calc.hist.breaks: no visible global function definition for ‘nclass.FD’
calc.hist.breaks: no visible global function definition for
  ‘nclass.scott’
check.class: no visible global function definition for ‘as.formula’
gtkColorSelectionForPlotGetColor: no visible global function definition
  for ‘rgb’
gtkColorSelectionWidgetNew: no visible global function definition for
  ‘colors’
gtkFileChooserDialogFilteredActivate: no visible binding for global
  variable ‘theme_grey’
localize: no visible global function definition for ‘localeToCharset’
summary.CrossTable : twoDimTable: no visible global function definition
  for ‘addmargins’
summary.CrossTable: no visible global function definition for
  ‘assocstats’
write.spss: no visible global function definition for ‘write.table’
write.stata: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  addmargins as.formula assocstats colors localeToCharset nclass.FD
  nclass.Sturges nclass.scott rgb theme_grey write.table
Consider adding
  importFrom("grDevices", "colors", "nclass.FD", "nclass.Sturges",
             "nclass.scott", "rgb")
  importFrom("stats", "addmargins", "as.formula")
  importFrom("utils", "localeToCharset", "write.table")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Package suggested but not available for checking: ‘org.Sc.sgd.db’
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sandwich-OOP.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 ...<bb>[<cf>^^VZ^^X!=<cf><cb>d2<f8><8e>TND<b5>Z<ed><83>^^O><c0> @u<ea><b2>@<ce>y<96><d7>\<bd>
                                                  ^^Q<d0>^^BT<f8><97>K<a1>P^^@q^^?Q^<f3>ػ<88>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.19 ...<ee>`0 "<c4>^^L3^^R<dc>[^^Ha<db>v.<97>øa^^X<8e><c3>E<9d><e6>y<9d>_^^?<ed>^
                                                  <bf><fe><ae>a\<95>RJ)<85><82><94>Ҷ<ed>b<b1>H<a1>^^N<8a>a^...
! Undefined control sequence.
l.19 ...^^L3^^R<dc>[^^Ha<db>v.<97>øa^^X<8e><c3>E<9d><e6>y<9d>_^^?<ed>^<bf><fe><ae>a\<95>
                                     
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
    opponent.vote, turnout, winner, winner.bmi, winner.height,
    winner.party, winner.vote

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

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

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

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

The following object is masked from package:SciencesPo:

    turnout

.data was converted to a dataframe
Warning: New theme missing the following elements: axis.line.x, axis.line.y, panel.grid.major, panel.grid.minor
Quitting from lines 1090-1091 (SciencesPo.Rmd) 
Error: processing vignette 'SciencesPo.Rmd' failed with diagnostics:
invalid 'times' argument
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    libs   2.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SDD.Rcheck/00install.out’ for details.
Found the following executable file:
  inst/external/env/bio14.bil
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/semiArtificial.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 439 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 447 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 448 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 456 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'semPLS-intro.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<f4><af>i<9a>^^X<a2><94>m<db>['<8c>^^N<e9><85><de><eb><fd>ư<b0><b0><c0>^^X<b3>,<eb><e4>ɓW<ae>\1
                                                  M<f3><fe><fd><fb>W<af>^^^UB<98><a6><f9><f8><f1><e3><c9><c9>I<a5>T<bd>^<bf>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ^^E^^\^^R<c2>^^[<fe>.,,<80>^^Y<a5><d4><e5>˗<a5><94>+++<b6>m^^S\<95>
                                           RB<88><f9><f9><f9>~<ad><a7><cf>ҋK<c4><d2>><cd><ff><8e><d9><db>o^^ZڽA<a6>=<a9>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 <82>?s<b9><94>m<bb><8d><c6><fb><9c>^^_<e5><fc>^^?^^WS<c3>0<94>R<8e><e3><cc><ce>΢^^Ec<b1>\<f2>
                                             E<a4><94><89>Db}}}bb<a2><d9>l&^^R<89>f<b3>)<84><a8>T
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 128.5Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    libs  122.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sgPLS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/shinyRGL.Rcheck/00install.out’ for details.
randomDAG: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbinom
Consider adding
  importFrom("stats", "rbinom")
to your NAMESPACE file.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.0Mb
Error in re-building vignettes:
  ...
  input string 420 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 421 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'smacof.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.22 ...<97><d7><de>׽<9d><f4><82><b1>~<c5><d3>u^^]R<f9><fd>~EQ8<e7>D<f4><f8><f1><e3><d5><d5>Uo3UU!9^^Q}
                                                  <f1><c5>^^W^^X<d3><c6><c6><c6><ec><ec><ec><f2><f2><f2>^^O?<fc><b0><ba><ba>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.22 ...<f5><d5>W<90>jii	<ed>!<c0><e3>Ǐ^^[<8d><c6><ed>۷!6^^Q<ed><ef><ef>omm<a9><aa><ba><b4><b4><d4><fb>h}
                                                  o0 <ca>d2<9a><a6>a<82>^^F<84>7)<de>^^E`D-Ì<be>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/smint.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/smoothtail.Rcheck/00install.out’ for details.
Running examples in ‘soilphysics-Ex.R’ failed
The error most likely occurred in:

> ### Name: fitsoilwater
> ### Title: Interactive Estimation of van Genuchten's (1980) Model
> ###   Parameters
> ### Aliases: fitsoilwater
> 
> ### ** Examples
> 
> # Liu et al. (2011)
> h <- c(0.001, 50.65, 293.77, 790.14, 992.74, 5065, 10130, 15195)
> w <- c(0.5650, 0.4013, 0.2502, 0.2324, 0.2307, 0.1926, 0.1812, 0.1730)
> fitsoilwater(w, h)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: fitsoilwater ... handshake -> fun -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Running examples in ‘SPACECAP-Ex.R’ failed
The error most likely occurred in:

> ### Name: SPACECAP
> ### Title: Fits spatially-explicit capture recapture models
> ### Aliases: SPACECAP
> 
> ### ** Examples
> 
> SPACECAP()
Invalid MIT-MAGIC-COOKIE-1 keyError in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: SPACECAP ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...

    RFoptions

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

    atan2

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

    abs, acosh, asin, asinh, atan, atan2, atanh, cos, cosh, exp,
    expm1, floor, gamma, lgamma, log, log1p, log2, logb, max, min,
    round, sin, sinh, sqrt, tan, tanh, trunc

Loading required package: grid

Attaching package: 'grid'

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

    gpar

Quitting from lines 352-356 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotc2412bdcf402.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc2412bdcf402.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sparr.Rcheck/00install.out’ for details.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/spatgraphs.Rcheck/00install.out’ for details.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.1Mb
    libs   1.6Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: 'lgamma' declared at (1) is also the name of an intrinsic.  It can only be called via an explicit interface or if declared EXTERNAL.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SPECIES.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rgdal’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sphereplot.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
  input string 415 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingSpikeSlabGAM.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<c1>
          k^^[W^^S<9f>H5<89><88>><ad>^^_	qm<b3><de><f5><83>^^^<fa><d5><c8>^^B^^]J^^N<a9>|0^^T<f7><90>[(<f4>\^^D<fd>z<ed><b5><87><9e>K}O...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<ad>^^_	qm<b3><de><f5><83>^^^<fa><d5><c8>^^B^^]J^^N<a9>|0^^T<f7><90>[(<f4>\^^D
                                                  <fd>z<ed><b5><87><9e>K}O/<ba><f9><d0>@<bd>^^D;<82><86><84>,]<ab>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...^D^^V<ad>^^WU<95><a9><fd><bc>k<c5>]<b7>X<fa>^^N?4<ec><e7>ږ<94>ڎ<e5>j^^Nb<f5><f6
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sprint.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RPostgreSQL’
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages which this enhances but not available for checking:
  ‘RPostgreSQL’ ‘RODBC’
Running examples in ‘SRRS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SRRS-package
> ### Title: The Stepwise Response Refinement Screener (SRRS)
> ### Aliases: SRRS-package
> 
> ### ** Examples
> 
> SRRS()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: SRRS ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   8.4Mb
    lib       1.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/StatDA.Rcheck/00install.out’ for details.
File ‘stepPlr/libs/stepPlr.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘cg_descent.o’
  Found ‘__gfortran_stop_string’, possibly from ‘stop’ (Fortran)
    Object: ‘cg_descent.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 examples in ‘stepwise-Ex.R’ failed
The error most likely occurred in:

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


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

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

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

> WinHalfWidth<-30

> permReps<-10

> a<-maxchi(inputFile, breaks, WinHalfWidth, permReps)
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=georgia&zoom=5&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=georgia&sensor=false
Quitting from lines 220-233 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyDetailOpLines: no visible global function definition for
  ‘tkProgressBar’
DetailOpLines: no visible global function definition for
  ‘setTkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘tkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘setTkProgressBar’
SimHistory: no visible global function definition for ‘tkProgressBar’
SimHistory: no visible global function definition for
  ‘setTkProgressBar’
Undefined global functions or variables:
  setTkProgressBar tkProgressBar
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Number of test functions: 18 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  stremr unit testing - 18 test functions, 1 error, 0 failures
  ERROR in test.speedglm.allestimators10Kdata: Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 7
  1. Error: basic (@test-strip.R#11) 
  2. Error: big (@test-strip.R#18) 
  3. Error: libre (@test-strip.R#25) 
  4. Error: abiword (@test-strip.R#35) 
  5. Error: Japanese (cp932) (@test-strip.R#45) 
  6. Error: Chinese and Korean (@test-strip.R#55) 
  7. Error: Europe (@test-strip.R#65) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘subspaceMOA-Ex.R’ failed
The error most likely occurred in:

> ### Name: DSC_HDDStream
> ### Title: Density-based Projected Clustering over High-Dimensional Data
> ### Aliases: DSC_HDDStream
> 
> ### ** Examples
> 
> dsc <- DSC_HDDStream()
Error in rJava::.jcall("SubspaceClustererBuilder", returnSig = "Lmoa/clusterers/hddstream/HDDStream;",  : 
  RcallMethod: cannot determine object class
Calls: DSC_HDDStream -> <Anonymous> -> .External
Execution halted
Package required but not available: ‘d3r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.2Mb
Package suggested but not available for checking: ‘RTCGA.clinical’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Quitting from lines 55-64 (Informative_Survival_Plots.Rmd) 
Error: processing vignette 'Informative_Survival_Plots.Rmd' failed with diagnostics:
there is no package called 'RTCGA.clinical'
Execution halted
File ‘survrec/libs/survrec.so’:
  Found ‘__gfortran_rand’, possibly from ‘rand’ (Fortran)
    Object: ‘bootstrap.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keydlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
File ‘svmpath/libs/svmpath.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyprocessSocket: no visible global function definition for ‘URLdecode’
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
  Warning: 'erfc' declared at (1) is also the name of an intrinsic.  It can only be called via an explicit interface or if declared EXTERNAL.
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1)
  apply.f:86:0: warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  burnop.f:29:0: warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  harvestop.f:166:0: warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  harvestop.f:195:0: warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  harvgrainop.f:168:0: warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  harvkillop.f:175:0: warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  plantop.f:87:0: warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  rewind_init.f:171:0: warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1)
  sweep.f:56:0: warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
  rewind_init.f:172:0: warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SWATmodel.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘cplexAPI’ ‘clpAPI’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sybilSBML.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/symbolicDA.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 426 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'symmoments.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Ol
           ^^S<cb>^^Y<ff>b;^^?^^\<c0><bb>+^^^<90><86>8<b1><b6><e5>E<b4><c1><a1><b2>z^^H^^R5<95>,UBꡕ,<bd>'<ae>O^^QG<de>^^A<e5>^^]...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 <e9>j^^Op<b9>\<82>
               <94><ac><aa><a2><de><d7>^^?<fc>à<89>f<b3><db><d0>y<88><eb><d2>-f=<99><d1>M]<dd>9<bd><b3><a7><fb><f0><f6><f7><f1>o<be><f2>5A<e0><86><a1><8a>zg<b7><95>.=<f7><e7><bf><fe><fb>?<e9><cd>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...<9e><be>x<f1><a2>,<cb>^^V<8b><85><e7><
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Package suggested but not available for checking: ‘GISTools’
Running examples in ‘tbart-Ex.R’ failed
The error most likely occurred in:

> ### Name: allocate
> ### Title: Teitz-Bart algorithm applied to Spatial* and Spatial*DataFrame
> ###   objects
> ### Aliases: allocate
> 
> ### ** Examples
> 
> data(meuse)
> coordinates(meuse) <- ~x+y
> allocate(meuse,p=5)
  [1]   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9  23
 [19]  23  23  23  23  23   9   9   9  23  23  23   9  23  23  23  23  23  23
 [37]  23  23  23  23  23 132 132 132 132 132 132 132 132 132 132 132 132 132
 [55] 132 132 132 132 132 132 132 113 113 113 113 113 113 113 113  77  77  77
 [73]  77  77  77  77  77  77  77  77  77 113 113   9 113 113  77  77  77  77
 [91]  77  77  77  77  77  77  77  77  77  77  77 113 113 113 113 132 113 113
[109] 113 113 113 113 113 113 113 113 113 113 132 132 132 132 132 132 132 132
[127] 132 132   9  23 113 132  23 132 113 113 113  77  77  77  77  77  77  77
[145]  77  77  77  77  77  77  77  77  77  77 113
> 
> 
> 
> require(RColorBrewer)
Loading required package: RColorBrewer
> require(GISTools)
Loading required package: GISTools
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GISTools’
> data(georgia)
Warning in data(georgia) : data set ‘georgia’ not found
> allocations.list <- allocate(georgia2,p=5)
Error in allocate(georgia2, p = 5) : object 'georgia2' not found
Execution halted
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  34.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TDMR.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyaniplotevents: no visible global function definition for ‘plot’
aniplotevents: no visible global function definition for ‘lines’
cbfs: no visible global function definition for ‘rnorm’
cbfs: no visible global function definition for ‘runif’
cbfs_red: no visible global function definition for ‘arima.sim’
cbfs_red: no visible global function definition for ‘runif’
eventCluster: no visible global function definition for ‘princomp’
eventCluster: no visible global function definition for ‘kmeans’
measures: no visible global function definition for ‘sd’
measures: no visible global function definition for ‘var’
measures: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘Box.test’
noiseTests: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘ar’
plotevents: no visible global function definition for ‘plot’
plotevents: no visible global function definition for ‘lines’
ur.za.fast : roll: no visible global function definition for ‘coef’
ur.za.fast : roll: no visible global function definition for ‘lm’
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Running examples in ‘TELP-Ex.R’ failed
The error most likely occurred in:

> ### Name: telp
> ### Title: The Base Function of This Package The Free Evocation of Words
> ###   Technique
> ### Aliases: telp
> ### Keywords: function
> 
> ### ** Examples
> 
> telp()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: telp ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/termstrc.Rcheck/00install.out’ for details.
installed size is 37.8Mb
  sub-directories of 1Mb or more:
    libs       6.7Mb
    tessdata  31.0Mb
Error in re-building vignettes:
  ...
  input string 398 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'texreg.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[<d7>^^V?<95><f2><d1>!A<d2>}-AQQ,.^^D<c3>Kp^^D^^C<85>^^Z<8a>C0Y4P^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.18 RJ<a5><94>^^P^^BS<e7><f3>y)<a5><e3>8B^^H<c3>0<94>R/^
                                 <bc>8s<e6><cc>ݻw<85><82>^^P<c2>4M)<e5><ec>쬮<eb><85>B<81><88><a4><94>RJ<d3>4<85>^^PJ<a9><d5><d5><d5>...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.21 ...<8b>MMM^^]dÃa<ce>a<db>VG<86><c3>1<a7><94>ҶmP	<e4><c2>/3-^^X<8c>y<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.5Mb
    libs   6.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/textTinyR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because Tigger-Vignette.Rmd appears to be an R Markdown v2 document.
Loading required package: ggplot2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

sh: sysctl: command not found
Quitting from lines 111-116 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command
Execution halted
drawGraph: no visible global function definition for ‘eqmcc’
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘plot’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off eqmcc lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running the tests in ‘tests/simple.R’ failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > 
  > ## run in the R session temp.dir. which gets cleaned
  > setwd(tempdir())                        
  > 
  > ## process html -- should work everywhere
  > file.copy(system.file("examples", "simpleHtml.Rmd", package="tint"), "simpleHtml.Rmd")
  [1] TRUE
  > rmarkdown::render("simpleHtml.Rmd")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tkrgl.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘rgl’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key.my.tkdev: no visible global function definition for ‘X11’
tkpersp : draw: no visible global function definition for ‘par’
tkpersp : draw: no visible global function definition for ‘persp’
Undefined global functions or variables:
  X11 par persp
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
Running examples in ‘tm.plugin.dc-Ex.R’ failed
The error most likely occurred in:

> ### Name: tm_map.DCorpus
> ### Title: Transformations on Distributed Corpora
> ### Aliases: tm_map.DCorpus
> 
> ### ** Examples
> 
> data("crude")
> tm_map(as.DCorpus(crude), content_transformer(tolower))
Warning in file(con, "w") :
  cannot open file '/var/folders/8q/c881c7rn7_x34vj58f4ywhvm0000h3/T//Rtmpb0djBE/DSL-20160505-034420-gjoxfxyrqb/chunk-15dc814df4a7b': No such file or directory
Error in file(con, "w") : cannot open the connection
Calls: tm_map ... DS_write_lines -> <Anonymous> -> <Anonymous> -> file
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘TeachingDemos’ ‘ash’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘tpr/libs/tpr.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

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

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

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

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

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Quitting from lines 90-91 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Package suggested but not available for checking: ‘OpenStreetMap’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TraMineR-state-sequence.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 xí\Ï
          k^^[×^^V>^^]÷áêEñÅ}&ÏA28´`#»^^Hº(¸rÀÝtÿnJ¡Yµ.^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.18 ...l4^^ZDBJùÝwßÝ¿^^?_^^H.¼-eMNNîXVrr2pÝ×^
                                                  O$îæa^^Táú©óo³{ë^^RÑ^^[B...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.23 ^^G^^G^^GRÊ7oÎÌÌ^^XqæÌz½n^^X^^F|ù\.w
                                      
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TSclust.Rcheck/00install.out’ for details.
Packages which this enhances but not available for checking:
  ‘TSPostgreSQL’ ‘TSodbc’
Packages suggested but not available for checking: ‘TSodbc’ ‘RODBC’
Packages unavailable to check Rd xrefs: ‘TSodbc’, ‘RODBC’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/datastructure/ESTAT/DSD_ei_nama_q/1.0
Feb 15, 2017 7:33:57 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/data/ESTAT,ei_nama_q,1.0/Q.MIO-EUR.NSA.CP.NA-P72.IT
Feb 15, 2017 7:33:57 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData
INFO: The sdmx call returned messages in the footer:
 Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]]

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.util.SdmxException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider.
Execution halted
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

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

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

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted
Package unavailable to check Rd xrefs: ‘TSPostgreSQL’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TSdist.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.3Mb
Running examples in ‘uplift-Ex.R’ failed
The error most likely occurred in:

> ### Name: checkBalance
> ### Title: Standardized Differences for Stratified Comparisons
> ### Aliases: checkBalance
> ### Keywords: uplift xBalance
> 
> ### ** Examples
> 
> library(uplift)
> 
> set.seed(12345)
> dd <- sim_pte(n = 1000, p = 20, rho = 0, sigma =  sqrt(2), beta.den = 4)
> dd$treat <- ifelse(dd$treat == 1, 1, 0) 
> 
> checkBalance(treat ~ X1 + X2 + X3 + X4 + X5 + X6 , data = dd)
     strata  unstrat                                                              
     stat    treat=0  treat=1 adj.diff adj.diff.null.sd std.diff     z            
vars                                                                              
X1          0.01152  -0.00596 -0.01748         0.06006  -0.01840 -0.29103         
X2          0.03160  -0.02812 -0.05972         0.06236  -0.06057 -0.95778         
X3          0.01145  -0.02242 -0.03387         0.06355  -0.03370 -0.53303         
X4          0.01533  -0.03551 -0.05083         0.06370  -0.05046 -0.79801         
X5          -0.06440 0.02370  0.08810          0.06153  0.09060  1.43175          
X6          0.02237  -0.02177 -0.04414         0.06308  -0.04425 -0.69980         
---Overall Test---
        chisquare df p.value
unstrat      4.54  6   0.604
---
Signif. codes:  0 ‘***’ 0.001 ‘** ’ 0.01 ‘*  ’ 0.05 ‘.  ’ 0.1 ‘   ’ 1 
Error in ncol(DT) : object 'DT' not found
Calls: <Anonymous> ... withOptions -> tryCatch -> do.call -> <Anonymous> -> ncol
Execution halted
Package unavailable to check Rd xrefs: ‘rgdal’
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
         list(call = mc, handlers = handlers, levels = levels(mf[[1L]]), terms = attr(mf, 
             "terms"))), class = classes)
  5: RWeka_build_classifier(mf, control, name, handlers, options, init)
  6: read_model_frame_into_Weka(mf)
  7: read_data_into_Weka(mf, 1L)
  8: .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List"))
  
  testthat results ================================================================
  OK: 1068 SKIPPED: 20 FAILED: 1
  1. Error: test train/prediction base learner methods (@test_base_learner.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘uuid/libs/uuid.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 428 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vars.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ?<f1><8b><96><eb><96>;<d9>l6^^V<8b>uM<<c3>0n޼<99>N<a7>1\Y
                                 <96><f1><a6><96><fb><9a><a6><a5>R)<88>^^Z<8f><c7><f9>D^^D<83><c1>D"<a1><eb><ba>,˲,뺎6<f8><9a>J<a5>^^N...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 <bd>MMM<e1><9a>c^^?^^?<ff><ee>ݻ^^O^^_><9c><9b><9b><8b><c7>㌱<d9><d9>Y<bc><e8>$^^L\<cc>
                                                <84>H<d7><f5><d3><c7><dd>!<ba>,<9e><ae><eb>D<f4><e1><87>^^_z<9e>G<c7><fa><a1>cB...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 0<c6>X<b5>ZE\<e6>
             <a7>.<98>L<c7>[H~n<c7><e3>q<90><b6><a5>^^_<f4><cf>?<fd>!<de>)<8c><b8><88><a6><a5><8b>^^\n<e3>^^X^^Xc<b0>^^G|<c7>^^X^^[<94><f3><f3><f3>t<ec>	^...
The control sequence at the end o
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   3.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VDA.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keycv.vda.le.default: no visible global function definition for ‘predict’
cv.vda.r.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VecStatGraphs3D.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyDrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in ‘VecStatGraphs3D-Ex.R’ failed
The error most likely occurred in:

> ### Name: DrawModuleAndAngleDistribution3D
> ### Title: Graphic representation of Module and Angle Distribution.
> ### Aliases: DrawModuleAndAngleDistribution3D
> ### Keywords: graphics
> 
> ### ** Examples
> 
>    FileName<-system.file("data/XYZcoor.txt", package="VecStatGraphs3D")
>    dat<-LoadData3D(FileName, Type=1)
>    DrawModuleAndAngleDistribution3D(dat, plane="XY");
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: DrawModuleAndAngleDistribution3D ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/vegan3d.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.6Mb
Error in re-building vignettes:
  ...
  input string 373 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'categoricalVGAM.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.24 ...<d5>j<95><9f>e<db>v<a9>T^^Z^^]^^]<c5><ef><b9>^^P<81>=ʳ]H<e9><a2>^^^<d2>_<a6><89>`L^
                                                  <8e>B<d4>b^^X^^@^^NII^^Fv2<f2>"3r...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.30 ...<93><ee><d0>Nx^^?^^^<f3>Y|<c0>cE1<ca><fb>J9<a0>C<98><ae>ŧ`<c8><e3>"<91>^^H<ca>\t<e2>
                                                  <e7><bc>;<e8><dd>z<bd>>??<8f>^^O^^B<89>^^H^^Xv<fc>...
! Missing { inserted.
<to be read again> 
                   \edef 
l.30 ...<93><ee><d0>Nx^^?^^^<f3>Y|<c0>cE1<ca>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘VisuClust-Ex.R’ failed
The error most likely occurred in:

> ### Name: FuzzyPlot
> ### Title: Displays a Fuzzy Plot
> ### Aliases: FuzzyPlot
> 
> ### ** Examples
> 
> 
> library(cluster)
> library(MASS)
> 
> # The example data
> data("MilchSmall")
> 
> M <- scale(MilchSmall[3:6])
> D <- dist(M)
> S <- sammon(D)
Initial stress        : 0.00738
stress after  10 iters: 0.00227, magic = 0.500
stress after  20 iters: 0.00204, magic = 0.500
stress after  30 iters: 0.00203, magic = 0.500
> F <- fanny(D, 6)
> 
> FuzzyPlot(S$points, F$membership, labels=MilchSmall[,2], 
+ 	clusterColors=c("red", "green", "magenta", "yellow", "blue", "black"))
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: FuzzyPlot ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
File ‘waffect/libs/waffect.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wand.Rcheck/00install.out’ for details.
Running examples in ‘wbsts-Ex.R’ failed
The error most likely occurred in:

> ### Name: tau.fun
> ### Title: Universal thresholds
> ### Aliases: tau.fun
> ### Keywords: threshold
> 
> ### ** Examples
>  
> 
> cps=c(400,470)
> set.seed(101)
> y=sim.pw.ar(N =2000,sd_u = 1,b.slope=c(0.4,-0.6,0.5),br.loc=cps)[[2]]
> #tau.fun(y) is the default value for C_i
> #Binary segmentation
> wbs.lsw(y,M=1)$cp.aft
NULL
> #Wild binary segmentation
> wbs.lsw(y,M=3500)$cp.aft
Error in while (ind.max < 0 | ind.max > e) { : 
  missing value where TRUE/FALSE needed
Calls: wbs.lsw -> uh.wbs
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/WMCapacity.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-54 (Automat.Rmd) 
Error: processing vignette 'Automat.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wnominate.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because wordcloud.Rmd appears to be an R Markdown v2 document.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 432 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WRS2.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.19 ...VB<e0>+W^^L<ce>O?<fd>^^T^^X[^^&"<ec>^^G"<82>p<e5>rYJ	<81><98>x&<b9>\<ce>
                                                  <f3><bc>d2	A<85>^^PA^^P<94>J%<f4><80>^^[<ef>g<a5>T...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 <95>l<f1><81><93>T*<85>ꥮ<eb>^^T<b9>^^]<88>sv<df><f7><85>^^P<cb><cb>˨^^Qan<9c><d7>an\2
                                                <8b><a6>s<b6>m+<a5><82>  "]<d7><f9><e4><bd><d1>h^^Pѩ<ca><ea>)<fa><b0>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.29 èV<ab><8b><8b><8b>tb<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/x12GUI.Rcheck/00install.out’ for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java        4.6Mb
    unitTests   1.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/YplantQMC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/YuGene.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: D:/temp/RtmpAFsgBH/R.INSTALL2244144d7e99/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
Running examples in 'ActuDistns-Ex.R' failed
The error most likely occurred in:

> ### Name: dgumbeld
> ### Title: Gumbel pdf
> ### Aliases: dgumbeld
> ### Keywords: Gumbel distribution
> 
> ### ** Examples
> x=runif(10,min=0,max=1)
> y=dgumbeld(x)
Error in dgumbel(x, mu = mu, sigma = sigma) : 
  unused arguments (mu = mu, sigma = sigma)
Calls: dgumbeld -> ifelse -> dgumbel
Execution halted
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
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.
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/BACA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BayClone2.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/BiSEp.Rcheck/00install.out' for details.
installed size is 72.4Mb
  sub-directories of 1Mb or more:
    include   2.7Mb
    lib      69.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BRugs.Rcheck/00install.out' for details.
Package required but not available: 'OpenCL'

See section 'The DESCRIPTION file' 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.
Running examples in 'chipPCR-Ex.R' failed
The error most likely occurred in:

> ### Name: amptest
> ### Title: Class '"amptest"'
> ### Aliases: amptest amptest-class summary.amptest summary,amptest-method
> ###   show.amptest show,amptest-method plot.amptest plot,amptest-method
> ###   plot,amptest,ANY-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> # Compare a positive and a negative amplification reaction.
> # First simulate positive reaction (fluo.pos) and than the 
> # negative reaction (fluo.neg).
> # Simulation of an amplifiaction curve with some noise and a high signal.
> 
> fluo.pos <- AmpSim(cyc = 1:40, noise = TRUE)[, 2]
> ampt.pos <- amptester(fluo.pos, manual = TRUE, background = c(0, 15), 
+ 		      noiselevel = 0.15)
Error in validObject(.Object) : 
  invalid class "amptest" object: superclass "Mnumeric" not defined in the environment of the object's class
Calls: amptester -> new -> initialize -> initialize -> validObject
Execution halted
Error in re-building vignettes:
  ...

Loading required package: XML

Attaching package: 'XML'

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

    toHTML

Loading required package: GO.db
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moe430a.db'
Loading required package: RankAggreg
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.2/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'clValid.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE (file ./clValid-022.pdf): PDF inclusion: required p
age does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Execution halted
Error in re-building vignettes:
  ...
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Warning in grid.Call.graphics(L_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  font family not found in Windows font database
Quitting from lines 775-800 (CopulaDTA_Vignette.Rmd) 
Error: processing vignette 'CopulaDTA_Vignette.Rmd' failed with diagnostics:
formal argument "axis.title.y" matched by multiple actual arguments
Execution halted
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   6.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cplexAPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cudaBayesreg.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > test_check("dataone")
  Loading required package: dataone
  1. Failure: CNode object index query works with query list param (@test.D1Node.R#37) 
  result[[1]]$abstract does not match "chlorophyll".
  Actual value: "Two YSI water quality sondes and loggers were installed onto a navigation light pole in Kentucky Lake KY, one at a depth of one meter below the lake surface, the other at one meter above the lake bottom in February 2005.  Water Temperature, pH, dissolved oxygen, conductivity, oxidation reduction potential, and turbidity data are collected from each sonde every 15 minutes.  Chlorophyll a data are collected from the one meter depth.  Lake elevations are estimated from depth data collected from the sonde anchored near the lake bottom."
  
  
  testthat results ================================================================
  OK: 197 SKIPPED: 31 FAILED: 1
  1. Failure: CNode object index query works with query list param (@test.D1Node.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    help   1.3Mb
    libs   1.5Mb
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/DGCA.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/Difdtl.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/DNAprofiles.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/DNLC.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: running command 'domino help' had status 127
See 'd:/Rcompile/CRANpkg/local/3.3/domino.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: domino.runCommand(loginCommand, domino.OK, "Login failed", theinput)
  3: domino.runCommandFromDefaultPath(commandAndArgs, successCallback, failureMessage, 
         stdInput)
  4: domino.handleCommandNotFound(failureMessage)
  5: stop(paste("Couldn't find domino client in the PATH or in default locations.\n  Add domino client directory path to PATH environment variable.\n  If you don't have domino client installed follow instructions on 'http://help.dominodatalab.com/client'.\n  If you use R-Studio Domino on GNU/Linux through a desktop launcher, add domino path to the .desktop file.\n\n  If you need more help, email support@dominodatalab.com or visit http://help.dominodatalab.com/troubleshooting\n\n  - ", 
         failureMessage), call. = FALSE)
  
  testthat results ================================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: The login command works (@test-login.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
  
  
  Executing test function test.registerDoRNG  ...  done successfully.
  
  ------------------- UNIT TEST SUMMARY ---------------------
  
  Error in .local(x, ...) : Functions: 2 | Errors: 1 | Failures: 0 
  ERROR in runit.dorng.R::test.dorng: Error in mpi.comm.spawn(slave = rscript, slavearg = args, nslaves = count,  : 
    Other MPI error, error stack:
  MPI_Comm_spawn(cmd="D:/RCompile/recent/R-33~1.2/bin/Rscript", argv=0x00000000069D9AA0, maxprocs=2, MPI_INFO_NULL, root=0, MPI_COMM_SELF, intercomm=0x000000000A18BF60, errors=0x000000000AA0DDE8) failed
  Function not implemented
  Calls: <Anonymous> -> <Anonymous> -> .local -> utest -> utest -> .local
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.9Mb
    libs   2.5Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: compare(object, expected, ...)
  3: EnsRoca(fcst4, obs2)
  4: count2prob(ens, type = 4)
  5: stopifnot(is.wholenumber(rowSums(x)))
  6: stop(sprintf(ngettext(length(r), "%s is not TRUE", "%s are not all TRUE"), ch), call. = FALSE, 
         domain = NA)
  
  testthat results ================================================================
  OK: 119 SKIPPED: 0 FAILED: 1
  1. Error: ROC area values (@test_Roc.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    xsd   5.5Mb
Running examples in 'etl-Ex.R' failed
The error most likely occurred in:

> ### Name: smart_download
> ### Title: Download only those files that don't already exist
> ### Aliases: smart_download
> 
> ### ** Examples
> 
> cars <- etl("mtcars")
Not a valid src. Creating a src_sqlite for you at:
D:\temp\Rtmp8ATktP\file1c7cce47422.sqlite3
> urls <- c("http://www.google.com", "http://www.nytimes.com")
> smart_download(cars, src = urls)
trying URL 'http://www.google.com'
Content type 'text/html; charset=ISO-8859-1' length unknown
.......... 
downloaded 10 KB

trying URL 'http://www.nytimes.com'
Error in download.file(url, method = method, ...) : 
  cannot open URL 'http://www.nytimes.com'
Calls: smart_download -> mapply -> <Anonymous>
Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             download.file(url, ...)
         }
     })(dots[[1L]][[2L]], dots[[2L]][[2L]])
  9: suppressWarnings(download.file(url, method = method, ...))
  10: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  11: download.file(url, method = method, ...)
  
  testthat results ================================================================
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: smart_download works (@test-etl.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FastRWeb.Rcheck/00install.out' for details.
Running examples in 'fheatmap-Ex.R' failed
The error most likely occurred in:

> ### Name:  Column Annotations 
> ### Title: Annotations of columns in "fheatmap_data"
> ### Aliases: ' annotation_col '
> ### Keywords: annotation_col
> 
> ### ** Examples
> 
> data(annotation_col)
> fheatmap(fheatmap_data,annotation_col=annotation_col)
Error in theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(),  : 
  formal argument "plot.margin" matched by multiple actual arguments
Calls: fheatmap -> draw_tree -> theme_blank -> theme
Execution halted
Running examples in 'fractal-Ex.R' failed
The error most likely occurred in:

> ### Name: findNeighbors
> ### Title: Nearest neighbor search in a multidimensional space
> ### Aliases: findNeighbors
> ### Keywords: distribution
> 
> ### ** Examples
> 
> ## Calculate the 10 nearest neighbors for each 
> ## point of 3-dimensional delayed coordinate 
> ## embedding of the beamchaos data. Exclude 
> ## self-neighbors from the output. 
> embedding <- embedSeries( beamchaos, dim = 3, tlag = 10 )
> nn <- findNeighbors( embedding, n.neighbor=10, olag=1 )
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/fuzzyforest.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/gamsel.Rcheck/00install.out' for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data    3.7Mb
    doc     2.9Mb
    tests   2.6Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: generate_grViz(x, ...)
  6: do.call(DiagrammeR::create_nodes, create_nodes_call)
  7: DiagrammeR::create_nodes
  8: getExportedValue(pkg, name)
  9: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 118 SKIPPED: 0 FAILED: 1
  1. Error: plotting a tree works (@test_plot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  [new]     a98c658afa4e0c096550 refs/tags/v0.2.10
  [new]     1bdc18280bdba8058e70 refs/tags/v0.2.12
  [new]     e066e5cfcc0028d5fe91 refs/tags/v0.2.15
  [new]     d3888ce03c9cf7d8f470 refs/tags/v0.2.5
  Adding metadata to DESCRIPTION for package ghit...
  
  
  testthat results ================================================================
  OK: 68 SKIPPED: 0 FAILED: 1
  1. Error: Install from a tag (@test_install.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/gmum.r.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/GOGANPA.Rcheck/00install.out' for details.
Warning: no function found corresponding to methods exports from 'gpclib' for: 'coerce', 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
read.polyfile: no visible global function definition for 'as'
write.polyfile: no visible global function definition for 'is'
write.polyfile: no visible global function definition for 'as'
[,gpc.poly: no visible global function definition for 'new'
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for 'new'
coerce,data.frame-gpc.poly: no visible global function definition for
  'as'
coerce,list-gpc.poly: no visible global function definition for 'as'
coerce,matrix-gpc.poly: no visible global function definition for 'new'
coerce,numeric-gpc.poly: no visible global function definition for
  'new'
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for 'new'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'as'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'new'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'as'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'new'
tristrip,gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for
  'new'
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running the tests in 'tests/bug1.R' failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gpuR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gputools.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.2/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

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

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/hBayesDM.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.2Mb
    libs   1.0Mb
NB: this package is only installed for sub-architecture 'x64'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(ids)
  > 
  > test_check("ids")
  1. Failure: functional interface (@test-adjective-animal.R#64) -----------------
  all(grepl(re, x)) isn't true.
  
  
  testthat results ================================================================
  OK: 97 SKIPPED: 0 FAILED: 1
  1. Failure: functional interface (@test-adjective-animal.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  13.4Mb
Running examples in 'inarmix-Ex.R' failed
The error most likely occurred in:

> ### Name: diagnose
> ### Title: Diagnostics for the model fit.
> ### Aliases: diagnose
> ### Keywords: print
> 
> ### ** Examples
> 
> XX <- cbind(rep(1,9),c(0:8)/4)
> colnames(XX) <- c("const","time")
> coefs <- rbind(c(-.2,0),c(1.2,.3))
> alpha <- c(.2,.2)
> scale <- c(2,2)
> mix.prop <- c(.8,.2)
> 
> testdat <- GenerateMixData(200,coefs,alpha,scale,mix.prop,XX)
> testfit <- inarmix(y~time,nclasses=2,id=subject,data=testdat,maxiter=3)
Iteration:  1 
Iteration:  2 
Iteration:  3 
[1] 1.766754e-224
[1] 1.766754e-224
Error in solve.default(hh$dermat, hh$sqmat) : 
  system is computationally singular: reciprocal condition number = 1.76675e-224
Calls: inarmix -> tcrossprod -> solve -> solve -> solve.default
Execution halted
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/LANDD.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/largeVis.Rcheck/00install.out' for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    geojson  12.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.3Mb
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/maGUI.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/medSTC.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '.DollarNames.C++Object', '.DollarNames.Module', 'print.bytes', 'format.Rcpp_stack_trace', 'str.Rcpp_stack_trace', 'print.Rcpp_stack_trace' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.3/memisc.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
    misc   1.1Mb
Found the following significant warnings:
  mmap.c:223:48: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  mmap.c:226:46: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/mmap.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Error: `mapped_plot` not equal to lazyLoadDBfetch(c(36521L, 321L), datafile, compressed, envhook).
  Component "layers": Component 1: Component 3: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 3: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 7: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 7: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 9: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 9: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 12: Modes of target, current: function, environment
  Component "layers": Component 1: Component 12: target, current do not match when deparsed
  Component "layers": Component 2: Component 3: Component 2: Modes of target, current: fun
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/nettools.Rcheck/00install.out' for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    CppCode   1.8Mb
    R         2.4Mb
    include   3.7Mb
    libs      1.5Mb
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.2/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.2/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

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

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

Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    help   2.1Mb
    libs   1.2Mb
Running examples in 'oec-Ex.R' failed
The error most likely occurred in:

> ### Name: treemap
> ### Title: Creates a treemap for a given year
> ### Aliases: treemap
> ### Keywords: functions
> 
> ### ** Examples
> 
> treemap("chl", "chn", "exports", 6, 2014)
[1] "HS92 (6 characters) files already exists. skipping."
[1] "creating treemap..."
[1] "writing html file..."
[1] "opening html files in the browser."
serving the directory d:\RCompile\CRANpkg\local\3.3\oec.Rcheck at http://127.0.0.1:4859

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Assertion failed!

Program: D:\RCompile\recent\R-33~1.2\bin\x64\Rterm.exe
File: src/win/tcp.c, Line 1107

Expression: handle->reqs_pending > 0
Assertion failed!

Program: D:\RCompile\recent\R-33~1.2\bin\x64\Rterm.exe
File: src/win/tcp.c, Line 1107

Expression: handle->reqs_pending > 0
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/OpenCL.Rcheck/00install.out' for details.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs     5.0Mb
    models   4.5Mb
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, xtabs

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

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

Welcome to Bioconductor

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

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: httr::GET(query)
  3: request_perform(req, hu$handle$handle)
  4: request_fetch(req$output, req$url, handle)
  5: request_fetch.write_memory(req$output, req$url, handle)
  6: curl::curl_fetch_memory(url, handle = handle)
  
  testthat results ================================================================
  OK: 167 SKIPPED: 0 FAILED: 2
  1. Error: invalid key (@test-extract-objects.R#21) 
  2. Error: valid key (@test-extract-objects.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Checking rgeos availability: TRUE
Loading osmplotr
Quitting from lines 338-342 (basic-maps.Rmd) 
Error: processing vignette 'basic-maps.Rmd' failed with diagnostics:
Couldn't connect to server
Execution halted
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/PANDA.Rcheck/00install.out' for details.
Running examples in 'partools-Ex.R' failed
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  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: 15 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    lib    5.5Mb
    libs   4.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   2.1Mb
    libs   2.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Failure: createTable (@test-poplite.R#252) 
  2. Failure: createTable (@test-poplite.R#252) 
  3. Failure: createTable (@test-poplite.R#252) 
  4. Failure: createTable (@test-poplite.R#252) 
  5. Failure: insertStatement (@test-poplite.R#330) 
  6. Failure: insertStatement (@test-poplite.R#350) 
  7. Failure: insertStatement (@test-poplite.R#330) 
  8. Failure: insertStatement (@test-poplite.R#350) 
  9. Failure: insertStatement (@test-poplite.R#330) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/ppiPre.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: initialize(value, ...)
  10: initialize(value, ...)
  11: callNextMethod()
  12: .nextMethod(.Object = .Object, ... = ...)
  13: validObject(.Object)
  14: stop(msg, ": ", errors, domain = NA)
  
  testthat results ================================================================
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: Small example works (@test_factorial_preprocessing.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/qtbase.Rcheck/00install.out' for details.
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.3Mb
    libs   2.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/Rblpapi.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rcplex.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib       3.7Mb
    libs      2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/RcppOctave.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RDieHarder.Rcheck/00install.out' for details.
Package required but not available: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running the tests in 'tests/reconstruct.R' failed.
Last 13 lines of output:
        k =   34 ; sb/Sb = 0 ; sb = 0
        k =  414 ; sb/Sb = 0.60237132329825 ; sb = 387.816744112795
        Creating new point: f = 0.830052794117553
  Triangulating...
  Internal error in finddirection():  Unable to find a
    triangle leading from (-195.467775468, 4725.74636175) to  (192.266112266, 4832.37318087).
    Please report this bug to jrs@cs.berkeley.edu
    Include the message above, your input data set, and the exact
      command line you used to run Triangle.
  Error in RTriangle::triangulate(RTriangle::pslg(P = out$P, S = out$S[out$SB ==  : 
    Triangle exit, code $i
  Calls: retistruct.reconstruct ... ReconstructedOutline -> TriangulatedOutline -> <Anonymous> -> .Call
  Execution halted
Error in re-building vignettes:
  ...
mpiler/texmf/fonts/type1/public/amsfonts/cm/cmr8.pfb><D:/Compiler/texmf/fonts/t
ype1/public/amsfonts/cm/cmr9.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts
/cm/cmsltt10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss10.pfb><
D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss8.pfb><D:/Compiler/texmf/f
onts/type1/public/amsfonts/cm/cmss9.pfb><D:/Compiler/texmf/fonts/type1/public/a
msfonts/cm/cmsy10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti10.
pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti12.pfb><D:/Compiler/t
exmf/fonts/type1/public/amsfonts/cm/cmtt10.pfb><D:/Compiler/texmf/fonts/type1/p
ublic/amsfonts/cm/cmtt8.pfb><D:/Compiler/texmf/fonts/type1/public/mathpazo/fplm
ri.pfb><D:/Compiler/texmf/fonts/type1/public/cm-super/sfrm0900.pfb><D:/Compiler
/texmf/fonts/type1/public/cm-super/sfrm1000.pfb><D:/Compiler/texmf/fonts/type1/
urw/palatino/uplr8a.pfb><D:/Compiler/texmf/fonts/type1/urw/palatino/uplri8a.pfb
>
Output written on rgp_introduction.pdf (16 pages, 430970 bytes).
Transcript written on rgp_introduction.log.
"D:/RCompile/recent/R-33~1.2/bin/Rscript" -e "tools::compactPDF('rgp_introduction.pdf', gs_quality='ebook')"
  compacted 'rgp_introduction.pdf' from 421Kb to 205Kb
rm -f Rplots.pdf
rm: cannot remove 'Rplots.pdf': Device or resource busy
make[1]: *** [pdf] Error 1
make[1]: Leaving directory `/cygdrive/d/RCompile/CRANpkg/local/3.3/rgp.Rcheck/vign_test/rgp/vignettes'
Warning: running command 'make' had status 2
Error in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.3/rgp.Rcheck/vign_test/rgp") : 
  running 'make' failed
Execution halted
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.
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.
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    exe  45.1Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("rmapshaper")
  1. Failure: ms_simplify works with lines (@test-simplify.R#442) ----------------
  ms_simplify(line_list) not equal to geojson_list(expected_json).
  Component "features": Component 1: Component 2: Component 2: Component 2: Component 2: Mean relative difference: 1.985531e-08
  
  
  testthat results ================================================================
  OK: 252 SKIPPED: 0 FAILED: 1
  1. Failure: ms_simplify works with lines (@test-simplify.R#442) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    java   4.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rmosek.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/ROracle.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
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.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  7. Error: loo/waic for stan_lm works (@test_loo.R#162) 
  8. Error: loo/waic for stan_lm works (@test_loo.R#162) 
  9. Error: loo/waic for stan_lm works (@test_loo.R#162) 
  1. ...
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: There were 10 divergent transitions after warmup. Increasing adapt_delta above 0.95 may help. See
  http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup 
  2: Examine the pairs() plot to diagnose sampling problems
   
  3: Markov chains did not converge! Do not analyze results! 
  Execution halted
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()
Found the following significant warnings:
  Warning: S3 methods 'anova.merMod', 'as.data.frame.boot', 'as.data.frame.thpr', 'as.data.frame.VarCorr.merMod', 'as.function.merMod', 'coef.lmList4', 'coef.merMod', 'confint.lmList4', 'confint.merMod', 'confint.thpr', 'densityplot.thpr', 'deviance.merMod', 'df.residual.merMod', 'dotplot.coef.mer', 'dotplot.ranef.mer', 'drop1.merMod', 'extractAIC.merMod', 'family.glmResp', 'family.lmResp', 'family.merMod', 'family.nlsResp', 'fitted.merMod', 'fixef.merMod', 'formula.lmList4', 'formula.merMod', 'getME.merMod', 'hatvalues.merMod', 'isGLMM.merMod', 'isLMM.merMod', 'isNLMM.merMod', 'isREML.merMod', 'log.thpr', 'logLik.merMod', 'model.frame.merMod', 'model.matrix.merMod', 'ngrps.factor', 'ngrps.merMod', 'nobs.merMod', 'plot.coef.mer', 'plot.lmList4.confint', 'plot.merMod', 'plot.ranef.mer', 'predict.merMod', 'print.merMod', 'print.ranef.mer', 'print.summary.merMod', 'print.VarCorr.merMod', 'profile.merMod', 'qqmath.merMod', 'qqmath.ranef.mer', 'ranef.merMod', 'refit.merMod', 'refitML.merMod', 'residua [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.3/Rz.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    sample_data   3.2Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: lapply(dates, find_for_date, id = id, version = version)
  3: FUN(X[[i]], ...)
  4: validate_ftp_request(id, date, version)
  5: validate_date(id, version, date)
  6: stop(paste(prefix, suffix))
  
  testthat results ================================================================
  OK: 9 SKIPPED: 14 FAILED: 2
  1. Error: invalid output directories cause errors (@test-download_smap.R#4) 
  2. Error: invalid datasets cause errors (@test-extract_smap.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.0Mb
    libs   1.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/sybilSBML.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/TipDatingBeast.Rcheck/00install.out' for details.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    examples  19.1Mb
    include    2.9Mb
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/TROM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/uaparserjs.Rcheck/00install.out' for details.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(ubeR)
  > 
  > test_check("ubeR")
  1. Failure: raise error on fail to geocode (@test_utils.R#4) -------------------
  geocode("The Old Biscuit Mill") did not throw an error.
  
  
  testthat results ================================================================
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Failure: raise error on fail to geocode (@test_utils.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/uroot.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
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Quitting from lines 934-939 (walkr.Rnw) 
Error: processing vignette 'walkr.Rnw' failed with diagnostics:
The inequality constraints cannot be all satisfied!
                                   Sampling in this solution space is not possible!
Execution halted
Found the following significant warnings:
  Warning: vfs customization not available on this platform. Ignoring value: vfs = unix-none
See 'd:/Rcompile/CRANpkg/local/3.3/WGCNA.Rcheck/00install.out' for details.
newXMLDoc: no visible binding for global variable 'doc'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
[[,XMLCodeFile: possible error in updateIds(doc, save = x): unused
  argument (save = x)
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   5.0Mb
BFD_Processor: no visible global function definition for 'levelplot'
BFD_Processor: no visible global function definition for 'corrplot'
FBA_solve: no visible global function definition for 'Rglpk_solve_LP'
PHPP: no visible global function definition for 'levelplot'
PHPP: no visible global function definition for 'persp3d'
PHPP: no visible global function definition for 'play3d'
PHPP: no visible global function definition for 'spin3d'
Found the following significant warnings:
  Warning: D:/temp/RtmpIBWRxW/R.INSTALL590433ee2391/ACEt/man/ACEt-package.Rd:1: All text must be in a section
See 'd:/Rcompile/CRANpkg/local/3.2/ACEt.Rcheck/00install.out' for details.
clusters: no visible global function definition for 'write.matrix'
copNormal : pcopula: no visible global function definition for
  'pmvnorm'
copNormal : rcopula: no visible global function definition for
  'rmvnorm'
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R  14.3Mb
Namespaces in Imports field not imported from:
  'plotly' 'shinydashboard'
  All declared Imports should be used.
aspm: no visible binding for global variable 'X.Declan'
aspm: no visible binding for global variable 'Z.Jaida'
aspm: no visible binding for global variable 'group.vec.Handan'
rCSL: no visible global function definition for 'ginv'
rCSL: no visible global function definition for 'expand'
rCSL: no visible global function definition for 'lu'
adaptiveGMRF2COVAR: no visible global function definition for
  'mcparallel'
adaptiveGMRF2COVAR: no visible global function definition for
  'mccollect'
sim.adaptiveGMRF2COVAR: no visible global function definition for
  'mcparallel'
sim.adaptiveGMRF2COVAR: no visible global function definition for
  'mccollect'
ov.p.grid: no visible global function definition for 'cloud'
ov.p.grid: no visible global function definition for 'wireframe'
Namespace in Imports field not imported from: 'filehash'
  All declared Imports should be used.
checkDNAbcd: no visible global function definition for 'haplotype'
denoise: no visible global function definition for 'ebayesthresh'
denoise2: no visible global function definition for 'ebayesthresh'
denoisehetero: no visible global function definition for 'ebayesthresh'
denoisehetero2: no visible global function definition for
  'ebayesthresh'
denoiseheteromp: no visible global function definition for
  'ebayesthresh'
denoiseheteroprop: no visible global function definition for
  'ebayesthresh'
denoiseheteroprop2: no visible global function definition for
  'ebayesthresh'
Namespaces in Imports field not imported from:
  'fields' 'knitr'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/agRee.Rcheck/00install.out' for details.
backfit.logistic.interaction: warning in glm(y ~ trt, family =
  "binomial", weight = wt): partial argument match of 'weight' to
  'weights'
backfit.logistic.main: warning in glm(y ~ 1, family = "binomial",
  weight = wt): partial argument match of 'weight' to 'weights'
logistic.interaction: warning in glm(y ~ trt, family = "binomial",
  weight = wt): partial argument match of 'weight' to 'weights'
logistic.main: warning in glm(y ~ 1, family = "binomial", weight = wt):
  partial argument match of 'weight' to 'weights'
backfit.cox.interaction: no visible global function definition for
  'coxph'
cox.interaction: no visible global function definition for 'coxph'
cv.cox.interaction: no visible global function definition for 'coxph'
cv.cox.main: no visible global function definition for 'coxph'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/AlignStat.Rcheck/00install.out' for details.
pedigree.summary: no visible global function definition for 'orderPed'
pedigree.summary: no visible global function definition for
  'calcInbreeding'
batch.possSpells.fnc: no visible binding for global variable 'words'
possSpells.fnc: no visible binding for global variable 'len.phons'
possSpells.fnc: no visible binding for global variable 'phon1'
possSpells.fnc: no visible binding for global variable 'len.total'
possSpells.fnc: no visible binding for global variable 'poss.spells'
sigma.hat: no visible global function definition for 'sigmaHat'
Package required and available but unsuitable version: 'tcltk'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
LBI: warning in png(file = paste(graphout, ".png", sep = "")): partial
  argument match of 'file' to 'filename'
normalisation: warning in read.table(as.character(nom[i]), nrow = 1,
  skip = 1, sep = sep): partial argument match of 'nrow' to 'nrows'
aode: no visible global function definition for 'Compose'
mdl: no visible global function definition for 'cutPoints'
setVar: no visible global function definition for 'Compose'
plot,ANFIS : .local: no visible binding for global variable 'X'
varbin: no visible global function definition for 'boot'
apple: no visible global function definition for 'ginv'
deri: no visible global function definition for 'ginv'
y.app: no visible global function definition for 'ginv'
bookTheme: no visible global function definition for 'trellis.par.set'
transparentTheme: no visible global function definition for
  'trellis.par.set'
upperp: no visible global function definition for 'ellipse'
upperp: no visible global function definition for 'panel.xyplot'
upperp: no visible global function definition for 'trellis.par.get'
Afun: no visible global function definition for 'corr.matrix'
betahat.app.H: no visible global function definition for 'quad.form'
betahat.app.H: no visible global function definition for
  'quad.form.inv'
cdash.fun: no visible global function definition for 'quad.3form'
cdash.fun: no visible global function definition for 'quad.form'
generate.toy.observations : delta: no visible global function
  definition for 'rmvnorm'
generate.toy.observations : delta: no visible global function
  definition for 'corr.matrix'
object: no visible global function definition for 'quad.form'
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
apsrtableSummary.lrm: no visible binding for global variable 'est.exp'
pval.note: no visible binding for global variable 'se'
se.note: no visible binding for global variable 'se'
se.note: no visible binding for global variable 'nmodels'
stars.note: no visible binding for global variable 'lev'
aqDayOfWeekStat: no visible global function definition for 'index'
aqDropHour: no visible global function definition for 'index'
aqHourIndex: no visible global function definition for 'index'
aqHourlyStat: no visible global function definition for 'index'
aqStoreSeriesField: no visible global function definition for 'index'
ginv.zalphasfn: no visible global function definition for 'ginv'
tspsimplex_projection: no visible global function definition for
  'solve_TSP'
tspsimplex_projection: no visible global function definition for 'TSP'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.4Mb
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for lhs since lhs is already defined in the 'lazyeval' namespace
  Warning: failed to assign NativeSymbolInfo for rhs since rhs is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/arulesCBA.Rcheck/00install.out' for details.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    bin   11.7Mb
    misc   2.1Mb
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for lhs since lhs is already defined in the 'lazyeval' namespace
  Warning: failed to assign NativeSymbolInfo for rhs since rhs is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/arulesViz.Rcheck/00install.out' for details.
Asciidoc: no visible binding for global variable 'RweaveAsciidoc'
Org: no visible binding for global variable 'RweaveOrg'
Pandoc: no visible binding for global variable 'RweavePandoc'
ReST: no visible binding for global variable 'RweaveReST'
T2t: no visible binding for global variable 'RweaveT2t'
Textile: no visible binding for global variable 'RweaveTextile'
weaverAsciiFinish: no visible global function definition for
  'resetStorage'
weaverAsciiFinish: no visible binding for global variable 'cache_expr'
weaverAsciiRuncode: Error while checking: object 'weaverEvalWithOpt'
  not found
weaverAsciiSetup: no visible global function definition for 'log_debug'
weaverOrgSetup: no visible global function definition for 'log_debug'
weaverPandocSetup: no visible global function definition for
  'log_debug'
weaverReSTSetup: no visible global function definition for 'log_debug'
weaverT2tSetup: no visible global function definition for 'log_debug'
weaverTextileSetup: no visible global function definition for
  'log_debug'
CF: no visible binding for global variable 'activities'
CF2PTS: no visible binding for global variable 'activities'
CF2PTS: no visible binding for global variable 'activities2'
CMD: no visible binding for global variable 'activities'
CMD: no visible global function definition for 'gridpts'
calc_box: no visible binding for global variable 'activities'
calc_box: no visible global function definition for 'wtd.var'
calc_sdd: no visible binding for global variable 'activities'
calc_sde: no visible binding for global variable 'activities'
distances: no visible binding for global variable 'centre'
distances: no visible binding for global variable 'activities'
mean_centre: no visible binding for global variable 'activities'
median_centre: no visible binding for global variable 'activities'
plot_box: no visible binding for global variable 'r.BOX'
plot_centres: no visible binding for global variable 'r.SDE'
plot_centres: no visible binding for global variable 'r.CF'
plot_centres: no visible binding for global variable 'r.median'
plot_centres: no visible binding for global variable 'r.CMD'
plot_centres: no visible binding for global variable 'r.CF2PTS'
plot_sdd: no visible binding for global variable 'r.SDD'
plot_sde: no visible binding for global variable 'r.SDE'
Missing link or links in documentation object 'is_s3_generic.Rd':
  '[utils]{isS3method}'

See section 'Cross-references' in the 'Writing R Extensions' manual.
my_uminp_method: no visible global function definition for 'pmvnorm'
audioHist: no visible global function definition for 'rescale'
audioHist: no visible global function definition for 'toJSON'
audioScatter: no visible global function definition for 'hexbinplot'
audioScatter: no visible global function definition for 'toJSON'
audioSplom: no visible global function definition for 'hexplom'
audioSplom: no visible binding for global variable 'BTY'
audioSplom: no visible binding for global variable 'panel.hexboxplot'
audioSplom : <anonymous>: no visible global function definition for
  'toJSON'
matricize: no visible global function definition for 'hexbin'
panel.audiolyzR: no visible global function definition for
  'panel.hexbinplot'
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/3.2/audio.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/auRoc.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'htmlwidgets'
  All declared Imports should be used.
Package suggested but not available for checking: 'gpclib'
cv.compare.ggplot: no visible global function definition for 'ggplot'
cv.compare.ggplot: no visible global function definition for
  'aes_string'
cv.compare.ggplot: no visible global function definition for
  'facet_wrap'
cv.compare.ggplot: no visible global function definition for
  'scale_x_continuous'
cv.compare.ggplot: no visible global function definition for
  'scale_y_continuous'
cv.compare.ggplot: no visible global function definition for
  'coord_equal'
cv.compare.ggplot: no visible global function definition for
  'scale_color_gradient2'
cv.compare.ggplot: no visible global function definition for
  'scale_size_continuous'
cv.compare.ggplot: no visible global function definition for 'fortify'
cv.compare.ggplot: no visible global function definition for
  'geom_path'
cv.compare.ggplot: no visible global function definition for
  'geom_point'
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.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BACCT.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'osd'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bamdit.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BANOVA.Rcheck/00install.out' for details.
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: gcrma
Loading required package: preprocessCore
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Loading required package: gcrma
Loading required package: preprocessCore
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Loading required package: gcrma
Loading required package: preprocessCore
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: gcrma
Loading required package: preprocessCore
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
barcode: no visible global function definition for 'unit'
barcode: no visible global function definition for 'grid.newpage'
barcode: no visible global function definition for 'grid.text'
barcode: no visible global function definition for 'gpar'
barcode: no visible global function definition for 'pushViewport'
barcode: no visible global function definition for 'viewport'
barcode: no visible global function definition for 'convertHeight'
barcode: no visible global function definition for 'convertWidth'
barcode: no visible global function definition for 'grid.rect'
barcode: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for 'unit'
barcode.panel: no visible global function definition for 'pushViewport'
barcode.panel: no visible global function definition for 'viewport'
barcode.panel: no visible global function definition for 'grid.xaxis'
barcode.panel: no visible global function definition for 'gpar'
barcode.panel: no visible global function definition for 'grid.text'
barcode.panel: no visible global function definition for 'popViewport'
barcode.panel: no visible global function definition for
  'grid.segments'
barcode.panel: no visible global function definition for 'grid.points'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bayescount.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BayesMed.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bayesmix.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
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.
gibbs: no visible global function definition for 'permn'
hmflatlogit: no visible global function definition for 'rmnorm'
hmflatloglin: no visible global function definition for 'mvrnorm'
hmflatprobit: no visible global function definition for 'rmnorm'
hmnoinflogit: no visible global function definition for 'rmnorm'
hmnoinfloglin: no visible global function definition for 'mvrnorm'
hmnoinfprobit: no visible global function definition for 'rmnorm'
ACGaussian: no visible global function definition for 'ginv'
ACGaussian: no visible global function definition for 'rmvnorm'
ACt: no visible global function definition for 'ginv'
ACt: no visible global function definition for 'rmvnorm'
MCGaussian: no visible global function definition for 'ginv'
MCGaussian: no visible global function definition for 'rmvnorm'
MCGaussian: no visible global function definition for 'vec'
MCt: no visible global function definition for 'ginv'
MCt: no visible global function definition for 'rmvnorm'
MCt: no visible global function definition for 'vec'
NCGaussian: no visible global function definition for 'ginv'
NCGaussian: no visible global function definition for 'rmvnorm'
NCGaussian: no visible global function definition for 'rdiric'
NCt: no visible global function definition for 'ginv'
NCt: no visible global function definition for 'rmvnorm'
NCt: no visible global function definition for 'rdiric'
coef.Bayesthresh: no visible global function definition for 'mcmc'
lmerFactorList : <anonymous>: no visible binding for global variable
  'rBind'
lmerFactorList : <anonymous>: no visible global function definition for
  'drop0'
mkZt: no visible binding for global variable 'rBind'
predict.Bayesthresh: no visible global function definition for
  'rankMatrix'
random.effects: no visible global function definition for 'mcmc'
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
File 'BayHap/libs/i386/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'
File 'BayHap/libs/x64/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
BPSpost2mcmc: no visible global function definition for 'mcmc'
CPPpost2mcmc: no visible global function definition for 'mcmc'
LittleMCAR: no visible global function definition for 'mlest'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BaySIC.Rcheck/00install.out' for details.
semimetric.deriv: no visible global function definition for
  'splineDesign'
BBRecap: no visible global function definition for 'arms'
LBRecap: no visible global function definition for 'findbars'
LBRecap: no visible global function definition for 'glmer'
LBRecap: no visible global function definition for 'fixef'
LBRecap: no visible global function definition for 'ranef'
plot,BCDating-ts : .local: no visible binding for global variable
  'na.rm'
Running examples in 'BCEA-Ex.R' failed
The error most likely occurred in:

> ### Name: evppi
> ### Title: Expected Value of Perfect Partial Information (EVPPI) for
> ###   selected parameters
> ### Aliases: evppi evppi.default
> ### Keywords: Health economic evaluation Expected value of partial
> ###   information
> 
> ### ** Examples
> 
> # See Baio G., Dawid A.P. (2011) for a detailed description of the 
> # Bayesian model and economic problem
> #
> # Load the processed results of the MCMC simulation model
> data(Vaccine)
Warning: namespace 'rjags' is not available and has been replaced
by .GlobalEnv when processing object 'vaccine'
> # 
> # Runs the health economic evaluation using BCEA
> m <- bcea(e,c,ref=2,interventions=treats)
> #
> # Computes the EVPPI for a bunch of parameters
> inp <- CreateInputs(vaccine)
Error in CreateInputs(vaccine) : 
  You need to install the package 'R2jags'. Please run in your R terminal:
 install.packages('R2jags')
Execution halted
Running examples in 'BCEs0-Ex.R' failed
The error most likely occurred in:

> ### Name: bces0
> ### Title: Bayesian Cost-Effectiveness models in the presence of structural
> ###   zeros
> ### Aliases: bces0 bces0.default
> ### Keywords: JAGS Markov Chain Monte Carlo Bayesian models for
> ###   cost-effectiveness analysis
> 
> ### ** Examples
> 
> data(acupuncture)
> m <- bces0(data,dist.c="gamma",dist.e="beta",n.iter=1000,n.burnin=500,n.chains=2)
> print(m)
NULL
> plot(m)
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Warning in min(x) : no non-missing arguments to min; returning Inf
Warning in max(x) : no non-missing arguments to max; returning -Inf
Error in plot.window(...) : need finite 'xlim' values
Calls: plot -> plot.default -> localWindow -> plot.window
Execution halted
Namespace in Imports field not imported from: 'inline'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'ggplot2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'readxl'
  All declared Imports should be used.
beadtypeFilter: no visible global function definition for 'exprs'
beadtypeFilter: no visible global function definition for 'se.exprs'
beadtypeFilter: no visible global function definition for 'beadNum'
beadtypeFilter: no visible global function definition for 'fData'
emCDF: no visible global function definition for 'brewer.pal'
Found the following significant warnings:
  Warning: 'loadRcppModules' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.2/beanz.Rcheck/00install.out' for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Found the following significant warnings:

  Warning: 'loadRcppModules' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Namespaces in Imports field not imported from:
  'Rcpp' 'chron' 'colorspace' 'gtable' 'htmltools' 'htmlwidgets'
  'httpuv' 'magrittr' 'munsell' 'plyr' 'scales' 'stringi' 'xtable'
  'yaml'
  All declared Imports should be used.
boxplot.AlgorithmPerformance: no visible binding for global variable
  'algorithms'
boxplot.AlgorithmPerformance: no visible binding for global variable
  'value'
boxplot.AlgorithmPerformance: no visible binding for global variable
  'samples'
bsgraph0.dist: no visible global function definition for 'addEdge'
bsgraph0.graphNEL: no visible global function definition for
  'getDefaultAttrs'
bsgraph0.graphNEL: no visible global function definition for 'agopen'
densityplot.AlgorithmPerformance: no visible binding for global
  variable 'value'
densityplot.AlgorithmPerformance: no visible binding for global
  variable 'algorithms'
mi: no visible global function definition for 'mi.plugin'
patch.relation_class_ids: no visible global function definition for
  'relation_is_strict_weak_order'
plot.DatasetCharacterization: no visible binding for global variable
  'characteristics'
plot.DatasetCharacterization: no visible binding for global variable
  'value'
plot.DatasetCharacterization: no visible binding for global variable
  'samples'
plot.DatasetCharacterization: no visible global function definition for
  'theme_text'
plot.TestResult: no visible binding for global variable 'samples'
plot.TestResult: no visible binding for global variable 'value'
stripchart.AlgorithmPerformance: no visible binding for global variable
  'algorithms'
stripchart.AlgorithmPerformance: no visible binding for global variable
  'value'
stripchart.AlgorithmPerformance: no visible binding for global variable
  'samples'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/benchr.Rcheck/00install.out' for details.
bI: no visible global function definition for 'mpfr'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BEST.Rcheck/00install.out' for details.
betafam: no visible global function definition for 'glmnet'
cca.pertables : cca.var: no visible binding for global variable
  'cca.formula'
cca.pertables: no visible binding for global variable 'cca.formula'
rda.pertables : rda.var: no visible binding for global variable
  'rda.formula'
rda.pertables: no visible binding for global variable 'rda.formula'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/betategarch.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'FinTS' 'Rcpp' 'TSA' 'TTR' 'colorspace' 'fpp' 'fracdiff' 'gtable'
  'htmlwidgets' 'lmtest' 'normtest' 'quadprog' 'rugarch' 'scales'
  'stringi' 'testthat' 'timeDate' 'tseries' 'viridis'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'maptools'
  All declared Imports should be used.
maxstudent2 : padj.fun: no visible global function definition for
  'pmvnorm'
pvstudent2 : padj.fun: no visible global function definition for
  'pmvnorm'
File 'bifactorial/libs/i386/bifactorial.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'misc.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'krit.o', 'pv.o'
File 'bifactorial/libs/x64/bifactorial.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'misc.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'krit.o', 'pv.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bife.Rcheck/00install.out' for details.
lasso.stars: no visible global function definition for 'glmnet'
bigglm.RODBC: no visible global function definition for 'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'sqlGetResults'
bigglm,ANY-DBIConnection : .local: no visible global function
  definition for 'dbSendQuery'
bigglm,ANY-DBIConnection : .local: no visible global function
  definition for 'dbClearResult'
bigglm,ANY-DBIConnection : .local : chunk: no visible global function
  definition for 'dbClearResult'
bigglm,ANY-DBIConnection : .local : chunk: no visible global function
  definition for 'dbSendQuery'
bigglm,ANY-DBIConnection : .local : chunk: no visible global function
  definition for 'fetch'
Namespace in Imports field not imported from: 'R6'
  All declared Imports should be used.
LDCAEst: no visible global function definition for 'glmnet'
cv.LDCA: no visible global function definition for 'cv.glmnet'
tsp.gbm: no visible global function definition for 'gbm.fit'
tsp.randomForest: no visible global function definition for
  'randomForest'
tsp.tree: no visible global function definition for 'tree.control'
tsp.tree: no visible global function definition for 'tree'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
ebayesthresh.wavelet.wd: no visible global function definition for
  'ebayesthresh'
hfdenoise: no visible global function definition for
  'ebayesthresh.wavelet'
negloglik.laplace: no visible global function definition for 'wfromt'
negloglik.laplace: no visible global function definition for
  'beta.laplace'
wandafromx: no visible global function definition for 'wfromt'
HLtest.Rsq: warning in pchisq(X2, 10 - 2, lower = FALSE): partial
  argument match of 'lower' to 'lower.tail'
X2GOFtest.Rsq: warning in pnorm(abs(z), lower = FALSE): partial
  argument match of 'lower' to 'lower.tail'
Packages required and available but unsuitable versions:
  'spatstat' 'grDevices' 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace in Imports field not imported from: 'stringi'
  All declared Imports should be used.
dis: no visible binding for global variable 'sub.mat'
mat.dis: no visible binding for global variable 'sub.mat'
mmds.3D.plot: no visible global function definition for 'box3d'
mmds.3D.plot: no visible global function definition for 'axes3d'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BiSEp.Rcheck/00install.out' for details.
biwt.cor: no visible global function definition for 'covMcd'
biwt.est: no visible global function definition for 'covMcd'
Namespaces in Imports field not imported from:
  'glmnet' 'gtools' 'knitr' 'nnet' 'parallel' 'rJava' 'reshape'
  'rmarkdown' 'shinyjs'
  All declared Imports should be used.
'library' or 'require' calls in package code:
  'Matrix' 'sna'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
gplot1: warning in grep(pat = "block", search()): partial argument
  match of 'pat' to 'pattern'
gplot2: warning in grep(pat = "block", search()): partial argument
  match of 'pat' to 'pattern'
loadnetwork2: warning in grep(patt = "^ *$", x = as.character(line)):
  partial argument match of 'patt' to 'pattern'
loadpajek: warning in grep(patt = "^ *$", x = as.character(line)):
  partial argument match of 'patt' to 'pattern'
savecluster: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
savematrix: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
savenetwork: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
savepajek: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
savevector: warning in grep(patt = "w32", x = version["os"]): partial
  argument match of 'patt' to 'pattern'
check.these.par: no visible global function definition for
  'crit.fun.tmp'
check.these.par: no visible binding for global variable 'useM'
crit.fun: no visible global function definition for 'crit.fun.tmp'
crit.fun: no visible binding for global variable 'useM'
gen.crit.fun: no visible binding for global variable 's'
gplot1: no visible global function definition for 'gplot'
gplot2: no visible global function definition for 'gplot'
loadnetwork: no visible global function definition for 'Matrix'
loadnetwork2: no visible global function definition for 'Matrix'
opt.par: no visible global function definition for 'opt.par.tmp'
opt.random.par: no visible global function definition for 'opt.par.tmp'
opt.these.par: no visible global function definition for 'opt.par.tmp'
opt.these.par: no visible binding for global variable 'm'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
      as.Date, as.Date.numeric
  
  trying URL 'http://www.bls.gov/web/metro/laucntycur14.txt'
  Error in download.file("http://www.bls.gov/web/metro/laucntycur14.txt",  : 
    cannot open URL 'http://www.bls.gov/web/metro/laucntycur14.txt'
  Calls: test_check ... force -> source_file -> eval -> eval -> download.file
  In addition: Warning message:
  In download.file("http://www.bls.gov/web/metro/laucntycur14.txt",  :
    InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
bmd: no visible global function definition for 'LL.2'
bmd: no visible global function definition for 'LN.2'
bmd: no visible global function definition for 'W1.2'
bmd: no visible global function definition for 'W2.2'
bmd: no visible global function definition for 'LL.5'
bmd: no visible global function definition for 'LN.4'
bmd: no visible global function definition for 'W1.4'
bmd: no visible global function definition for 'W2.4'
bmd: no visible global function definition for 'FPL.4'
bmd: no visible global function definition for 'maED'
bmd: no visible global function definition for 'ED'
bmem.bs: no visible global function definition for 'sem'
bmem.em.rcov: no visible global function definition for 'cov.rob'
bmem.mi.cov: no visible global function definition for 'amelia'
bmem.sem: no visible global function definition for 'sem'
bmem.sobel: no visible global function definition for 'sem'
power.basic: no visible global function definition for 'simulateData'
power.basic: no visible global function definition for 'lavaanNames'
power.basic : runonce: no visible global function definition for
  'simulateData'
power.basic: no visible global function definition for 'sfInit'
power.basic: no visible global function definition for 'sfLibrary'
power.basic: no visible binding for global variable 'lavaan'
power.basic: no visible global function definition for 'sfLapply'
power.boot: no visible global function definition for 'simulateData'
power.boot: no visible global function definition for 'lavaanNames'
power.boot : runonce: no visible global function definition for
  'simulateData'
power.boot : runonce: no visible global function definition for
  'bootstrapLavaan'
power.boot: no visible global function definition for 'sfInit'
power.boot: no visible global function definition for 'sfLibrary'
power.boot: no visible binding for global variable 'lavaan'
power.boot: no visible global function definition for 'sfLapply'
summary.power: no visible global function definition for 'lavaanNames'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bmeta.Rcheck/00install.out' for details.
bmkconverge: no visible global function definition for 'Compose'
bmksensitive: no visible global function definition for 'Compose'
bmksummary: no visible global function definition for 'Compose'
bmksummary: no visible global function definition for 'Curry'
bmksummary: no visible global function definition for 'mcmc'
bmksummary: no visible global function definition for 'mcmc.list'
bmksummary: no visible global function definition for 'effectiveSize'
bmksummary: no visible global function definition for 'gelman.diag'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/bmlm.Rcheck/00install.out' for details.
File 'BMN/libs/i386/BMN.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'JunctionTree.o', 'pseudoLikelihood.o'
File 'BMN/libs/x64/BMN.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'JunctionTree.o', 'pseudoLikelihood.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.
Namespace in Imports field not imported from: 'compiler'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/Boom.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'Boom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
alleleEnrichment.data.alleles : <anonymous>: no visible global function
  definition for 'allele.count'
alleleEnrichment.lp: no visible global function definition for
  'make.lp'
alleleEnrichment.lp : <anonymous>: no visible global function
  definition for 'set.column'
alleleEnrichment.lp : <anonymous>: no visible global function
  definition for 'set.type'
alleleEnrichment.lp: no visible global function definition for
  'set.objfn'
alleleEnrichment.lp: no visible global function definition for
  'set.constr.type'
alleleEnrichment.lp: no visible global function definition for
  'set.rhs'
alleleEnrichment.lp: no visible global function definition for
  'lp.control'
alleleEnrichment.lp: no visible global function definition for
  'get.variables'
getGenotypes : <anonymous>: no visible global function definition for
  'genotype'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/boral.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'rgdal' 'tidyr'
  All declared Imports should be used.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

const.cor.list: no visible global function definition for
  'wave.correlation'
const.var.list: no visible global function definition for
  'wave.variance'
wave.trans: no visible global function definition for 'dwt'
wave.trans: no visible global function definition for 'modwt'
wave.trans: no visible global function definition for 'brick.wall'
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
confint.profile.brglm: no visible global function definition for
  'profConfint'
profile.brglm: no visible global function definition for 'profileModel'
Foreign function calls to a different package:
  .C("CharArray", ..., PACKAGE = "libOpenBUGS")
  .C("CmdInterpreter", ..., PACKAGE = "libOpenBUGS")
  .C("Integer", ..., PACKAGE = "libOpenBUGS")
  .C("RealArray", ..., PACKAGE = "libOpenBUGS")
  .C("SetTempDir", ..., PACKAGE = "libOpenBUGS")
  .C("SetWorkingDir", ..., PACKAGE = "libOpenBUGS")
Undeclared package in foreign function calls:
   'libOpenBUGS'
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
BOOTSimpsonD : BSimpson: no visible global function definition for
  'estSimpsonf'
BOOTSimpsonR : BSimpson: no visible global function definition for
  'estSimpsonf'
CIGLM: no visible global function definition for 'univariate_calpha'
CIGLM: no visible global function definition for 'adjusted_calpha'
EDA: no visible global function definition for 'kurtosis'
EDA: no visible global function definition for 'skewness'
bs.design: no visible global function definition for 'spline.des'
Packages required and available but unsuitable versions:
  'BoomSpikeSlab' 'Boom' 'Boom'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/BTSPAS.Rcheck/00install.out' for details.
File 'C50/libs/i386/C50.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'getdata.o'
File 'C50/libs/x64/C50.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'getdata.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.
Namespace in Imports field not imported from: 'utils'
  All declared Imports should be used.
CADFpvalues: no visible binding for global variable 'coeffs_ct'
CADFpvalues: no visible binding for global variable 'coeffs_c'
CADFpvalues: no visible binding for global variable 'coeffs_nc'
estmodel: no visible global function definition for 'dynlm'
estmodel: no visible global function definition for 'punitroot'
estmodel: no visible global function definition for 'kernHAC'
plot.CADFtest: no visible global function definition for
  'jarque.bera.test'
MH: no visible global function definition for 'rmvnorm'
computer.model: no visible global function definition for 'rmvnorm'
model.inadequacy: no visible global function definition for 'rmvnorm'
prob.psi1: no visible global function definition for 'dmvnorm'
prob.psi2: no visible global function definition for 'dmvnorm'
prob.theta: no visible global function definition for 'dmvnorm'
sample.theta: no visible global function definition for 'rmvnorm'
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.
bestBy: no visible global function definition for 'dbConnect'
bestBy: no visible global function definition for 'dbDriver'
bestBy: no visible global function definition for 'dbWriteTable'
bestBy: no visible global function definition for 'dbGetQuery'
dbWriteTable2: no visible global function definition for 'dbListFields'
dbWriteTable2: no visible global function definition for 'dbGetQuery'
dbWriteTable2: no visible global function definition for 'dbSendQuery'
dbWriteTable2: no visible global function definition for 'dbColumnInfo'
dbWriteTable2: no visible global function definition for
  'dbClearResult'
dbWriteTable2: no visible global function definition for 'dbWriteTable'
groupBy: no visible global function definition for 'dbConnect'
groupBy: no visible global function definition for 'dbDriver'
groupBy: no visible global function definition for 'dbWriteTable'
groupBy: no visible global function definition for 'dbGetQuery'
spie: no visible global function definition for 'grid.newpage'
spie: no visible global function definition for 'pushViewport'
spie: no visible global function definition for 'viewport'
spie: no visible global function definition for 'grid.layout'
spie: no visible global function definition for 'dataViewport'
spie: no visible global function definition for 'grid.circle'
spie: no visible global function definition for 'gpar'
spie: no visible global function definition for 'grid.polygon'
spie: no visible global function definition for 'grid.rect'
spie: no visible global function definition for 'stringWidth'
spie: no visible global function definition for 'stringHeight'
spie: no visible global function definition for 'grid.text'
spie: no visible global function definition for 'grid.lines'
spie: no visible global function definition for 'unit'
spie: no visible global function definition for 'upViewport'
Namespace in Imports field not imported from: 'Matrix'
  All declared Imports should be used.
File 'CausalGAM/R/zzz.R':
  .onAttach calls:
    cat("##\n## CausalGAM Package\n")
    cat("## Copyright (C) 2009", " Adam Glynn and Kevin Quinn\n",     sep = "")
    require(gam, quietly = TRUE)

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/CCTpack.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/cda.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'RCurl' 'rgdal'
  All declared Imports should be used.
fitVolDist: no visible global function definition for 'nls.lm'
fitVolDist: no visible global function definition for 'nls.lm.control'
centrality: no visible global function definition for 'vcount'
centrality: no visible global function definition for 'degree'
centrality: no visible global function definition for 'betweenness'
cepa.all.parallel.by.snow: no visible global function definition for
  'makeCluster'
cepa.all.parallel.by.snow: no visible global function definition for
  'clusterCall'
cepa.all.parallel.by.snow: no visible global function definition for
  'clusterApply'
cepa.all.parallel.by.snow: no visible global function definition for
  'stopCluster'
generate.pathway: no visible global function definition for
  'graph.edgelist'
pathway.nodes: no visible global function definition for 'vcount'
pathway.nodes: no visible global function definition for
  'get.vertex.attribute'
plot.igraph2: no visible binding for global variable 'layout.random'
plot.igraph2: no visible global function definition for 'V'
plot.igraph2: no visible global function definition for 'E'
plot.igraph2: no visible global function definition for 'get.edgelist'
plot.igraph2: no visible global function definition for 'ecount'
plotGraph: no visible global function definition for 'V'
plotGraph: no visible global function definition for 'V<-'
plotGraph: no visible global function definition for 'E'
plotGraph: no visible global function definition for 'E<-'
plotGraph : layout.method: no visible global function definition for
  'layout.reingold.tilford'
radiality: no visible global function definition for 'shortest.paths'
radiality: no visible global function definition for 'vcount'
radiality: no visible global function definition for 'diameter'
reach: no visible global function definition for 'E'
reach: no visible global function definition for 'shortest.paths'
report: no visible global function definition for 'write.graph'
spread: no visible global function definition for 'E'
spread: no visible global function definition for 'shortest.paths'
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of 'int' to
  'interval'
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of 'label' to 'labels'
plot.cggd: no visible global function definition for 'gen.beta'
plotCVcggd: no visible binding for global variable 'cv'
plotCVcggd: no visible binding for global variable 'cv.error'
predict.cggd: no visible binding for global variable 'max.tk'
predict.cggd: no visible global function definition for 'gen.beta'
L2L1ExpandFit: no visible global function definition for
  'L2L1PathExtract'
Namespace in Imports field not imported from: 'grDevices'
  All declared Imports should be used.
Hartree2Joule: no visible binding for global variable
  'universalConstants'
Hertz2Joule: no visible binding for global variable
  'universalConstants'
Joule2Hartree: no visible binding for global variable
  'universalConstants'
Joule2Hertz: no visible binding for global variable
  'universalConstants'
Joule2Kelvin: no visible binding for global variable
  'universalConstants'
Joule2centimeterMinusOne: no visible binding for global variable
  'universalConstants'
Joule2electronVolt: no visible binding for global variable
  'universalConstants'
Joule2kiloCaloriePerMole: no visible binding for global variable
  'universalConstants'
Joule2kiloJoulePerMole: no visible binding for global variable
  'universalConstants'
Kelvin2Joule: no visible binding for global variable
  'universalConstants'
LandauZener: no visible binding for global variable
  'universalConstants'
LandauZenerProbability: no visible binding for global variable
  'universalConstants'
Marcus: no visible binding for global variable 'universalConstants'
MarcusLevichJortner: no visible binding for global variable
  'universalConstants'
centimeterMinusOne2Joule: no visible binding for global variable
  'universalConstants'
electronVolt2Joule: no visible binding for global variable
  'universalConstants'
kiloCaloriePerMole2Joule: no visible binding for global variable
  'universalConstants'
kiloJoulePerMole2Joule: no visible binding for global variable
  'universalConstants'
DPfitSamples: no visible global function definition for 'mclapply'
getCCF: no visible global function definition for 'mclapply'
getDiploidOrigin: no visible global function definition for 'mclapply'
getSegChr.CBS: no visible global function definition for 'mclapply'
getSegPurity: no visible global function definition for 'mclapply'
downloadMaster: no visible global function definition for
  'getURLContent'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/cheddar.Rcheck/00install.out' for details.
Running examples in 'chipPCR-Ex.R' failed
The error most likely occurred in:

> ### Name: amptest
> ### Title: Class '"amptest"'
> ### Aliases: amptest amptest-class summary.amptest summary,amptest-method
> ###   show.amptest show,amptest-method plot.amptest plot,amptest-method
> ###   plot,amptest,ANY-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> # Compare a positive and a negative amplification reaction.
> # First simulate positive reaction (fluo.pos) and than the 
> # negative reaction (fluo.neg).
> # Simulation of an amplifiaction curve with some noise and a high signal.
> 
> fluo.pos <- AmpSim(cyc = 1:40, noise = TRUE)[, 2]
> ampt.pos <- amptester(fluo.pos, manual = TRUE, background = c(0, 15), 
+ 		      noiselevel = 0.15)
Error in validObject(.Object) : 
  invalid class "amptest" object: superclass "replValueSp" not defined in the environment of the object's class
Calls: amptester -> new -> initialize -> initialize -> validObject
Execution halted
chngpt.test.2: no visible global function definition for 'startsWith'
sim.chngpt: no visible global function definition for 'startsWith'
sim.my: no visible global function definition for 'endsWith'
sim.my: no visible global function definition for 'startsWith'
Running examples in 'chngpt-Ex.R' failed
The error most likely occurred in:

> ### Name: chngpt.test
> ### Title: Change Point Tests
> ### Aliases: antoch.test chngpt.test plot.chngpt.test
> 
> ### ** Examples
> 
> 
> dat=sim.chngpt("sigmoid4", type="step", n=200, seed=1, beta=1, alpha=-1, x.distr="norm", e.=4)
Loading required namespace: mvtnorm
Error in sim.chngpt("sigmoid4", type = "step", n = 200, seed = 1, beta = 1,  : 
  could not find function "startsWith"
Execution halted
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
  
   
  1 Test Suite : 
  chngpt unit testing - 2 test functions, 2 errors, 0 failures
  ERROR in test.chngpt.test: Error in sim.chngpt("sigmoid4", type = "step", n = 250, seed = 1, beta = 0,  : 
    could not find function "startsWith"
  ERROR in test.chngptm: Error in sim.chngpt("sigmoid2", type = "hinge", n = 250, seed = 1, beta = log(0.4),  : 
    could not find function "startsWith"
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 2)
  
  Execution halted
correctData: no visible global function definition for 'wd'
correctData: no visible global function definition for 'threshold'
correctData: no visible binding for global variable 'madmad'
correctData: no visible global function definition for 'wr'
Namespaces in Imports field not imported from:
  'Matrix' 'stringr'
  All declared Imports should be used.
print.rao.spacing.test: no visible binding for global variable
  'rao.table'
cit.assignBcmst: no visible binding for global variable 'citbcmst'
cit.assignCcmst: no visible binding for global variable 'citccmst'
Namespace in Imports field not imported from: 'Rcpp'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/classify.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: eval(expr, envir, enclos)
  6: samplerate2d(tb$torigin)
  7: rbind(sample.rate.table, data.frame(item = stname2longname(code2stname(i)), hiccode = as.number(StdId(i)), 
         sr = sr))
  8: rbind(deparse.level, ...)
  9: stop("numbers of columns of arguments do not match")
  
  testthat results ================================================================
  OK: 207 SKIPPED: 0 FAILED: 1
  1. Error: calculate 2D sample rate (@test_report.r#36) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: 'survival'
  All declared Imports should be used.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
cfly_dist: no visible global function definition for 'ggplot'
cfly_dist: no visible global function definition for 'aes_string'
cfly_dist: no visible global function definition for 'geom_density'
cfly_dist: no visible global function definition for 'facet_grid'
cfly_fluct: no visible global function definition for 'ggplot'
cfly_fluct: no visible global function definition for 'aes_string'
cfly_fluct: no visible global function definition for 'geom_tile'
cfly_fluct: no visible global function definition for
  'scale_y_discrete'
cfly_fluct: no visible global function definition for
  'scale_x_discrete'
cfly_fluct: no visible global function definition for 'theme'
cfly_pcp: no visible global function definition for 'ggplot'
cfly_pcp: no visible global function definition for 'aes_string'
cfly_pcp: no visible global function definition for 'geom_line'
cfly_pcp: no visible global function definition for 'facet_wrap'
som_iterate: no visible global function definition for 'unit.distances'
Package required but not available: 'OpenImageR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
Namespace in Imports field not imported from: 'tidyr'
  All declared Imports should be used.
BHI: no visible global function definition for 'getGO'
BHI: no visible binding for global variable 'dropECode'
BSI: no visible global function definition for 'getGO'
BSI: no visible binding for global variable 'dropECode'
vClusters: no visible global function definition for 'Mclust'
vClusters: no visible global function definition for 'som'
Error in re-building vignettes:
  ...
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Loading required package: XML

Attaching package: 'XML'

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

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moe430a.db'
Loading required package: RankAggreg
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.2.5/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.2.5/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'clValid.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE (file ./clValid-022.pdf): PDF inclusion: required p
age does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Execution halted
ControlCharts: no visible global function definition for
  'com.log.density'
COBRA : COBRA.lars: no visible global function definition for 'lars'
COBRA : COBRA.lars: no visible global function definition for
  'predict.lars'
COBRA : COBRA.tree: no visible global function definition for 'tree'
COBRA : COBRA.ridge: no visible global function definition for
  'linearRidge'
COBRA : COBRA.randomForest: no visible global function definition for
  'randomForest'
COBRA: no visible global function definition for 'sfInit'
COBRA: no visible global function definition for 'sfLibrary'
COBRA: no visible global function definition for 'sfExportAll'
COBRA: no visible global function definition for 'sfSapply'
COBRA: no visible global function definition for 'sfStop'
autocorr1: no visible global function definition for 'is.mcmc'
autocorr1: no visible global function definition for 'as.mcmc'
autocorr1: no visible global function definition for 'autocorr'
bridgestat.diag: no visible global function definition for
  'is.mcmc.list'
bridgestat.diag: no visible global function definition for 'as.mcmc'
bridgestat.diag: no visible global function definition for 'nvar'
bridgestat.diag: no visible global function definition for 'varnames'
bridgestat.diag: no visible global function definition for 'niter'
bridgestat.diag: no visible global function definition for
  'spectrum0.ar'
transient.test: no visible global function definition for 'as.mcmc'
coloc.abf.snpStats: no visible global function definition for
  'single.snp.tests'
coloc.abf.snpStats: no visible global function definition for
  'col.summary'
fillin: no visible global function definition for 'col.summary'
fillin: no visible global function definition for 'snp.imputation'
fillin: no visible global function definition for 'impute.snps'
plot,colocPCs-missing : .local: no visible binding for global variable
  'object'
plotVenn2d : twoWayOverlap: no visible global function definition for
  'grid.polygon'
plotVenn2d : twoWayOverlap: no visible global function definition for
  'gpar'
plotVenn2d: no visible global function definition for 'grid.text'
plotVenn2d: no visible global function definition for 'gpar'
plotVenn2d: no visible global function definition for 'grid.polygon'
plotVenn3d : twoWayOverlap: no visible global function definition for
  'grid.polygon'
plotVenn3d : twoWayOverlap: no visible global function definition for
  'gpar'
plotVenn3d: no visible global function definition for 'grid.text'
plotVenn3d: no visible global function definition for 'gpar'
plotVenn3d: no visible global function definition for 'grid.polygon'
plotVenn4d : region.polygon: no visible global function definition for
  'grid.polygon'
plotVenn4d : region.polygon: no visible global function definition for
  'gpar'
plotVenn4d: no visible global function definition for 'grid.text'
plotVenn4d: no visible global function definition for 'gpar'
plotVenn4d: no visible global function definition for 'pushViewport'
plotVenn4d: no visible global function definition for 'viewport'
plotVenn4d: no visible global function definition for 'grid.polygon'
plotVenn4d: no visible global function definition for 'upViewport'
splitTrainTest: warning in ts(dat[1:numTrain], start = props[1], freq =
  props[3]): partial argument match of 'freq' to 'frequency'
splitTrainTest: warning in ts(dat[(numTrain + 1):length(dat)], start =
  (props[1] + numTrain/props[3]), freq = props[3]): partial argument
  match of 'freq' to 'frequency'
plot.msc : showResults: no visible global function definition for
  'rgl.open'
plot.msc : showResults: no visible global function definition for
  'rgl.clear'
plot.msc : showResults: no visible global function definition for
  'rgl.bg'
plot.msc : showResults: no visible global function definition for
  'rgl.light'
plot.msc : showResults: no visible global function definition for
  'rgl.bbox'
plot.msc : showResults: no visible global function definition for
  'rgl.surface'
plot.msc : showResults: no visible global function definition for
  'rgl.spheres'
plot.msc : showResults: no visible global function definition for
  'axes3d'
plot.msc : showResults: no visible global function definition for
  'title3d'
plot.msc : showResults: no visible global function definition for
  'rgl.viewpoint'
plot.msc: no visible global function definition for 'xyplot'
plot.msc : mypanel: no visible global function definition for
  'panel.fill'
plot.msc : mypanel: no visible global function definition for
  'panel.grid'
plot.msc : mypanel: no visible global function definition for
  'panel.levelplot'
plot.msc: no visible global function definition for 'levelplot'
plot.msc : <anonymous>: no visible global function definition for
  'axis.default'
plot.msc : <anonymous>: no visible global function definition for
  'panel.text'
plot.msc: no visible global function definition for 'shingle'
plot.msc: no visible global function definition for 'strip.custom'
Running examples in 'compareDF-Ex.R' failed
The error most likely occurred in:

> ### Name: compare_df
> ### Title: Compare Two dataframes
> ### Aliases: compare_df
> 
> ### ** Examples
> 
> old_df = data.frame(var1 = c("A", "B", "C"),
+                     val1 = c(1, 2, 3))
> new_df = data.frame(var1 = c("A", "B", "C"),
+                     val1 = c(1, 2, 4))
> ctable = compare_df(new_df, old_df, c("var1"))
Creating comparison table...
Loading required namespace: htmlTable
Creating HTML table for first 100 rows
Error in compare_df(new_df, old_df, c("var1")) : 
  Assertion failed. One of the following must apply:
 * check_matrix(css.cell): Must be of type 'matrix', not 'data.frame'
 * check_character(css.cell): Must be of type 'character', not
 * 'data.frame'
Calls: compare_df ... htmlTable.data.frame -> htmlTable.default -> assert -> mstop
Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  Creating comparison table...
  Loading required namespace: htmlTable
  Creating HTML table for first 100 rows
  Error in test_check("compareDF") : 
    Assertion failed. One of the following must apply:
   * check_matrix(css.cell): Must be of type 'matrix', not 'data.frame'
   * check_character(css.cell): Must be of type 'character', not
   * 'data.frame'
  Calls: test_check ... htmlTable.data.frame -> htmlTable.default -> assert -> mstop
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
compareODM: no visible global function definition for 'xmlRoot'
compareODM: no visible global function definition for 'xmlTreeParse'
compareODM: no visible global function definition for 'xmlChildren'
compareODM: no visible global function definition for 'xmlAttrs'
compareODM: no visible global function definition for 'xmlValue'
dcomplnorm: no visible global function definition for 'grad'
pcomplnorm: no visible global function definition for 'grad'
qcomplnorm: no visible global function definition for 'grad'
arrows3D.default: no visible global function definition for 'texts3d'
arrows3D.default: no visible global function definition for
  'segments3d'
axis3D: no visible global function definition for 'bbox3d'
biplot3D.default: no visible global function definition for 'points3d'
biplot3D.default: no visible global function definition for 'texts3d'
biplot3D.princomp: no visible global function definition for 'texts3d'
biplot3D.princomp: no visible global function definition for 'par3d'
plot3D.acomp: no visible global function definition for 'points3d'
plot3D.acomp: no visible global function definition for 'lines3d'
plot3D.acomp: no visible global function definition for 'texts3d'
plot3D.acomp: no visible global function definition for 'rgl.viewpoint'
plot3D.acomp: no visible global function definition for 'bbox3d'
plot3D.default: no visible global function definition for 'rgl.bbox'
plot3D.rcomp: no visible global function definition for 'points3d'
plot3D.rcomp: no visible global function definition for 'lines3d'
plot3D.rcomp: no visible global function definition for 'texts3d'
plot3D.rcomp: no visible global function definition for 'rgl.viewpoint'
plot3D.rcomp: no visible global function definition for 'bbox3d'
plot3D.rmult: no visible global function definition for 'points3d'
plot3D.rmult: no visible global function definition for 'par3d'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/CompQuadForm.Rcheck/00install.out' for details.
dhpareto: no visible global function definition for 'pgpd'
dhpareto: no visible global function definition for 'dgpd'
hpareto.gamma: no visible global function definition for 'pgpd'
phpareto: no visible global function definition for 'pgpd'
qhpareto: no visible global function definition for 'qgpd'
rhpareto: no visible global function definition for 'qgpd'
rhpareto: no visible global function definition for 'pgpd'
Namespace in Imports field not imported from: 'graphics'
  All declared Imports should be used.
Package required and available but unsuitable version: 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ConjointChecks: no visible global function definition for 'makeCluster'
ConjointChecks: no visible global function definition for
  'clusterSetRNGStream'
ConjointChecks: no visible global function definition for
  'clusterApply'
ConjointChecks: no visible global function definition for 'stopCluster'
Namespaces in Imports field not imported from:
  'Hmisc' 'MASS' 'geepack'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'knitr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Rtsne' 'scatterplot3d'
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'loadRcppModules' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.2/CorrectOverloadedPeaks.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'xtable'
  All declared Imports should be used.
Package in Depends field not imported from: 'calibrate'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
correlogram: no visible global function definition for 'textxy'
correlogram: no visible global function definition for 'circle'
linangplot: no visible global function definition for 'rad2degree'
linangplot: no visible global function definition for 'ginv'
linangplot: no visible global function definition for 'calibrate'
cosinor_analyzer: no visible binding for global variable 'vitamind'
AntiAR: no visible global function definition for 'first.last'
BootTOS: no visible global function definition for 'ewspec'
BootTOS : bsfn: no visible global function definition for 'LSWsim'
BootTOS : bsfn: no visible global function definition for 'ewspec'
EWSsmoothRM: no visible global function definition for 'accessD'
EWSsmoothRM: no visible global function definition for 'putD'
LCTS: no visible global function definition for 'ewspec'
LCTSres: no visible global function definition for 'ewspec'
coeftofn: no visible global function definition for 'wd'
coeftofn: no visible global function definition for 'wr'
findstysols: no visible global function definition for 'IsPowerOfTwo'
lacv: no visible global function definition for 'ewspec'
lacv: no visible global function definition for 'PsiJmat'
cotrend.default: no visible global function definition for 'coredata'
covLCA: no visible global function definition for 'ginv'
covLCA.initialAlphaGamma: no visible global function definition for
  'mlogit.data'
covLCA.initialAlphaGamma: no visible global function definition for
  'mlogit'
covLCA.initialBeta: no visible global function definition for 'poLCA'
covLCA.initialBeta: no visible global function definition for
  'mlogit.data'
covLCA.initialBeta: no visible global function definition for 'mlogit'
covLCA.paramVariance: no visible global function definition for 'ginv'
covLCA.varianceFirst: no visible global function definition for 'bdiag'
calcz02: no visible global function definition for 'coxph'
covTest: no visible global function definition for 'Surv'
CoxBoost: no visible global function definition for 'Matrix'
cv.CoxBoost: no visible global function definition for 'mclapply'
estimPVal: no visible global function definition for 'mclapply'
iCoxBoost: no visible global function definition for 'Matrix'
plot.coxr: warning in close.screen(all = TRUE): partial argument match
  of 'all' to 'all.screens'
cpa : OpenX: no visible global function definition for 'tclvalue'
cpa : OpenX: no visible global function definition for 'tkgetOpenFile'
cpa : OpenV: no visible global function definition for 'tclvalue'
cpa : OpenV: no visible global function definition for 'tkgetOpenFile'
cpa : OpenA: no visible global function definition for 'tclvalue'
cpa : OpenA: no visible global function definition for 'tkgetOpenFile'
cpa : Close: no visible global function definition for 'tkdestroy'
cpa : OnOK: no visible global function definition for 'tkmessageBox'
cpa : OnOK: no visible global function definition for 'tclvalue'
cpa : OnOK: no visible global function definition for 'tktoplevel'
cpa : OnOK: no visible global function definition for 'tclVar'
cpa : OnOK: no visible global function definition for 'tkentry'
cpa : OnOK: no visible global function definition for 'tkgrid'
cpa : OnOK: no visible global function definition for 'tklabel'
cpa : OnOK : Save: no visible global function definition for 'tclvalue'
cpa : OnOK : Save: no visible global function definition for
  'tkdestroy'
cpa : OnOK: no visible global function definition for 'tkbutton'
cpa : OnOK: no visible global function definition for 'tkbind'
cpa : OnOK: no visible global function definition for 'tkfocus'
cpa: no visible global function definition for 'tktoplevel'
cpa: no visible global function definition for 'tkwm.title'
cpa: no visible global function definition for 'tkbutton'
cpa: no visible global function definition for 'tkgrid'
cpa: no visible global function definition for 'tklabel'
cpa: no visible global function definition for 'tkfocus'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/crmPack.Rcheck/00install.out' for details.
getUrlsCRN: no visible global function definition for 'getURL'
BootC: no visible global function definition for 'boot'
BootC: no visible global function definition for 'boot.ci'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespace in Imports field not imported from: 'httpcode'
  All declared Imports should be used.
GMLDfct: no visible global function definition for 'clusterApplyLB'
SNPgenmap: no visible binding for global variable 'RutgersMapB36'
doGeneDrops: no visible global function definition for 'write.pedfile'
doGeneDrops: no visible global function definition for 'GeneDrops'
doGeneDrops: no visible global function definition for 'read.pedfile'
flagAllPairs: no visible global function definition for 'showLabels'
flagPairs: no visible global function definition for 'showLabels'
gendrp: no visible global function definition for 'clusterApply'
get.ellipse: no visible global function definition for 'ellipse'
parfile.fitLD: no visible global function definition for
  'write.pedfile'
parfile.fitLD: no visible global function definition for
  'write.parfile'
parfile.fitLD: no visible global function definition for 'FitGMLD'
parfile.noLD: no visible global function definition for 'write.parfile'
snpfilter: no visible global function definition for 'row.summary'
File 'Cubist/libs/i386/Cubist.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'getdata.o'
File 'Cubist/libs/x64/Cubist.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'getdata.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/CuCubes.Rcheck/00install.out' for details.
cudiaDet: no visible global function definition for 'rdirichlet'
cudiaDet: no visible global function definition for 'lm.ridge'
getoptimalalpha: no visible global function definition for 'gcvplot'
.klogreg: no visible global function definition for 'Matrix'
.klogreg: no visible global function definition for 'kernelMatrix'
.klogreg: no visible global function definition for 'Diagonal'
.klogreg.predict: no visible global function definition for
  'kernelMult'
.krr: no visible global function definition for 'kernelMatrix'
.krr: no visible global function definition for 'Matrix'
.krr.predict: no visible global function definition for 'kernelMatrix'
constructSVMLearner : learn.svm: no visible global function definition
  for 'ksvm'
constructSVRLearner : learn.svr: no visible global function definition
  for 'ksvm'
cxxfunctionplus: no visible global function definition for 'getPlugin'
cxxfunctionplus: no visible global function definition for
  'cxxfunction'
get.trans: no visible global function definition for
  'create.bspline.basis'
get.trans: no visible global function definition for 'smooth.basis'
get.trans: no visible global function definition for 'deriv.fd'
get.trans: no visible global function definition for 'eval.fd'
initialize,D2C : .local: warning in sort(IM, decr = TRUE, ind = TRUE):
  partial argument match of 'decr' to 'decreasing'
updateD2C,D2C : .local: warning in sort(IM, decr = TRUE, ind = TRUE):
  partial argument match of 'decr' to 'decreasing'
compute,DAG.network : .local: no visible global function definition for
  'numNodes'
compute,DAG.network : .local: no visible global function definition for
  'inEdges'
initialize,D2C : .local: no visible binding for global variable 'i'
initialize,D2C : .local: no visible global function definition for
  'nodes'
initialize,D2C : .local: no visible global function definition for
  'subGraph'
initialize,D2C : .local: no visible global function definition for
  'inEdges'
initialize,simulatedDAG : .local: no visible binding for global
  variable 'i'
initialize,simulatedDAG : .local: no visible global function definition
  for 'edges'
updateD2C,D2C : .local: no visible binding for global variable 'i'
updateD2C,D2C : .local: no visible global function definition for
  'nodes'
updateD2C,D2C : .local: no visible global function definition for
  'subGraph'
updateD2C,D2C : .local: no visible global function definition for
  'inEdges'
compareModels: no visible binding for global variable 'fgl'
compareModels: no visible global function definition for 'rlm'
Daim: no visible global function definition for 'mclapply'
Daim: no visible global function definition for 'clusterSetRNGStream'
Daim: no visible global function definition for 'clusterEvalQ'
Daim: no visible global function definition for 'clusterApplyLB'
The following files are already in R: 'jss.bst', 'jss.cls'
Please remove them from your package.
.onLoad : <anonymous>: no visible global function definition for
  'dbConnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbListTables'
.onLoad : <anonymous>: no visible global function definition for
  'dbExistsTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbReadTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbWriteTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbDisconnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbRemoveTable'
meta,SftpLocation : .local: no visible global function definition for
  'basicTextGatherer'
meta,SftpLocation : .local: no visible binding for global variable
  'isdir'
meta,SftpLocation : .local: no visible binding for global variable
  'name'
put,BlogPostTarget-Blogger : .local: no visible global function
  definition for 'toJSON'
Package suggested but not available for checking: 'nanotime'
DAT : DATrun: no visible global function definition for 'rot90'
DAT : DATrun: no visible global function definition for 'locfit.robust'
DAT : DATrun: no visible global function definition for 'writeMat'
DAT: no visible binding for global variable 'DAT.simData'
plot.pcobiplot: no visible binding for global variable 'sveg'
getCutoff: no visible binding for global variable 'unifCut'
getCutoff: no visible binding for global variable 'normCut'
getCutoff: no visible binding for global variable 'distEqCut'
getPval: no visible binding for global variable 'unifCut'
getPval: no visible binding for global variable 'normCut'
getPval: no visible binding for global variable 'distEqCut'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dclone.Rcheck/00install.out' for details.
Plot.triangle: no visible global function definition for 'cloud'
Plot.triangle: no visible binding for global variable 'panel.3dbars'
Plot.triangle: no visible global function definition for 'level.colors'
Plot.triangle: no visible global function definition for 'do.breaks'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dcmle.Rcheck/00install.out' for details.
plot,attribute.class-missing : .local: no visible binding for global
  variable 'attr.number'
plot,attribute.class-missing : .local: no visible binding for global
  variable 'mean.attr'
plot,attribute.profile.class-missing : .local: no visible binding for
  global variable 'attr.profile.number'
plot,attribute.profile.class-missing : .local: no visible binding for
  global variable 'mean.attr.profile'
summary,attribute.class : .local: no visible binding for global
  variable 'value'
summary,attribute.profile.class : .local: no visible binding for global
  variable 'max.class'
.onLoad: no visible binding for global variable 'jgr.addMenuItem'
.onLoad : gui.addSeperator: no visible global function definition for
  'jgr.addMenuSeparator'
.factorAnalysisRunFunction: no visible global function definition for
  'execute'
.onLoad: no visible binding for global variable '.deducer'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.registerDialog'
.onLoad: no visible global function definition for 'deducer.addMenu'
.onLoad: no visible global function definition for
  'deducer.addMenuItem'
.onLoad: no visible binding for global variable '.windowsGUI'
.onLoad: no visible binding for global variable '.jgr'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
makeFactorAnalysisDialog: no visible binding for global variable
  'SimpleRDialog'
makeFactorAnalysisDialog: no visible binding for global variable
  'VariableSelectorWidget'
makeFactorAnalysisDialog: no visible global function definition for
  'addComponent'
makeFactorAnalysisDialog: no visible binding for global variable
  'VariableListWidget'
makeFactorAnalysisDialog: no visible binding for global variable
  'CheckBoxesWidget'
makeFactorAnalysisDialog: no visible global function definition for
  'toJava'
makeListExampleDialog: no visible binding for global variable
  'ListWidget'
makeListExampleDialog: no visible global function definition for
  'setSize'
makeListExampleDialog: no visible binding for global variable
  'AddRemoveButtons'
makeListExampleDialog: no visible binding for global variable
  'SimpleRDialog'
makeListExampleDialog: no visible global function definition for
  'addComponent'
makeListExampleDialog: no visible global function definition for
  'toJava'
makeScatterPlotDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
'library' or 'require' call to 'UScensus2010' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: 'UScensus2010'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'JavaGD' 'OpenStreetMap' 'maptools' 'rgdal' 'scales' 'sp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.containedBy: no visible global function definition for
  'projectMercator'
.makeCensusDialog: no visible global function definition for 'J'
.makeCensusDialog: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.jengine'
.onLoad: no visible global function definition for 'J'
.subsetLines: no visible global function definition for
  'projectMercator'
.subsetPoints: no visible global function definition for
  'projectMercator'
.subsetPoly: no visible global function definition for
  'projectMercator'
spatialBubblePlot: no visible global function definition for
  'coordinates'
spatialChoropleth: no visible global function definition for
  'manual_pal'
spatialChoropleth: no visible global function definition for
  'gradient_n_pal'
spatialChoropleth: no visible global function definition for 'cscale'
spatialColoredPoints: no visible global function definition for
  'manual_pal'
spatialColoredPoints: no visible global function definition for
  'gradient_n_pal'
spatialColoredPoints: no visible global function definition for
  'cscale'
spatialTextPlot: no visible global function definition for
  'coordinates'
.CompareRunFunction: no visible global function definition for
  'execute'
.KMRunFunction: no visible global function definition for 'execute'
.onLoad: no visible binding for global variable '.deducer'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.registerDialog'
.onLoad: no visible global function definition for 'deducer.addMenu'
.onLoad: no visible global function definition for
  'deducer.addMenuItem'
.onLoad: no visible binding for global variable '.windowsGUI'
.onLoad: no visible binding for global variable '.jgr'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
makeCompareDialog: no visible binding for global variable
  'SimpleRDialog'
makeCompareDialog: no visible binding for global variable
  'VariableSelectorWidget'
makeCompareDialog: no visible global function definition for
  'addComponent'
makeCompareDialog: no visible binding for global variable
  'SingleVariableWidget'
makeCompareDialog: no visible binding for global variable
  'ButtonGroupWidget'
makeCompareDialog: no visible global function definition for 'toJava'
makeKMDialog: no visible binding for global variable 'SimpleRDialog'
makeKMDialog: no visible binding for global variable
  'VariableSelectorWidget'
makeKMDialog: no visible global function definition for 'addComponent'
makeKMDialog: no visible binding for global variable
  'SingleVariableWidget'
makeKMDialog: no visible binding for global variable 'TextAreaWidget'
makeKMDialog: no visible binding for global variable
  'ButtonGroupWidget'
makeKMDialog: no visible binding for global variable 'TextFieldWidget'
makeKMDialog: no visible global function definition for 'toJava'
.makeQuickWordcloud: no visible global function definition for 'J'
.makeQuickWordcloud: no visible global function definition for '.jnull'
.makeTextPlot: no visible global function definition for 'J'
.makeTextPlot: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for '.jpackage'
.onLoad: no visible global function definition for '.jnew'
.onLoad: no visible global function definition for 'J'
bpstrip: no visible binding for global variable 'panel.polygon'
bpstrip: no visible binding for global variable 'panel.segments'
bpstrip: no visible global function definition for
  'current.panel.limits'
bpstrip: no visible global function definition for 'trellis.par.get'
cistrip: no visible binding for global variable 'panel.points'
cistrip: no visible binding for global variable 'panel.segments'
denstrip: no visible binding for global variable 'panel.rect'
denstrip: no visible binding for global variable 'panel.segments'
denstrip: no visible global function definition for
  'current.panel.limits'
denstrip: no visible global function definition for 'trellis.par.get'
denstrip.legend: no visible binding for global variable 'panel.polygon'
denstrip.legend: no visible binding for global variable
  'panel.segments'
denstrip.legend: no visible binding for global variable 'panel.text'
denstrip.legend: no visible global function definition for
  'current.panel.limits'
denstrip.legend: no visible global function definition for
  'trellis.last.object'
denstrip.legend: no visible global function definition for
  'trellis.par.get'
sectioned.density: no visible binding for global variable 'panel.rect'
sectioned.density: no visible global function definition for
  'current.panel.limits'
sectioned.density: no visible global function definition for
  'trellis.par.get'
vwstrip: no visible binding for global variable 'panel.polygon'
vwstrip: no visible binding for global variable 'panel.segments'
vwstrip: no visible global function definition for
  'current.panel.limits'
vwstrip: no visible global function definition for 'trellis.par.get'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/DEploid.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    help   1.3Mb
    libs   1.4Mb
Missing link or links in documentation object 'StrRep.Rd':
  'strrep'

See section 'Cross-references' in the 'Writing R Extensions' manual.
compute.p.values: no visible global function definition for 'ash2'
draw.single.detsel.graph: no visible global function definition for
  'ash2'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    bin   3.7Mb
    doc   1.7Mb
Namespace in Imports field not imported from: 'mgcv'
  All declared Imports should be used.
sectionview,function : .local: warning in sectionview.fun(fun = model,
  dim = dim, center = center, axis = axis, npoints = npoints, col =
  col, mfrow = mfrow, Xname = Xname, yname = yname, Xscale = Xscale,
  yscale = yscale, xlim = xlim, ylim = ylim, title = title, ...):
  partial argument match of 'col' to 'col_surf'
view,character-function : .local: warning in sectionview.fun(fun =
  model, dim = dim, center = center, axis = axis, npoints =
  ifelse(is.null(npoints), 100, npoints), col = col, mfrow = mfrow,
  Xname = Xname, yname = yname, Xscale = Xscale, yscale = yscale, xlim
  = xlim, ylim = ylim, title = title, ...): partial argument match of
  'col' to 'col_surf'
L2eV: no visible binding for global variable 'constants'
L2w: no visible binding for global variable 'constants'
eV2L: no visible binding for global variable 'constants'
t2eV: no visible binding for global variable 'constants'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/Difdtl.Rcheck/00install.out' for details.
diffpci: no visible global function definition for 'diffpropci.Wald.mp'
diffpci: no visible global function definition for 'diffpropci.mp'
diffpci: no visible global function definition for 'scoreci.mp'
wilson: no visible global function definition for 'uniroot.all'
wilson.cc: no visible global function definition for 'uniroot.all'
wilson.phi: no visible global function definition for 'uniroot.all'
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.3Mb
fAssocmatrix : fAssocmatrix1: no visible global function definition for
  'coordinates<-'
fAssocplot: no visible global function definition for 'coordinates'
fDrawfigure: no visible global function definition for
  'SpatialPolygons'
fDrawfigure: no visible global function definition for 'spsample'
fRanXY : <anonymous>: no visible global function definition for
  'spsample'
EdgelistFromIgraph: no visible global function definition for
  'get.adjacency'
EdgelistFromIgraph: no visible global function definition for 'V'
EdgelistFromIgraph: no visible global function definition for 'vcount'
IgraphFromEdgelist: no visible global function definition for
  'graph.adjacency'
IgraphFromEdgelist: no visible global function definition for 'V'
IgraphFromEdgelist: no visible global function definition for 'V<-'
MeasureNetworkInformation: no visible binding for global variable
  'betweenness'
MeasureNetworkInformation: no visible global function definition for
  'vcount'
MeasureNetworkInformation : SampleIgraph: no visible global function
  definition for 'ecount'
MeasureNetworkInformation : SampleIgraph: no visible global function
  definition for 'delete.edges'
MeasureNetworkInformation : SampleIgraph: no visible global function
  definition for 'E'
RelativeNetworkInformation: no visible binding for global variable
  'betweenness'
RssSuggestedNetwork: no visible global function definition for
  'get.adjacency'
RssSuggestedNetwork: no visible global function definition for
  'is.directed'
RssSuggestedNetwork: no visible global function definition for 'vcount'
RssSuggestedNetwork: no visible global function definition for
  'graph.adjacency'
RssSuggestedNetwork: no visible global function definition for
  'graph.density'
plot.discrimARTs: no visible global function definition for 'grid.text'
plot.discrimARTs: no visible global function definition for 'gpar'
GraphDistatisAll: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisBoot: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisBoot: no visible global function definition for
  'dataEllipse'
GraphDistatisBoot: no visible global function definition for
  'peeledHull'
GraphDistatisCompromise: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisCompromise: no visible global function definition for
  'prettyPlot'
GraphDistatisPartial: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisPartial: no visible global function definition for
  'prettyPlot'
GraphDistatisRv: no visible global function definition for
  'createColorVectorsByDesign'
GraphDistatisRv: no visible global function definition for 'prettyPlot'
momIntegrated: multiple local function definitions for 'ddist' with
  different formal arguments
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   1.2Mb
hip: no visible global function definition for 'adiag'
.addEq: no visible global function definition for '.Eq'
.addSt: no visible global function definition for '.St'
plot.compExp: no visible global function definition for 'grid.newpage'
plot.compExp: no visible global function definition for 'pushViewport'
plot.compExp: no visible global function definition for 'viewport'
plot.compExp: no visible global function definition for 'grid.layout'
plot.compExp: no visible global function definition for 'bwplot'
plot.compExp : <anonymous>: no visible global function definition for
  'panel.grid'
plot.compExp : <anonymous>: no visible global function definition for
  'panel.bwplot'
plot.compExp: no visible global function definition for 'upViewport'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/DNAprofiles.Rcheck/00install.out' for details.
network.modules: no visible global function definition for
  'graph.empty'
network.modules: no visible global function definition for
  'add.vertices'
network.modules: no visible global function definition for 'add.edges'
network.modules: no visible global function definition for 'tkplot'
network.modules: no visible global function definition for 'V'
Namespaces in Imports field not imported from:
  'GOstats' 'caTools' 'fdrtool'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'tibble'
  All declared Imports should be used.
.randomize: no visible global function definition for '[.coded.data'
Found the following significant warnings:
  Warning: running command 'domino help' had status 127
See 'd:/Rcompile/CRANpkg/local/3.2/domino.Rcheck/00install.out' for details.
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
  
  
  Executing test function test.registerDoRNG  ...  done successfully.
  
  ------------------- UNIT TEST SUMMARY ---------------------
  
  Error in .local(x, ...) : Functions: 2 | Errors: 1 | Failures: 0 
  ERROR in runit.dorng.R::test.dorng: Error in mpi.comm.spawn(slave = rscript, slavearg = args, nslaves = count,  : 
    Other MPI error, error stack:
  MPI_Comm_spawn(cmd="D:/RCompile/recent/R-32~1.5/bin/Rscript", argv=0x000000000A614710, maxprocs=2, MPI_INFO_NULL, root=0, MPI_COMM_SELF, intercomm=0x000000000A5C1818, errors=0x000000000A32E980) failed
  Function not implemented
  Calls: <Anonymous> -> <Anonymous> -> .local -> utest -> utest -> .local
  Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
dpmixsim: no visible global function definition for 'clara'
postkcluster: no visible global function definition for 'clara'
readsliceimg: no visible global function definition for 'readNIfTI'
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.
depratio: warning in match.call(expand = FALSE): partial argument match
  of 'expand' to 'expand.dots'
drm: warning in match.call(expand = FALSE): partial argument match of
  'expand' to 'expand.dots'
Namespace in Imports field not imported from: 'shapefiles'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dSVA.Rcheck/00install.out' for details.
perturbFBM: warning in circFBM(n, H, plot = FALSE): partial argument
  match of 'plot' to 'plotfBm'
filt: no visible global function definition for 'wavDaubechies'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/dynamichazard.Rcheck/00install.out' for details.
bootstrapCI: no visible global function definition for 'lpepa'
dynamicCorrelation: no visible global function definition for 'lpepa'
PredictPropen,modelObjFit-data.frame : .local: no visible global
  function definition for 'level'
PlotPotential: no visible global function definition for 'aes'
PlotPotential: no visible global function definition for 'geom_tile'
PlotPotential: no visible global function definition for
  'scale_fill_gradient'
PlotPotential: no visible global function definition for 'stat_contour'
PlotPotential: no visible global function definition for 'xlab'
PlotPotential: no visible global function definition for 'ylab'
PlotPotential: no visible global function definition for 'labs'
Namespaces in Imports field not imported from:
  'ggplot2' 'reshape2' 'scales' 'xtable'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'base64enc' 'knitr' 'markdown'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.file_attachment: no visible global function definition for
  'base64encode'
easyHtmlReport: no visible global function definition for 'knit'
easyHtmlReport: no visible global function definition for
  'markdownToHTML'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/EasyMARK.Rcheck/00install.out' for details.
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.
decdfHT: possible error in findInterval(x[i], ecdfHT.fit$xsort,
  rightmost.closed = TRUE, all.inside = TRUE, left.open = FALSE):
  unused argument (left.open = FALSE)
Running examples in 'ecdfHT-Ex.R' failed
The error most likely occurred in:

> ### Name: pecdfHT
> ### Title: Compute cdf, pdf, quantiles, and simulate from a fitted
> ###   distribution
> ### Aliases: decdfHT pecdfHT qecdfHT recdfHT
> 
> ### ** Examples
> 
> x <- rcauchy(1000)
> a <- ecdfHT( x, show.plot=FALSE )
> fit <- ecdfHT.fit( c(.1,.9), a, add.to.plot=FALSE )
> pecdfHT( -3:3, fit )
[1] 0.08621799 0.12705058 0.23166862 0.47955015 0.72400844 0.82998740 0.87927967
> decdfHT( -3:3, fit )
Error in findInterval(x[i], ecdfHT.fit$xsort, rightmost.closed = TRUE,  : 
  unused argument (left.open = FALSE)
Calls: decdfHT -> findInterval
Execution halted
Package required and available but unsuitable version: 'RSQLite'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
ecipex: no visible binding for global variable 'nistiso'
Namespace in Imports field not imported from: 'magrittr'
  All declared Imports should be used.
.echCusum1: no visible global function definition for 'xcusum.arl'
.echCusum2: no visible global function definition for 'xcusum.arl'
.echEwma1: no visible global function definition for 'xewma.arl'
.echEwma2: no visible global function definition for 'xewma.arl'
echCusum: no visible global function definition for 'xcusum.arl'
echEwma: no visible global function definition for 'xewma.arl'
ecoCusum: no visible global function definition for 'xcusum.arl'
ecoEwma: no visible global function definition for 'xewma.arl'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/eggCounts.Rcheck/00install.out' for details.
Y_impute: no visible binding for global variable 'pp_zq'
Y_impute: no visible binding for global variable 'Ranks'
Y_impute: no visible binding for global variable 'Z'
eigenmodel_setup: no visible binding for global variable 'Y'
rUL_fc: no visible binding for global variable 'Z'
rUL_fc: no visible binding for global variable 'X'
rUL_fc: no visible binding for global variable 'b'
rUL_fc: no visible binding for global variable 'UL'
rUL_fc: no visible binding for global variable 'R'
rUL_fc: no visible binding for '<<-' assignment to 'mean_u'
rUL_fc: no visible binding for global variable 'var_u'
rUL_fc: no visible binding for global variable 'pp_mu'
rUL_fc: no visible binding for global variable 'pm_mu'
rUL_fc: no visible binding for global variable 'n'
rUL_fc: no visible binding for global variable 'mean_u'
rUL_fc: no visible binding for global variable 'pp_l'
rZ_fc: no visible binding for global variable 'X'
rZ_fc: no visible binding for global variable 'b'
rZ_fc: no visible binding for global variable 'UL'
rZ_fc: no visible binding for global variable 'pp_zq'
rZ_fc: no visible binding for global variable 'Ranks'
rZ_fc: no visible binding for global variable 'uRanks'
rZ_fc: no visible binding for global variable 'n'
rb_fc: no visible binding for global variable 'Z'
rb_fc: no visible binding for global variable 'UL'
rb_fc: no visible binding for global variable 'pm_b'
rb_fc: no visible binding for global variable 'xtx'
rb_fc: no visible binding for global variable 'pp_b'
rb_fc: no visible binding for global variable 'tx'
cluster.segment: no visible global function definition for 'knn'
quantreg.est: no visible global function definition for 'rq.fit.fnb'
ei.MD.bayes: warning in BayesMDei2(formula, data, total = total,
  lambda1 = lambda1, lambda2 = lambda2, tune.alpha = tune.alpha,
  tune.beta = tune.beta, start.alpha = start.alphas, start.betas =
  start.betas, sample = sample, thin = thin, burnin = burnin, verbose =
  verbose, ret.beta = ret.beta, ret.mcmc = ret.mcmc, usrfun = usrfun):
  partial argument match of 'start.alpha' to 'start.alphas'
tuneMD: warning in ei.MD.bayes(formula, covariate = covariate, data =
  data, sample = sample, thin = thin, burnin = burnin, tune = tl, ...):
  partial argument match of 'tune' to 'tune.list'
bayes.regress : truncMVRnorm: no visible global function definition for
  'mvrnorm'
bayes.regress: no visible binding for global variable 'mvrnorm'
cover.plot: no visible global function definition for 'is.mcmc'
density.plot.lambdaMD: no visible global function definition for
  'is.mcmc'
density.plot.lambdaRegBayes: no visible global function definition for
  'is.mcmc'
lambda.MD: no visible global function definition for 'is.mcmc'
lambda.MD: no visible global function definition for 'mcpar'
mergeMD: no visible global function definition for 'mcmc'
print.eiMD: no visible global function definition for 'is.mcmc'
read.betas: no visible global function definition for 'as.mcmc'
summary.eiMD: no visible global function definition for 'is.mcmc'
summary.lambdaRegBayes: no visible global function definition for
  'is.mcmc'
BaB: no visible binding for global variable 'calc.pairwise.e_p'
BaB: no visible global function definition for 'weight.function'
BaB: no visible global function definition for 'compute.stark.t'
LKPBound: no visible binding for global variable 'calc.pairwise.e_p'
LKPBound: no visible global function definition for 'weight.function'
LKPBound: no visible global function definition for 'compute.stark.t'
eqValBound: no visible binding for global variable 'calc.pairwise.e_p'
eqValBound: no visible global function definition for 'weight.function'
eqValBound: no visible global function definition for 'compute.stark.t'
getEbsMargin: no visible global function definition for 'is.elec.data'
getEbsMargin: no visible global function definition for
  'maximumMarginBound'
makeStratObj: no visible global function definition for 'is.elec.data'
makeStratObj: no visible global function definition for
  'maximumMarginBound'
strat.elec.data: no visible global function definition for 'elec.data'
takeOutZeroMMB: no visible global function definition for
  'maximumMarginBound'
withReplaceBound: no visible binding for global variable
  'calc.pairwise.e_p'
withReplaceBound: no visible global function definition for
  'weight.function'
withReplaceBound: no visible global function definition for
  'compute.stark.t'
Namespaces in Imports field not imported from:
  'prettyunits' 'ratelimitr' 'rgdal'
  All declared Imports should be used.
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.
Likelihood: no visible global function definition for
  'makePSOCKcluster'
Likelihood: no visible global function definition for 'clusterExport'
Likelihood: no visible global function definition for 'makeForkCluster'
Likelihood.first.run: no visible global function definition for
  'clusterApply'
Likelihood.next.runs: no visible global function definition for
  'clusterApply'
es.stopCluster: no visible global function definition for 'stopCluster'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/EMA.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: namespace 'embryogrowth' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/3.2/embryogrowth.Rcheck/00install.out' for details.
File 'EMC/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("##\n", "## Evolutionary Monte Carlo Package (EMC)\n",     "##\n", "## Functionality: random walk Metropolis, general Metropolis-Hastings\n",     "## parallel tempering, target oriented EMC (TOEMC), temperature ladder\n",     "## construction and placement\n", "##\n", "## Use: \"help(package = EMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

See section 'Good practice' in '?.onAttach'.

CigarShapedFuncGenerator1 : logTarDensFunc: no visible global function
  definition for 'dmvnorm'
CigarShapedFuncGenerator2 : logTarDensFunc: no visible global function
  definition for 'dmvnorm'
VShapedFuncGenerator : logTarDensFunc : <anonymous>: no visible global
  function definition for 'dmvnorm'
WShapedFuncGenerator : logTarDensFunc : <anonymous>: no visible global
  function definition for 'dmvnorm'
threeDimNormalFuncGenerator : logTarDensFunc: no visible global
  function definition for 'dmvnorm'
threeDimNormalFuncGenerator : propNewFunc: no visible global function
  definition for 'mvrnorm'
twentyModeFuncGenerator : logTarDensFunc : <anonymous>: no visible
  global function definition for 'dmvnorm'
uniModeFuncGenerator : logTarDensFunc: no visible global function
  definition for 'dmvnorm'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
'library' or 'require' calls to packages already attached by Depends:
  'clusterSim' 'earth'
  Please remove these calls from your code.
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'clusterSim' 'earth'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
distance: no visible global function definition for
  'data.Normalization'
estimateModel: no visible global function definition for 'earth'
estimateModel: no visible global function definition for 'plotmo'
MFFetch: no visible global function definition for 'melt'
drawScene.rgl: no visible global function definition for 'rgl.cur'
drawScene.rgl: no visible global function definition for 'open3d'
drawScene.rgl: no visible global function definition for 'clear3d'
drawScene.rgl: no visible global function definition for 'triangles3d'
fmmst.contour.3d: no visible global function definition for 'plot3d'
fmmst.contour.3d: no visible global function definition for 'points3d'
Error in re-building vignettes:
  ...
Quitting from lines 119-144 (emojifont.Rmd) 
Error: processing vignette 'emojifont.Rmd' failed with diagnostics:
StatTreeHorizontal was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
ENMCA : fn: no visible global function definition for 'assignCluster'
ENMCA : fn: no visible global function definition for 'catdes'
ENMCA : fn: no visible global function definition for 'plot.MCA'
ENdensity: no visible global function definition for 'kde2d'
ENlisib: no visible global function definition for 'plot.MCA'
MCA2: no visible global function definition for 'tab.disjonctif'
MCA2: no visible global function definition for 'PCA'
MCA2: no visible global function definition for 'CA'
MCA2: no visible global function definition for 'plot.MCA'
XvsYbarplot: possible error in hsv(h = 1, s = 1, v = 1, 1, 1): unused
  argument (1)
XvsYbarplot: possible error in hsv(h = 1, s = 0.4 + (height[i]/max) *
  0.6, v = 1, 1, 1): unused argument (1)
XvsYbarplot: possible error in hsv(h = a * i, s = 1, v = 1, 1, 1):
  unused argument (1)
barplot_function: possible error in hsv(h = a * m, s = 1, v = 1, 1, 1):
  unused argument (1)
barplot_function: possible error in hsv(h = a * m, s = 0.4 +
  (cont[j]/max) * 0.6, v = 1, 1, 1): unused argument (1)
barplot_sweave : set.X: no visible binding for global variable 'X'
chisq.function: no visible global function definition for 'coltable'
col.barplot: possible error in hsv(h = 1, s = 1, v = 1, 1, 1): unused
  argument (1)
col.barplot: possible error in hsv(h = 1, s = 0.4 + (height[i]/max) *
  0.6, v = 1, 1, 1): unused argument (1)
col.barplot: possible error in hsv(h = a * i, s = 1, v = 1, 1, 1):
  unused argument (1)
p_inertia: no visible global function definition for 'MCA'
tab_chi2: no visible global function definition for 'coltable'
KM.plot.ade : plot.box.ade: no visible global function definition for
  'axis.break'
KM.plot.ade: no visible global function definition for 'survfit'
KM.plot.ade: no visible global function definition for 'survdiff'
a.form.ade: no visible global function definition for 'cylindrect'
a.form.ade : sub.ellipse.ade : gradient.rect.ade: no visible global
  function definition for 'color.gradient'
box.plot.ade : a.draw.box: no visible global function definition for
  'cylindrect'
box.plot.wtd : wtd.sd: no visible global function definition for
  'wtd.var'
box.plot.wtd : a.draw.box: no visible global function definition for
  'wtd.mean'
box.plot.wtd : a.draw.box: no visible global function definition for
  'wtd.quantile'
box.plot.wtd : a.draw.box: no visible global function definition for
  'cylindrect'
histogram.ade: no visible global function definition for
  'weighted.hist'
pr2 : fa22: no visible global function definition for 'Anova'
eqs2lavaan: no visible binding for global variable 'r'
topoplot: no visible global function definition for 'interp'
esgplotshocks: no visible global function definition for 'geom_point'
esgplotshocks: no visible global function definition for 'aes'
esgplotshocks: no visible global function definition for 'theme'
esgplotshocks: no visible global function definition for
  'element_blank'
esgplotshocks: no visible global function definition for
  'scale_color_manual'
esgplotshocks: no visible global function definition for 'geom_density'
esgplotshocks: no visible global function definition for
  'scale_fill_manual'
esgplotshocks: no visible global function definition for 'coord_flip'
esgplotts: no visible global function definition for 'xlab'
esgplotts: no visible global function definition for 'ylab'
esgplotts: no visible global function definition for 'theme'
iqr_cell: no visible global function definition for 'wtd.quantile'
mean_sd_cell: no visible global function definition for 'wtd.mean'
mean_sd_cell: no visible global function definition for 'wtd.var'
mode_cell: no visible global function definition for 'wtd.table'
quantile_cell: no visible global function definition for 'wtd.quantile'
stat_cell: no visible global function definition for 'wtd.quantile'
stat_cell: no visible global function definition for 'wtd.mean'
stat_cell: no visible global function definition for 'wtd.var'
stat_cell: no visible global function definition for 'wtd.table'
Namespace in Imports field not imported from: 'EnvStats'
  All declared Imports should be used.
read_eventdata : read_ed_file: warning in read.csv(d, sep = sep, head =
  head, strip.white = TRUE, colClasses = "character"): partial argument
  match of 'head' to 'header'
ees: no visible global function definition for 'zoo'
eesPlot: no visible global function definition for 'index'
gen.data: no visible global function definition for 'index'
gen.data: no visible global function definition for 'coredata'
get.clusters.formatted: no visible global function definition for 'xts'
get.clusters.formatted: no visible global function definition for 'zoo'
inference.Ecar: no visible global function definition for 'boot'
inference.change.boot: no visible global function definition for 'boot'
inference.change.boot: no visible global function definition for
  'boot.ci'
phys2eventtime : timeshift: no visible global function definition for
  'index'
phys2eventtime : timeshift: no visible global function definition for
  'zoo'
phys2eventtime: no visible global function definition for 'zoo'
phys2eventtime: no visible global function definition for 'na.locf'
sumstat: no visible global function definition for 'xts'
yearly.exevent.summary: no visible global function definition for
  'apply.yearly'
yearly.exevent.summary: no visible global function definition for 'xts'
yearly.exevent.summary: no visible global function definition for
  'index<-'
yearly.exevent.summary: no visible global function definition for
  'as.yearmon'
yearly.exevent.summary: no visible global function definition for
  'index'
Namespace in Imports field not imported from: 'polynom'
  All declared Imports should be used.
expectreg.boost: no visible global function definition for 'mclapply'
expectreg.boost: no visible global function definition for
  'detectCores'
laws: no visible global function definition for 'mclapply'
laws: no visible global function definition for 'detectCores'
quant.boost: no visible global function definition for 'mclapply'
quant.boost: no visible global function definition for 'detectCores'
rb: no visible global function definition for 'cover.design'
ATEbounds: no visible global function definition for 'boot'
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
computeConstraints: no visible global function definition for
  'minmaxHelper'
coreCA: no visible global function definition for 'repmat'
coreMDS: no visible global function definition for 'repmat'
corePCA: no visible global function definition for 'repmat'
epGraphs: no visible global function definition for
  'createColorVectorsByDesign'
epGraphs: no visible global function definition for 'prettyPlot'
epGraphs: no visible global function definition for 'contributionBars'
makeNominalData: no visible global function definition for 'repmat'
mca.eigen.fix: no visible global function definition for 'repmat'
pcaSupplementaryColsPreProcessing: no visible global function
  definition for 'repmat'
pcaSupplementaryRowsPreProcessing: no visible global function
  definition for 'repmat'
rowNorms: no visible global function definition for 'repmat'
supplementalProjection: no visible global function definition for
  'repmat'
node.age: no visible global function definition for 'is.binary.tree'
node.age: no visible global function definition for 'multi2di'
DirichletPolygons,SpatialPointsBreeding-missing: no visible global
  function definition for 'ripras'
Namespace in Imports field not imported from: 'affy'
  All declared Imports should be used.
extfunnel: no visible global function definition for 'meta.summaries'
misc : q: no visible global function definition for 'name'
Namespace in Imports field not imported from: 'FactoMineR'
  All declared Imports should be used.
bayesQR : captureFormula: warning in match.call(expand = FALSE):
  partial argument match of 'expand' to 'expand.dots'
bayesQR: warning in matrix(beta, nc = 1): partial argument match of
  'nc' to 'ncol'
factorQR : captureFormula: warning in match.call(expand = FALSE):
  partial argument match of 'expand' to 'expand.dots'
factorQR: warning in matrix(rnorm(nObs * nFact), nr = nObs): partial
  argument match of 'nr' to 'nrow'
factorQR: warning in matrix(0, nr = nFact + xBetLen + numManInd, nc =
  nFact + xBetLen + numManInd): partial argument match of 'nr' to
  'nrow'
factorQR: warning in matrix(0, nr = nFact + xBetLen + numManInd, nc =
  nFact + xBetLen + numManInd): partial argument match of 'nc' to
  'ncol'
factorQR: warning in matrix(0, nr = nFact + xBetLen + 1, nc = nFact +
  xBetLen + 1): partial argument match of 'nr' to 'nrow'
factorQR: warning in matrix(0, nr = nFact + xBetLen + 1, nc = nFact +
  xBetLen + 1): partial argument match of 'nc' to 'ncol'
factorQR: warning in matrix(0, nr = xLength, nc = nFact): partial
  argument match of 'nr' to 'nrow'
factorQR: warning in matrix(0, nr = xLength, nc = nFact): partial
  argument match of 'nc' to 'ncol'
makeData: warning in matrix(0, nr = xLength, nc = nFact): partial
  argument match of 'nr' to 'nrow'
makeData: warning in matrix(0, nr = xLength, nc = nFact): partial
  argument match of 'nc' to 'ncol'
makeData: warning in matrix(rnorm(N * nFact), nc = nFact): partial
  argument match of 'nc' to 'ncol'
makeData: warning in matrix(rnorm(N * xLength), nc = xLength): partial
  argument match of 'nc' to 'ncol'
plot.bayesQR: warning in matrix(sampledVals, nc = 1): partial argument
  match of 'nc' to 'ncol'
plot.factorQR: warning in matrix(sampledVals, nc = 1): partial argument
  match of 'nc' to 'ncol'
factualGetSchema: no visible global function definition for 'fromJSON'
factualRead: no visible global function definition for 'curlEscape'
factualRead: no visible global function definition for 'fromJSON'
as.FAMTdata: no visible global function definition for 'impute.knn'
nbfactors : bivprob : <anonymous>: no visible global function
  definition for 'biv.nt.prob'
File 'fANCOVA/R/onload.R':
  .onLoad calls:
    packageStartupMessage("fANCOVA 0.5-1 loaded")

See section 'Good practice' in '?.onAttach'.
File 'fastmatch/libs/i386/fastmatch.dll':
  Found non-API call to R: 'match5'
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API call to R: 'match5'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
.run: no visible binding for global variable 'init'
.run: no visible global function definition for 'init'
.run: no visible binding for global variable 'run'
Namespace in Imports field not imported from: 'whisker'
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.5Mb
fcd.start: no visible global function definition for 'ginv'
fcd.start: no visible global function definition for 'glmnet'
mis.cluster: no visible global function definition for 'permn'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/fcros.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/fdasrvf.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/feather.Rcheck/00install.out' for details.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'base' 'graphics' 'stats'
A package should be listed in only one of these fields.
Namespace in Imports field not imported from: 'base'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'ncdf4' 'rgeos'
  All declared Imports should be used.
Conditional.MonteCarlo.ExpressCertificate.Classic: no visible global
  function definition for 'rnorm.halton'
Conditional.MonteCarlo.ExpressCertificate.Classic: no visible global
  function definition for 'rnorm.sobol'
EasyExpressCertificate: no visible global function definition for
  'CashOrNothingOption'
EasyExpressCertificate: no visible global function definition for
  'GBSOption'
ExpressCertificate: no visible global function definition for
  'GBSOption'
FFieldPtRepDemo: no visible global function definition for 'ggplot'
FFieldPtRepDemo: no visible global function definition for 'aes'
FFieldPtRepDemo: no visible binding for global variable 'mpg'
FFieldPtRepDemo: no visible global function definition for 'geom_point'
FFieldPtRepDemo: no visible global function definition for 'geom_text'
FFieldPtRepDemo: no visible global function definition for 'ggtitle'
FFieldPtRepDemo: no visible global function definition for
  'geom_segment'
FFieldPtRepDemo: no visible global function definition for
  'grid.arrange'
Namespace in Imports field not imported from: 'MASS'
  All declared Imports should be used.
garchFit: no visible binding for global variable 'dem2gbp'
fitted,fGARCH : .local: no visible binding for global variable 'fit'
dmymvnorm: no visible global function definition for 'dmvnorm'
dmymvt: no visible global function definition for 'dmvt'
gof.test : ecdf: no visible global function definition for 'mecdf'
gof.test: no visible global function definition for 'jacobian'
gradCdfT: no visible global function definition for 'pmvt'
influFun: no visible global function definition for 'jacobian'
plackettFormula: no visible global function definition for 'pmvt'
pmymvnorm: no visible global function definition for 'GenzBretz'
pmymvnorm: no visible global function definition for 'TVPACK'
pmymvnorm : <anonymous>: no visible global function definition for
  'pmvnorm'
pmymvt: no visible global function definition for 'GenzBretz'
pmymvt: no visible global function definition for 'TVPACK'
pmymvt : <anonymous>: no visible global function definition for 'pmvt'
rmymvnorm: no visible global function definition for 'rmvnorm'
rmymvt: no visible global function definition for 'rmvt'
createSQLite: no visible global function definition for 'dbDriver'
createSQLite: no visible global function definition for 'dbConnect'
createSQLite: no visible global function definition for
  'dbUnloadDriver'
createSQLite: no visible global function definition for 'dbGetQuery'
initializeSQLite: no visible global function definition for 'dbDriver'
initializeSQLite: no visible global function definition for 'dbConnect'
dbDelete,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
dbDisconnect,filehashSQLite: no visible global function definition for
  'dbUnloadDriver'
dbFetch,filehashSQLite-character: no visible global function definition
  for 'dbGetQuery'
dbInsert,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
dbList,filehashSQLite: no visible global function definition for
  'dbGetQuery'
dbMultiFetch,filehashSQLite-character: no visible global function
  definition for 'dbGetQuery'
Error in re-building vignettes:
  ...
Loading required package: RSQLite
Error: processing vignette 'Best_Prectices.Rmd' failed with diagnostics:
unused arguments (self_contained, lib_dir, output_dir)
Execution halted
FinTS.stats: no visible global function definition for 'skewness'
FinTS.stats: no visible global function definition for 'kurtosis'
Unitroot: no visible global function definition for 'adfTest'
Unitroot: no visible global function definition for 'unitrootTest'
plotArmaTrueacf: no visible global function definition for 'polynomial'
summary.fHTEST: no visible global function definition for 'padf'
fem.estep: no visible global function definition for 'ginv'
fem.loglik: no visible global function definition for 'ginv'
fstep.GramSc: no visible global function definition for 'ginv'
fstep.fisher: no visible global function definition for 'ginv'
fstep.qiao: no visible global function definition for 'ginv'
fstep.sparse: no visible global function definition for 'ginv'
fstep.sparse: no visible global function definition for 'enet'
fstep.sparse: no visible global function definition for 'predict.enet'
FitARMA: no visible global function definition for 'PacfDL'
FitARMA: no visible global function definition for 'GetARMeanMLE'
FitARMA: no visible global function definition for
  'BackcastResidualsAR'
FitARMA: no visible global function definition for 'LjungBoxTest'
GetFitARMA: no visible global function definition for 'LoglikelihoodAR'
GetFitARMA: no visible global function definition for 'ChampernowneD'
GetFitARMA : EntropyARMA: no visible global function definition for
  'PacfToAR'
GetFitARMA : EntropyARMA: no visible global function definition for
  'PacfDL'
GetFitARMA : EntropyARMA: no visible global function definition for
  'FastLoglikelihoodAR'
GetFitARMA: no visible global function definition for 'PacfToAR'
InformationMatrixARMA: no visible global function definition for
  'InvertibleQ'
TacvfARMA: no visible global function definition for 'InvertibleQ'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/FIT.Rcheck/00install.out' for details.
saveMarkerModels: no visible global function definition for
  'registerDoMC'
saveMarkerModels: no visible global function definition for '%dopar%'
saveMarkerModels: no visible global function definition for 'foreach'
start.plot: no visible global function definition for 'emf'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/flan.Rcheck/00install.out' for details.
getDifferentCluster: no visible global function definition for
  'solve_LSAP'
plot,FLXboot-missing : .local: no visible global function definition
  for 'rmvnorm'
plot,flexmix-missing : .local: no visible binding for global variable
  'cluster'
Namespace in Imports field not imported from: 'rgdal'
  All declared Imports should be used.
flip.adjust : <anonymous>: no visible global function definition for
  'adjusted'
mf.flux: no visible global function definition for 'runsd'
fmt.default: no visible global function definition for 'loessFit'
fmt.default: no visible global function definition for
  'trigammaInverse'
analyse.list: no visible binding for '<<-' assignment to 'files'
analyse.list: no visible binding for global variable 'files'
analyse.list: no visible binding for '<<-' assignment to 'foodweb'
analyse.list: no visible binding for '<<-' assignment to 'name'
analyse.list: no visible binding for global variable 'foodweb'
analyse.list: no visible binding for global variable 'name'
analyse.list: no visible binding for global variable 'indices'
analyse.seq: no visible binding for global variable 'indices'
analyse.single: no visible binding for global variable 'foodweb'
analyse.single: no visible binding for '<<-' assignment to 'foodweb'
analyse.single: no visible binding for '<<-' assignment to 'name'
analyse.single: no visible binding for global variable 'name'
analyse.single: no visible binding for global variable 'indices'
analyse.single: no visible binding for global variable 'levels.l'
analyse.single: no visible binding for global variable 'S'
analyse.single: no visible binding for global variable 'omn.l'
calculate.metrics: no visible binding for '<<-' assignment to 'S'
calculate.metrics: no visible binding for global variable 'S'
calculate.metrics: no visible binding for '<<-' assignment to 'indices'
calculate.metrics: no visible binding for global variable 'indices'
plotweb: no visible binding for global variable 'foodweb'
plotweb: no visible binding for global variable 'S'
INFCvpe: no visible binding for global variable 'INFCstats'
INFCvpe: no visible binding for global variable 'INFCdomain'
fwdglm: warning in glm.fit(x = x[bsb, ], y = y[bsb], w = weights[bsb],
  offset = obsb, family = family, control = glm.control(epsilon =
  epsilon, maxit = maxit)): partial argument match of 'w' to 'weights'
lmsglm : subset.median: warning in glm.fit(x[bsb, ], ybsb, family =
  family, w = weights[bsb], offset = obsb, control =
  glm.control(epsilon = epsilon, maxit = maxit)): partial argument
  match of 'w' to 'weights'
lmsglm: warning in glm.fit(x[bsb, ], y[bsb], family = family, w =
  weights[bsb], offset = obsb, control = glm.control(epsilon = epsilon,
  maxit = maxit)): partial argument match of 'w' to 'weights'
WaveVarFD: no visible global function definition for 'modwt'
do.fd.estimate: no visible global function definition for
  'performParallel'
fd.Genton: no visible global function definition for 'qn'
fd.estimate.matrix: no visible global function definition for
  'performParallel'
fractal.random: no visible global function definition for 'flog.debug'
fractal.random: no visible global function definition for 'xts'
fractal.uniform: no visible global function definition for 'flog.debug'
fractal.uniform: no visible global function definition for 'xts'
getPortfolioPrices: no visible binding for global variable
  'holidayNYSE'
getPortfolioPrices: no visible binding for global variable
  'sampleInitiators'
getPortfolioPrices: no visible global function definition for
  'anylength'
getPortfolioPrices: no visible binding for global variable
  'sampleGenerators'
getPortfolioPrices: no visible global function definition for 'index<-'
getPortfolioPrices: no visible global function definition for
  'anynames<-'
getTradingDates: no visible binding for global variable 'holidayNYSE'
getTradingDates: no visible global function definition for
  'timeSequence'
getTradingDates: no visible global function definition for 'isBizday'
getTradingDates: no visible global function definition for 'anylength'
next.seeds: no visible global function definition for 'flog.debug'
ou.process: no visible global function definition for 'xts'
plotReturns: no visible global function definition for 'Delt'
expandSlash : <anonymous>: no visible global function definition for
  'makeInteraction'
predict.FRBmultireg: no visible global function definition for
  'predict.mlm'
frcc: no visible global function definition for 'cor.shrink'
frcc: no visible global function definition for 'p.asym'
generate_multivariate_normal_sample: no visible global function
  definition for 'mvrnorm'
plot_units: no visible global function definition for 'textxy'
plot_variables: no visible global function definition for 'textxy'
chgbasismat: no visible global function definition for 'splineDesign'
coef.freekt: no visible global function definition for 'splineDesign'
fitted.freekt: no visible global function definition for 'splineDesign'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/FREGAT.Rcheck/00install.out' for details.
Bell : nways: no visible global function definition for 'setparts'
Bell: no visible global function definition for 'restrictedparts'
CalIncLapInt: no visible global function definition for 'is.whole'
CalIncLapInt: no visible global function definition for 'mpfr'
CalIncLapInt: no visible global function definition for 'chooseMpfr'
lrtest.frontier: no visible binding for global variable
  'lrtest.default'
Namespaces in Imports field not imported from:
  'R.utils' 'grDevices' 'graphics' 'matrixStats' 'stats'
  All declared Imports should be used.
.alignment: warning in lm(Y ~ X, dat = fr): partial argument match of
  'dat' to 'data'
.alignment: warning in lm(as.formula(form), dat = fr): partial argument
  match of 'dat' to 'data'
display.tests: no visible binding for global variable 'parameter.list'
display.tests: no visible binding for global variable 'sigs'
display.tests: no visible binding for global variable 'clust.mat'
display.tests : <anonymous>: no visible binding for global variable
  'clust.mat'
display.tests : <anonymous>: no visible binding for global variable
  'parameter.list'
run.analysis: no visible binding for global variable 'centers'
run.cluster.matrix: no visible binding for global variable 'amps'
run.cluster.matrix: no visible binding for global variable
  'clust.constant'
run.cluster.matrix: no visible binding for global variable 'spect.base'
run.lrg.peaks: no visible binding for global variable 'spect.base'
fugeR.sfRun: no visible global function definition for 'sfInit'
fugeR.sfRun: no visible global function definition for 'sfLibrary'
fugeR.sfRun: no visible global function definition for 'sfExport'
fugeR.sfRun: no visible global function definition for 'sfLapply'
fugeR.sfRun: no visible global function definition for 'sfStop'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'FunCluster/R/FunCluster.R':
  .First.lib calls:
    cat(paste("\nThis is FunCluster package version ", f.version,     " maintained by Corneliu Henegar.\n\n", "FunCluster(wd='', org='HS', go.direct=FALSE, clusterm='cc', compare='common.correl.genes',\n",     "\tcorr.met='greedy', corr.th=0.85, two.lists=TRUE, restrict=FALSE, alpha=0.05,\n",     "\tlocation=FALSE, details=FALSE)\n\n", sep = ""))

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

MiseEnFormeKegg: warning in gl(1, NbKmap, label = LL): partial argument
  match of 'label' to 'labels'
MiseEnFormeKeggSC: warning in gl(1, NbKmap, label = LL): partial
  argument match of 'label' to 'labels'
prop.alt: warning in matrix(seq(from = adjustment.args$edf.lower, by =
  stepsize, len = adjustment.args$num.steps), nr =
  adjustment.args$num.steps, nc = 1): partial argument match of 'nr' to
  'nrow'
prop.alt: warning in matrix(seq(from = adjustment.args$edf.lower, by =
  stepsize, len = adjustment.args$num.steps), nr =
  adjustment.args$num.steps, nc = 1): partial argument match of 'nc' to
  'ncol'
dualpathFusedX.mod: no visible global function definition for
  'graph.adjacency'
dualpathFusedX.mod: no visible global function definition for
  'clusters'
dualpathFusedX.mod: no visible global function definition for 'ginv'
dualpathFusedX.mod: no visible global function definition for
  'subcomponent'
dualpathFusedX.mod: no visible global function definition for 'rBind'
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable 'nn'
plotMF: no visible global function definition for 'interpSpline'
fxreturns: no visible binding for global variable 'FXRatesCHF'
gbreakpoints: no visible global function definition for '%dopar%'
gbreakpoints: no visible global function definition for 'foreach'
DBNScoreStep1: no visible global function definition for 'rlm'
DBNScoreStep2: no visible global function definition for 'rlm'
GAMBoost: no visible global function definition for 'Matrix'
cv.GAMBoost: no visible global function definition for 'mclapply'
estimPVal: no visible global function definition for 'mclapply'
nlgamlss: no visible global function definition for 'NO'
nlgamlss: no visible global function definition for 'as.gamlss.family'
gen.likelihood: no visible global function definition for 'startsWith'
getPEF: no visible global function definition for 'startsWith'
Running examples in 'gamlss-Ex.R' failed
The error most likely occurred in:

> ### Name: gen.likelihood
> ### Title: A function to generate the likelihood function from a GAMLSS
> ###   object
> ### Aliases: gen.likelihood
> ### Keywords: regression
> 
> ### ** Examples
> 
> data(aids)
> m1 <- gamlss(y~x+qrt, data=aids, family=NBI)
GAMLSS-RS iteration 1: Global Deviance = 492.7119 
GAMLSS-RS iteration 2: Global Deviance = 492.6375 
GAMLSS-RS iteration 3: Global Deviance = 492.6373 
> logL<-gen.likelihood(m1)
Error in gen.likelihood(m1) : could not find function "startsWith"
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/gamsel.Rcheck/00install.out' for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    data    3.7Mb
    doc     2.9Mb
    tests   2.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    1.0Mb
    libs   2.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      3.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.7Mb
gboot: no visible global function definition for 'boot'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/gbs2ploidy.Rcheck/00install.out' for details.
IsValidGDELT: no visible global function definition for 'md5sum'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.2Mb
Running examples in 'gemtc-Ex.R' failed
The error most likely occurred in:

> ### Name: mtc.hy.prior
> ### Title: Set priors for the heterogeneity parameter
> ### Aliases: mtc.hy.prior mtc.hy.empirical.lor
> 
> ### ** Examples
> 
> # NOTE: the mtc.run commands below are for illustrative purposes, such a small
> # number of iterations should obviously not be used in practice.
> 
> # set a uniform prior standard deviation
> model1 <- mtc.model(smoking, hy.prior=mtc.hy.prior("std.dev", "dunif", 0, 2))
> result <- mtc.run(model1, n.adapt=10, n.iter=10)
Error: .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
arrange_probabel_phe: no visible global function definition for
  'databel'
as.genotype.snp.data: no visible global function definition for
  'genotype'
check.marker.internal: no visible global function definition for
  'qvalue'
extract.annotation.impute: no visible global function definition for
  'extract_text_file_columns'
extract.annotation.mach: no visible global function definition for
  'extract_text_file_columns'
impute2databel: no visible global function definition for
  'get_temporary_file_name'
impute2databel: no visible global function definition for
  'text2databel'
impute2databel: no visible global function definition for
  'get_dimnames'
impute2databel: no visible global function definition for 'apply2dfo'
impute2databel: no visible global function definition for 'databel'
impute2databel: no visible global function definition for
  'set_dimnames<-'
impute2databel: no visible global function definition for 'disconnect'
impute2mach: no visible global function definition for 'get_dimnames'
impute2mach: no visible global function definition for 'disconnect'
mach2databel: no visible global function definition for
  'get_temporary_file_name'
mach2databel: no visible global function definition for 'text2databel'
mach2databel: no visible global function definition for 'get_dimnames'
minimac2databel: no visible global function definition for
  'get_temporary_file_name'
minimac2databel: no visible global function definition for
  'text2databel'
minimac2databel: no visible global function definition for
  'get_dimnames'
polygenic: no visible global function definition for 'ginv'
polygenic_hglm: no visible global function definition for 'hglm'
polygenic_hglm: no visible global function definition for 'ginv'
scan.haplo: no visible global function definition for
  'haplo.score.slide'
scan.haplo.2D: no visible global function definition for
  'haplo.score.slide'
scan.haplo.2D: no visible global function definition for
  'score.sim.control'
header.info: no visible global function definition for 'mmap'
header.info: no visible global function definition for 'char'
header.info: no visible global function definition for 'is.mmap'
header.info: no visible global function definition for 'munmap'
read.bin: no visible global function definition for 'mmap'
read.bin: no visible global function definition for 'char'
read.bin: no visible global function definition for 'is.mmap'
read.bin: no visible global function definition for 'munmap'
read.bin: no visible global function definition for 'uint8'
GeneFeST: no visible global function definition for 'as.mcmc'
NCPUS: no visible global function definition for 'detectCores'
NCPUS: no visible global function definition for 'makeCluster'
importance: no visible global function definition for 'clusterExport'
importance: no visible global function definition for 'clusterEvalQ'
importance: no visible global function definition for 'parApply'
importance: no visible global function definition for 'stopCluster'
parallelFindBest: no visible global function definition for 'parApply'
parallelSignatureFinder: no visible global function definition for
  'parApply'
puttingAllTogether: no visible global function definition for
  'makeCluster'
puttingAllTogether: no visible global function definition for
  'stopCluster'
seedsFinder: no visible global function definition for 'clusterExport'
seedsFinder: no visible global function definition for 'clusterEvalQ'
seedsFinder: no visible global function definition for 'parApply'
seedsFinder: no visible global function definition for 'stopCluster'
signatureFinder: no visible global function definition for
  'clusterExport'
signatureFinder: no visible global function definition for
  'clusterEvalQ'
signatureFinder: no visible global function definition for
  'stopCluster'
testGE: no visible global function definition for 'clusterExport'
testGE: no visible global function definition for 'parApply'
testGE: no visible global function definition for 'stopCluster'
groupGenotype: no visible global function definition for 'mapLevels<-'
groupGenotype: no visible global function definition for 'as.levelsMap'
bandwidthselect: no visible global function definition for 'dpik'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.0Mb
Package suggested but not available for checking: 'sf'
Namespace in Imports field not imported from: 'agricolae'
  All declared Imports should be used.
gTree: no visible global function definition for 'ctree'
gTree: no visible global function definition for 'ctree_control'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/gets.Rcheck/00install.out' for details.
gexmap : gexgraph: warning in axis(side = 2, at = min:max, tick = TRUE,
  lab = c(rep(min:max, 1)), cex.axis = 1): partial argument match of
  'lab' to 'labels'
gexmap : gexgraph: warning in axis(side = 1, at = seq(1, (may + 1), by
  = 5), tick = TRUE, lab = c(seq(0, may, by = 5)), cex.axis = 1):
  partial argument match of 'lab' to 'labels'
Namespace in Imports field not imported from: 'plotly'
  All declared Imports should be used.
macros/aesthetics.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'aesthetics.Rd'
Namespaces in Imports field not imported from:
  'dplyr' 'ggmap' 'gridExtra' 'scales' 'tnet'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/ggdmc.Rcheck/00install.out' for details.
Running examples in 'ggforce-Ex.R' failed
The error most likely occurred in:

> ### Name: facet_zoom
> ### Title: Facet data for zoom with context
> ### Aliases: facet_zoom
> 
> ### ** Examples
> 
> # Zoom in on the versicolor species on the x-axis
> ggplot(iris, aes(Petal.Length, Petal.Width, colour = Species)) +
+     geom_point() +
+     facet_zoom(x = Species == "versicolor")
Error in grid.Call.graphics(L_setviewport, vp, TRUE) : 
  INTEGER() can only be applied to a 'integer', not a 'NULL'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 336-339 (Visual_Guide.Rmd) 
Error: processing vignette 'Visual_Guide.Rmd' failed with diagnostics:
INTEGER() can only be applied to a 'integer', not a 'NULL'
Execution halted
Namespaces in Imports field not imported from:
  'gridExtra' 'lazyeval' 'readr'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'XML' 'mapproj' 'moonBook'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'NHANES' 'gridExtra'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'reshape2'
  All declared Imports should be used.
prepare_Rd: geom_bar.Rd:94: unknown macro '\aesthetics'
prepare_Rd: geom_bin2d.Rd:76: unknown macro '\aesthetics'
prepare_Rd: geom_boxplot.Rd:110: unknown macro '\aesthetics'
prepare_Rd: geom_contour.Rd:78: unknown macro '\aesthetics'
prepare_Rd: geom_count.Rd:66: unknown macro '\aesthetics'
prepare_Rd: geom_density.Rd:89: unknown macro '\aesthetics'
prepare_Rd: geom_density_2d.Rd:82: unknown macro '\aesthetics'
prepare_Rd: geom_dotplot.Rd:110: unknown macro '\aesthetics'
prepare_Rd: geom_errorbarh.Rd:59: unknown macro '\aesthetics'
prepare_Rd: geom_hex.Rd:74: unknown macro '\aesthetics'
prepare_Rd: geom_jitter.Rd:80: unknown macro '\aesthetics'
prepare_Rd: geom_linerange.Rd:80: unknown macro '\aesthetics'
prepare_Rd: geom_map.Rd:60: unknown macro '\aesthetics'
prepare_Rd: geom_path.Rd:89: unknown macro '\aesthetics'
prepare_Rd: geom_point.Rd:90: unknown macro '\aesthetics'
prepare_Rd: geom_polygon.Rd:62: unknown macro '\aesthetics'
prepare_Rd: geom_qq.Rd:68: unknown macro '\aesthetics'
prepare_Rd: geom_quantile.Rd:82: unknown macro '\aesthetics'
prepare_Rd: geom_ribbon.Rd:74: unknown macro '\aesthetics'
prepare_Rd: geom_rug.Rd:70: unknown macro '\aesthetics'
prepare_Rd: geom_segment.Rd:89: unknown macro '\aesthetics'
prepare_Rd: geom_smooth.Rd:107: unknown macro '\aesthetics'
prepare_Rd: geom_spoke.Rd:61: unknown macro '\aesthetics'
prepare_Rd: geom_text.Rd:91: unknown macro '\aesthetics'
prepare_Rd: geom_tile.Rd:82: unknown macro '\aesthetics'
prepare_Rd: geom_violin.Rd:89: unknown macro '\aesthetics'
prepare_Rd: stat_function.Rd:68: unknown macro '\aesthetics'
prepare_Rd: stat_summary.Rd:78: unknown macro '\aesthetics'
prepare_Rd: stat_unique.Rd:58: unknown macro '\aesthetics'
macros/aesthetics.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'aesthetics.Rd'
Namespace in Imports field not imported from: 'randomForest'
  All declared Imports should be used.
ggroc: no visible global function definition for 'ggplot'
ggroc: no visible global function definition for 'aes'
ggroc: no visible global function definition for 'geom_point'
ggroc: no visible global function definition for 'geom_line'
ggroc: no visible global function definition for 'theme'
ggroc: no visible global function definition for 'element_text'
ggroc: no visible global function definition for 'labs'
ggroc: no visible global function definition for 'ggsave'
Namespace in Imports field not imported from: 'lazyeval'
  All declared Imports should be used.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'gibbs.met/R/firstlib.R':
  .First.lib calls:
    cat("Naive Gibbs Sampling with Metropolis steps(gibbs.met) loaded\n",     "COPYRIGHT 2008 (c) Longhai Li (http://math.usask.ca/~longhai)\n",     "Type ?begin.gibbs.met for help to this package\n", sep = "")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
panel.pyramid: no visible global function definition for
  'trellis.par.get'
panel.pyramid: no visible global function definition for
  'current.panel.limits'
panel.pyramid: no visible global function definition for 'panel.abline'
panel.pyramid: no visible global function definition for 'panel.rect'
pyramid2.formula: no visible global function definition for
  'lattice.getOption'
pyramid2.formula: no visible global function definition for
  'is.shingle'
pyramid2.formula: no visible global function definition for
  'as.factorOrShingle'
useOuterStrips2 : new.strip: no visible global function definition for
  'strip.default'
useOuterStrips2 : new.strip.left: no visible global function definition
  for 'strip.default'
glm.fit2: no visible binding for global variable 'n'
el.CSW: no visible global function definition for 'logelr'
el.owen: no visible global function definition for 'logelr'
el.owen: no visible global function definition for 'llogp'
el.owen: no visible global function definition for 'llogpp'
el.owen: no visible global function definition for 'llog'
glmnet.cr: no visible global function definition for 'glmnet'
glmpath.cr: no visible global function definition for 'glmpath'
predict.coxpath: no visible global function definition for 'coxph'
glmulti,character-character-ANY-ANY: no visible global function
  definition for 'regsubsets'
installed size is 45.6Mb
  sub-directories of 1Mb or more:
    libs  44.6Mb
File 'gnmf/libs/i386/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'
File 'gnmf/libs/x64/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
predict.gnm: no visible binding for global variable 'eliminate'
cumres.lvmfit : myres: no visible global function definition for 'vars'
cumres.lvmfit: no visible global function definition for 'iid'
GOGANPA: no visible global function definition for 'GSE.Test.Main'
selectRho: no visible global function definition for
  'scaleFreeFitIndex'
goest,Goestica : .local: no visible global function definition for
  'fastICA'
Namespace in Imports field not imported from: 'googleCloudStorageR'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'R6' 'roxygen2'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'readr'
  All declared Imports should be used.
Resdata : prepdata: no visible global function definition for 'sqldf'
gpca : Build3d: no visible global function definition for
  'scatterplot3d'
gpca: no visible global function definition for 'scatterplot3d'
gpCovGrads: no visible global function definition for 'diag.spam'
gpUpdateAD: no visible global function definition for 'diag.spam'
gpUpdateKernels: no visible global function definition for 'diag.spam'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/gpuR.Rcheck/00install.out' for details.
Errors in running code in vignettes:
when running code in 'GRAN-Overview.Rnw'
  ...
Building 0 packages
starting migrateToFinalRepo 2017-02-11 18:28:19
Built 0 packages

  When sourcing 'GRAN-Overview.R':
Error: dims [product 0] do not match the length of object [1]
No traceback available 
> proc.time()
   user  system elapsed 
   1.13    0.43   22.86
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/graphql.Rcheck/00install.out' for details.
GrassmannOptim : <anonymous>: no visible global function definition for
  'expm'
GrassmannOptim : <anonymous>: no visible global function definition for
  'Matrix'
Namespace in Imports field not imported from: 'rgeos'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'BiasedUrn'
  All declared Imports should be used.
GriegSmith: no visible global function definition for 'is.ppp'
grouped: no visible binding for global variable 'n'
lL.gaussian: no visible binding for global variable 'p'
lL.gaussian: no visible binding for global variable 'X'
lL.gaussian: no visible binding for global variable 'qb'
lL.gaussian: no visible binding for global variable 'qa'
lL.logistic: no visible binding for global variable 'p'
lL.logistic: no visible binding for global variable 'X'
lL.logistic: no visible binding for global variable 'qb'
lL.logistic: no visible binding for global variable 'qa'
lL.t: no visible binding for global variable 'p'
lL.t: no visible binding for global variable 'X'
lL.t: no visible binding for global variable 'qb'
lL.t: no visible binding for global variable 'df.'
lL.t: no visible binding for global variable 'qa'
sc.gaussian: no visible binding for global variable 'p'
sc.gaussian: no visible binding for global variable 'X'
sc.gaussian: no visible binding for global variable 'qb'
sc.gaussian: no visible binding for global variable 'qa'
sc.gaussian: no visible binding for global variable 'qb.'
sc.gaussian: no visible binding for global variable 'qa.'
sc.logistic: no visible binding for global variable 'p'
sc.logistic: no visible binding for global variable 'X'
sc.logistic: no visible binding for global variable 'qb'
sc.logistic: no visible binding for global variable 'qa'
sc.logistic: no visible binding for global variable 'qb.'
sc.logistic: no visible binding for global variable 'qa.'
sc.t: no visible binding for global variable 'p'
sc.t: no visible binding for global variable 'X'
sc.t: no visible binding for global variable 'qb'
sc.t: no visible binding for global variable 'df.'
sc.t: no visible binding for global variable 'qa'
sc.t: no visible binding for global variable 'qb.'
sc.t: no visible binding for global variable 'qa.'
GSA: no visible global function definition for 'impute.knn'
plotgsCP: no visible global function definition for 'opts'
plotgsPower: no visible global function definition for 'opts'
qplotit: no visible global function definition for 'opts'
Namespace in Imports field not imported from: 'rrcov'
  All declared Imports should be used.
gee_wrap: no visible global function definition for 'gee'
geeglm_wrap: no visible global function definition for 'geeglm'
Found the following possibly unsafe calls:
File 'gtools/R/unByteCode.R':
  unlockBinding(name, env = env)
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.2.5/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.2.5/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-32\unhbox\voidb@x \penalty \@M \ {}1.
5/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
Namespace in Imports field not imported from: 'rvest'
  All declared Imports should be used.
normalweight: no visible binding for global variable 'NW_above'
normalweight: no visible binding for global variable 'NW_below'
obese: no visible binding for global variable 'OB_above'
obese: no visible binding for global variable 'OB_below'
overweight: no visible binding for global variable 'OW_above'
overweight: no visible binding for global variable 'OW_below'
gwl.beta: no visible global function definition for 'lars'
gwl.cv.err: no visible global function definition for 'lars'
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
AIC: no visible global function definition for 'hash'
AIC: no visible global function definition for 'values'
AIC: no visible global function definition for 'values<-'
ODS.ror: no visible global function definition for 'hash'
ODS.ror: no visible global function definition for 'values<-'
ODS.ror: no visible global function definition for 'keys'
ODS.ror: no visible global function definition for 'values'
ODS.ror: no visible global function definition for 'read.tree'
ODS.ror: no visible global function definition for 'nodelabels'
cc.sim: no visible global function definition for 'hash'
cc.sim: no visible global function definition for 'values<-'
cc.sim: no visible global function definition for 'values'
collapse: no visible global function definition for 'hash'
collapse: no visible global function definition for 'values<-'
collapse: no visible global function definition for 'keys'
collapse: no visible global function definition for 'values'
deletion: no visible global function definition for 'hash'
deletion: no visible global function definition for 'values<-'
deletion: no visible global function definition for 'keys'
deletion: no visible global function definition for 'values'
grp.list: no visible global function definition for 'hash'
grp.list: no visible global function definition for 'values'
Found the following significant warnings:
  readstat/stata/readstat_dta_read.c:181:25: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:366:21: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:584:21: warning: too many arguments for format [-Wformat-extra-args]
  readstat/stata/readstat_dta_read.c:831:21: warning: too many arguments for format [-Wformat-extra-args]
See 'd:/Rcompile/CRANpkg/local/3.2/haven.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'hms'
  All declared Imports should be used.
Package required and available but unsuitable version: 'methods'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
print.tsum: warning in print.default(x$resid, digits = digits, na = "",
  print.gap = 2): partial argument match of 'na' to 'na.print'
print.tsum: warning in symnum(correl, abbr.col = NULL): partial
  argument match of 'abbr.col' to 'abbr.colnames'
tlm: no visible binding for global variable 'response'
tlm: no visible binding for global variable 'dofse'
tscore: no visible binding for global variable 'response'
Btilde: no visible global function definition for 'bs'
hgam: no visible global function definition for 'LinReg'
hgam.fit: no visible global function definition for 'LinReg'
hgam.fit: no visible global function definition for 'grplasso'
hgam.fit: no visible global function definition for 'grpl.control'
hrisk: no visible binding for global variable 'mclapply'
hrisk : <anonymous>: no visible global function definition for
  'lambdamax'
plot.hrisk: no visible global function definition for 'plot3d'
plot.hrisk: no visible global function definition for 'levelplot'
gcline.fn: no visible global function definition for 'multinom'
Namespace in Imports field not imported from: 'colorspace'
  All declared Imports should be used.
hand1: no visible binding for global variable 'name1'
hotelling.stat: no visible global function definition for 'cov.shrink'
print.summary.hotspots: warning in sort(x$data, dec = TRUE): partial
  argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$positive, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$negative, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   1.1Mb
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.
get.pdf: no visible global function definition for 'dmvnorm'
hsmm.sim: no visible global function definition for 'rmvnorm'
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'phyloseq'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Namespace in Imports field not imported from: 'jsonlite'
  All declared Imports should be used.
humarray version 1.1

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
humarray version 1.1

The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
humarray version 1.1

See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
humarray version 1.1

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
humarray version 1.1

humarray version 1.1

humarray version 1.1
humarray version 1.1

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Error in re-building vignettes:
  ...
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 153-159 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
replacement has 0 rows, data has 4973
Execution halted
Warning in .doLoadActions(where, attach) :
  trying to execute load actions without 'methods' package
See sections 'The INDEX file' and 'Package subdirectories' in the
'Writing R Extensions' manual.
Warning in .doLoadActions(where, attach) :
  trying to execute load actions without 'methods' package
hybridMC: no visible global function definition for 'mcmc'
Running examples in 'HydeNet-Ex.R' failed
The error most likely occurred in:

> ### Name: HydePosterior
> ### Title: Posterior Distributions of a Decision Network
> ### Aliases: HydePosterior
> 
> ### ** Examples
> 
> data(PE, package="HydeNet")
> Net <- HydeNetwork(~ wells + 
+                      pe | wells + 
+                      d.dimer | pregnant*pe + 
+                      angio | pe + 
+                      treat | d.dimer*angio + 
+                      death | pe*treat,
+                      data = PE) 
>   
>                  
> compiledNet <- compileJagsModel(Net, n.chains=5)
Error: .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library("testthat")
  > library("HydeNet")
  Loading required package: nnet
  > 
  > test_check("HydeNet")
  Error: .onLoad failed in loadNamespace() for 'rjags', details:
    call: fun(libname, pkgname)
    error: The environment variable JAGS_HOME is set to
  c:/Program Files/JAGS/JAGS-4.0.0
  but no JAGS installation can be found there
  testthat results ================================================================
  OK: 3 SKIPPED: 0 FAILED: 0
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: nnet
Quitting from lines 314-325 (DecisionNetworks.Rmd) 
Error: processing vignette 'DecisionNetworks.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
hydromod: no visible global function definition for 'ggof'
plot_out: no visible global function definition for 'zoo'
plot_out: no visible global function definition for 'ggof'
plot_params.default: no visible global function definition for
  'vioplot'
plot_params.default: no visible global function definition for
  'hydropairs'
hyperbCvMTestPValue: no visible binding for global variable
  'hyperbWSqTable'
momIntegrated : ddist: no visible global function definition for 'dvg'
requiprobable: no visible global function definition for 'extract'
requiprobable : make.tree: no visible global function definition for
  'extract'
fitter.gen.rParam.uniform: no visible global function definition for
  '%do%'
fitter.gen.rParam.uniform: no visible global function definition for
  'foreach'
hzar.chain.doSeq: no visible global function definition for 'mcmc'
hzar.chain.doSeq: no visible global function definition for 'thin'
hzar.dataGroup.null: no visible global function definition for 'mcmc'
hzar.doChain.multi: no visible global function definition for '%dopar%'
hzar.doChain.multi: no visible global function definition for 'foreach'
hzar.doChain.multi: no visible global function definition for '%do%'
hzar.doFit: no visible global function definition for 'MCMCmetrop1R'
hzar.doFit.multi: no visible global function definition for '%dopar%'
hzar.doFit.multi: no visible global function definition for 'foreach'
hzar.doFit.multi: no visible global function definition for '%do%'
hzar.eval.clineLL: no visible global function definition for '%dopar%'
hzar.eval.clineLL: no visible global function definition for 'foreach'
hzar.eval.clineLL: no visible global function definition for '%do%'
hzar.fit2DataGroup: no visible global function definition for 'mcmc'
hzar.mcmc.bindLL: no visible global function definition for 'mcmc'
hzar.mcmc.bindLL: no visible global function definition for 'as.mcmc'
hzar.mcmc.bindLL: no visible global function definition for 'thin'
hzar.profile.dataGroup: no visible global function definition for
  'equal.count'
hzar.profile.dataGroup: no visible global function definition for
  'foreach'
hzar.profile.dataGroup: no visible global function definition for
  '%dopar%'
hzar.profile.dataGroup: no visible global function definition for
  '%do%'
optimizeTrace: no visible global function definition for 'as.mcmc'
Namespaces in Imports field not imported from:
  'Rcpp' 'ggplot2' 'pander'
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   1.9Mb
TrainIBHM: no visible global function definition for 'enableJIT'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for lhs since lhs is already defined in the 'lazyeval' namespace
  Warning: failed to assign NativeSymbolInfo for rhs since rhs is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/ibmdbR.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.1Mb
    libs   1.2Mb
NB: this package is only installed for sub-architecture 'x64'
str_match_all: possible error in regexec(pattern, x, perl = perl,
  useBytes = useBytes): unused argument (perl = perl)
str_pair_match : <anonymous>: possible error in regexec(pattern =
  pattern, text = x, perl = perl, useBytes = useBytes): unused argument
  (perl = perl)
Running the tests in 'tests/test-current-no-comorbid.R' failed.
Last 13 lines of output:
  unused argument (perl = perl)
  1: expect_identical(chapter_to_desc_range.icd10("jack (A10-A20)"), list(Jack = c(start = "A10", 
         end = "A20"))) at testthat/test-current-util.R:135
  2: identical(object, expected)
  3: chapter_to_desc_range.icd10("jack (A10-A20)")
  4: .chapter_to_desc_range(x, re_major = re_icd10_major_bare)
  5: str_match_all(x, re_code_range)
  6: regmatches(x, regexec(pattern, x, perl = perl, useBytes = useBytes))
  7: regexec(pattern, x, perl = perl, useBytes = useBytes)
  
  DONE ===========================================================================
  Error: Test failures
  Execution halted
plot.ICEepmap: no visible global function definition for 'contourplot'
plotHeatmap: no visible global function definition for 'bluered'
plotHeatmap : my.panel.levelplot: no visible global function definition
  for 'panel.levelplot'
plotHeatmap : my.panel.levelplot: no visible global function definition
  for 'panel.abline'
plotHeatmap : my.panel.levelplot.2: no visible global function
  definition for 'panel.levelplot'
plotHeatmap : my.panel.levelplot.2: no visible global function
  definition for 'panel.abline'
plotHeatmap: no visible global function definition for 'levelplot'
tune.iCluster2: no visible binding for global variable 'glp'
tune.iCluster2: no visible global function definition for 'mclapply'
agent_returnGridResolution: no visible global function definition for
  'xmlAttrs'
agent_returnIVoxels: no visible global function definition for
  'xmlAttrs'
agent_returnJVoxels: no visible global function definition for
  'xmlAttrs'
agent_returnKVoxels: no visible global function definition for
  'xmlAttrs'
agent_returnSimIteration: no visible global function definition for
  'xmlAttrs'
agent_returnSimTime: no visible global function definition for
  'xmlAttrs'
agent_returnSpeciesResultData: no visible global function definition
  for 'xmlSize'
agent_returnSpeciesResultData: no visible global function definition
  for 'xmlAttrs'
env_returnConcentrationAndRateChange: no visible global function
  definition for 'xmlSize'
env_returnConcentrationAndRateChange: no visible global function
  definition for 'xmlName'
env_returnConcentrationAndRateChange: no visible global function
  definition for 'xmlAttrs'
env_returnGlobalProductionRates: no visible global function definition
  for 'xmlSize'
env_returnGlobalProductionRates: no visible global function definition
  for 'xmlAttrs'
env_returnSimIteration: no visible global function definition for
  'xmlAttrs'
env_returnSimTime: no visible global function definition for 'xmlAttrs'
env_returnSoluteGridIVoxels: no visible global function definition for
  'xmlAttrs'
env_returnSoluteGridJVoxels: no visible global function definition for
  'xmlAttrs'
env_returnSoluteGridKVoxels: no visible global function definition for
  'xmlAttrs'
env_returnSoluteGridRes: no visible global function definition for
  'xmlAttrs'
env_returnSpecifiedSoluteData: no visible global function definition
  for 'xmlSize'
env_soluteProductionRateOverTime: no visible global function definition
  for 'xmlValue'
readSimResultFile: no visible global function definition for
  'xmlTreeParse'
readSimResultFile: no visible global function definition for 'xmlRoot'
simpsonIndex: no visible global function definition for 'diversity'
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs  12.8Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       3.4Mb
    include   2.6Mb
    libs      6.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.7Mb
select.lines: warning in symbols(long[segment[1:2]], lat[segment[1:2]],
  cir = c(1, 0.1), add = TRUE, col = 8): partial argument match of
  'cir' to 'circles'
IMIS: no visible global function definition for 'sample.prior'
IMIS: no visible global function definition for 'prior'
IMIS: no visible global function definition for 'likelihood'
IMIS : posterior: no visible global function definition for 'prior'
IMIS : posterior: no visible global function definition for
  'likelihood'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/ImportExport.Rcheck/00install.out' for details.
FctReducedNodevalues: no visible global function definition for
  'cfunction'
TotalVar: no visible global function definition for 'lp'
Namespace in Imports field not imported from: 'DBI'
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  'count_compare'
heal_data: no visible global function definition for 'optimum_k'
heal_data: no visible global function definition for 'optimum_w'
heal_data: no visible global function definition for 'pred_for_w'
initialize,Image : .local: no visible global function definition for
  'readJPEG'
initialize,Image : .local: no visible global function definition for
  'readPNG'
initialize,Image : .local: no visible global function definition for
  'read.bmp'
initialize,OrthIm : .local: no visible binding for global variable
  'obj'
dependogram: no visible global function definition for 'makeCluster'
dependogram: no visible global function definition for
  'clusterSetupSPRNG'
dependogram: no visible global function definition for 'clusterCall'
dependogram: no visible global function definition for 'stopCluster'
infer,coxph : .local: no visible global function definition for
  'sandwich'
infer,glm : .local: no visible global function definition for
  'sandwich'
infer,lm : .local: no visible global function definition for 'sandwich'
infer,lme : .local: no visible global function definition for
  'fixed.effects'
infer,mer : .local: no visible binding for global variable 'fm1'
est.expDeath : surv_p: no visible global function definition for
  'survfit'
function1: no visible global function definition for 'coxph.detail'
var.expDeath : surv_p: no visible global function definition for
  'survfit'
getFixEF.onePhase: no visible global function definition for
  'fractions'
getFixEF.twoPhase: no visible global function definition for
  'fractions'
getVcCoefMS.onePhase: no visible global function definition for
  'fractions'
getVcCoefMS.onePhase : <anonymous>: no visible global function
  definition for 'fractions'
getVcCoefMS.twoPhase: no visible global function definition for
  'fractions'
getVcCoefMS.twoPhase : <anonymous>: no visible global function
  definition for 'fractions'
projMat: no visible global function definition for 'ginv'
trtProkMat: no visible global function definition for 'ginv'
Package required and available but unsuitable version: 'Rmixmod'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
boot.compute.fj: no visible global function definition for
  'supplementaryCols'
epCA.inference.battery : permute.components.ca: no visible global
  function definition for 'epCA'
epCA.inference.battery: no visible global function definition for
  'epCA'
epGPCA.inference.battery : permute.components.pca: no visible global
  function definition for 'epGPCA'
epGPCA.inference.battery: no visible global function definition for
  'epGPCA'
epMCA.inference.battery : permute.components.mca: no visible global
  function definition for 'epMCA'
epMCA.inference.battery: no visible global function definition for
  'makeNominalData'
epMCA.inference.battery: no visible global function definition for
  'epMCA'
epPCA.inference.battery : permute.components.pca: no visible global
  function definition for 'epPCA'
epPCA.inference.battery: no visible global function definition for
  'epPCA'
inGraphs: no visible global function definition for
  'createColorVectorsByDesign'
inGraphs: no visible global function definition for
  'calculateConstraints'
inGraphs: no visible global function definition for 'prettyPlot'
inGraphs: no visible global function definition for 'prettyBars'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'insideRODE/R/zzz.r':
  .First.lib calls:
    require(nlme)
    require(lattice)
    require(deSolve)
    require(compiler)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.
cgrad: no visible global function definition for 'res'
doshade: no visible global function definition for 'projection'
doshade: no visible global function definition for 'extent'
doshade: no visible global function definition for 'res'
doshade: no visible global function definition for 'raster'
doshade: no visible global function definition for 'extent<-'
Namespace in Imports field not imported from: 'prodlim'
  All declared Imports should be used.
date.time: no visible global function definition for 'chron'
date.time: no visible global function definition for 'years'
date.time: no visible global function definition for 'days'
date.time: no visible global function definition for 'hours'
par_calibration: no visible global function definition for 'date.mdy'
par_calibration: no visible global function definition for 'as.date'
plot_meas_sim: no visible global function definition for 'as.date'
plot_meas_sim: no visible global function definition for 'date.mdy'
shape_calibration: no visible global function definition for 'date.mdy'
shape_calibration: no visible global function definition for 'as.date'
ILik: no visible global function definition for 'maxLik'
ILik: no visible global function definition for 'hessian'
f.grovest3 : f.est: no visible global function definition for 'survfit'
Namespace in Imports field not imported from: 'png'
  All declared Imports should be used.
File 'iotools/libs/i386/iotools.dll':
  Found non-API call to R: 'getConnection'
File 'iotools/libs/x64/iotools.dll':
  Found non-API call to R: 'getConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
summary,ipdlme: warning in pt(abs(stat), df = object@df, lower =
  FALSE): partial argument match of 'lower' to 'lower.tail'
.getListRegObjects: no visible global function definition for 'rmvnorm'
.getListRegObjectsFec: no visible global function definition for
  'rmvnorm'
diagnosticsPmatrix: no visible global function definition for
  'dtruncnorm'
sampleVitalRateObj: no visible global function definition for
  'rdirichlet'
sampleVitalRateObj: no visible global function definition for 'rmvnorm'
simulateCarlina: no visible global function definition for 'rmvnorm'
growth,numeric-numeric-data.frame-growthObjTruncIncr: no visible global
  function definition for 'dtruncnorm'
growthCum,numeric-numeric-data.frame-growthObjTruncIncr: no visible
  global function definition for 'ptruncnorm'
plot.htest: no visible global function definition for
  'normal.and.t.dist'
Namespaces in Imports field not imported from:
  'coda' 'lattice'
  All declared Imports should be used.
convert_edgeList_to_graph: no visible global function definition for
  'ftM2graphNEL'
convert_edgeList_to_graph: no visible global function definition for
  'graph.data.frame'
convert_graph_to_edgeList: no visible global function definition for
  'edgeWeights'
convert_graph_to_edgeList: no visible global function definition for
  'get.edgelist'
convert_graph_to_edgeList: no visible global function definition for
  'E'
summary_graph: no visible global function definition for
  'connectedComp'
summary_graph: no visible global function definition for 'subGraph'
summary_graph: no visible global function definition for 'clusters'
summary_graph: no visible global function definition for 'subgraph'
summary_graph: no visible binding for global variable
  'layout.fruchterman.reingold'
dendrify: no visible binding for global variable 'item'
dendrify: no visible binding for global variable 'node'
dendrify: no visible binding for global variable 'value'
exogenize: no visible binding for global variable 'item'
IS: no visible global function definition for 'mclapply'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/IUPS.Rcheck/00install.out' for details.
clusterVCV: no visible global function definition for 'estfun'
covc: no visible global function definition for 'sandwich'
ftest: no visible global function definition for 'vcovHC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/jagsUI.Rcheck/00install.out' for details.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

make_template: no visible global function definition for 'invalid'
.getJavaGDObject: no visible global function definition for '.jmkref'
JavaGD: no visible global function definition for '.jinit'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/jmotif.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'BayesFactor' 'GGally' 'GPArotation' 'PMCMR' 'afex' 'car' 'lsmeans'
  'lsr' 'multcomp' 'psych' 'vcd' 'vcdExtra'
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import 'lme4::sigma' by 'nlme::sigma' when loading 'joineRML'
See 'd:/Rcompile/CRANpkg/local/3.2/joineRML.Rcheck/00install.out' for details.
JointRegBC.default: no visible global function definition for 'fdHess'
JointRegBC.default: no visible global function definition for 'ginv'
JOP: no visible global function definition for 'dglm'
JOP: no visible global function definition for 'gosolnp'
JOP: no visible global function definition for 'solnp'
Found the following significant warnings:
  Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
See 'd:/Rcompile/CRANpkg/local/3.2/JWileymisc.Rcheck/00install.out' for details.
KappaV: no visible global function definition for 'over'
plot,kaps-missing : .local: no visible global function definition for
  'locfit.censor'
kcirt.fitMSS: no visible global function definition for 'sfInit'
kcirt.fitMSS: no visible global function definition for 'sfExport'
kcirt.fitMSS: no visible global function definition for 'sfIsRunning'
kcirt.fitMSS: no visible global function definition for 'sfStop'
epband.fun: no visible binding for global variable
  'critical.value.nair.90'
epband.fun: no visible binding for global variable
  'critical.value.nair.95'
epband.fun: no visible binding for global variable
  'critical.value.nair.99'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.90'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.95'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.99'
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Package in Depends field not imported from: 'cluster'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dataFiller: no visible global function definition for 'daisy'
theme_ms: possible error in theme(axis.text = element_text(size =
  rel(0.8)), axis.ticks = element_line(colour = "black"), legend.key =
  element_rect(colour = "grey80"), panel.background = element_rect(fill
  = "white", colour = NA), panel.border = element_rect(fill = NA,
  colour = "grey50"), panel.grid.major = element_line(colour =
  "grey90", size = 0.2), panel.grid.minor = element_line(colour =
  "grey98", size = 0.5), strip.background = element_rect(fill =
  "grey80", colour = "grey50"), strip.background = element_rect(fill =
  "grey80", : formal argument "strip.background" matched by multiple
  actual arguments
theme_ms: possible error in colour = "grey50")): formal argument
  "strip.background" matched by multiple actual arguments
kobe2sm,data.frame : .local: no visible global function definition for
  'kobe2smFn'
kobe,data.frame-missing : .local : <anonymous>: no visible global
  function definition for 'kobeFn'
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.0Mb
Package in Depends field not imported from: 'Sejong'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'rJava:::.jniInitialized'
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.KoNLPEnv'
Namespaces in Imports field not imported from:
  'dplyr' 'tibble'
  All declared Imports should be used.
plot.krls: no visible global function definition for 'histogram'
readSelexFile: no visible global function definition for 'startsWith'
ROC.offset: no visible global function definition for 'pData'
ROC.offset: no visible global function definition for 'exprs'
ROC.voting: no visible global function definition for 'pData'
ROC.voting: no visible global function definition for 'exprs'
bootstrap.ktsp: no visible global function definition for 'exprs'
bootstrap.ktsp: no visible global function definition for
  'featureNames'
bootstrap.ktsp: no visible global function definition for 'pData'
ktspcalc: no visible global function definition for 'exprs'
ktspcalc: no visible global function definition for 'featureNames'
ktspcalc: no visible global function definition for 'pData'
ktspcalc2: no visible global function definition for 'exprs'
ktspcalc2: no visible global function definition for 'featureNames'
ktspcalc2: no visible global function definition for 'pData'
predict.ktsp: no visible global function definition for 'featureNames'
predict.ktsp: no visible global function definition for 'exprs'
updatePackages: possible error in available.packages(repos = repos):
  unused argument (repos = repos)
Errors in running code in vignettes:
when running code in 'variablekey.Rnw'
  ...
Warning in file(outfile, "w") :
  cannot open file 'plots/t-Roptions.R': No such file or directory

  When tangling 'variablekey.Rnw':
Error: cannot open the connection
Execution halted
cv.l2boost: no visible global function definition for 'detectCores'
impute.cov: no visible global function definition for 'complete'
impute.cov: no visible global function definition for 'mice'
BSL: no visible global function definition for 'read.asciigrid'
PIF: no visible global function definition for 'read.asciigrid'
clouds: no visible global function definition for 'read.asciigrid'
geoshift: no visible global function definition for 'bbox'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/largeList.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/largeVis.Rcheck/00install.out' for details.
birthdeathSim: no visible global function definition for 'sim.bdtree'
birthdeathSim: no visible binding for global variable 'drop.tip'
birthdeathSim : fx: no visible global function definition for
  'branching.times'
getBtimes: no visible global function definition for 'read.tree'
getBtimes: no visible global function definition for 'is.ultrametric'
getBtimes: no visible global function definition for 'branching.times'
getBtimes.batch : btfx: no visible global function definition for
  'branching.times'
getBtimes.batch: no visible global function definition for 'read.tree'
getBtimes.batch: no visible binding for global variable
  'branching.times'
mccrTest: no visible global function definition for 'sim.bdtree'
mccrTest: no visible global function definition for 'drop.tip'
mccrTest: no visible global function definition for 'read.tree'
mccrTest: no visible binding for global variable 'gammaStat'
plotNodeNumbers.phylo: no visible global function definition for
  'plot.phylo'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    dataset   1.4Mb
    include   4.3Mb
    libs      2.0Mb
Tkp: no visible global function definition for 'is.spam'
addObservations: no visible global function definition for 'bbox'
addObservations: no visible global function definition for 'as.ppp'
addObservations: no visible global function definition for 'nncross'
addQuantVar: no visible global function definition for 'bbox'
addQuantVar: no visible global function definition for 'as.ppp'
addQuantVar: no visible global function definition for 'nncross'
areaRegion: no visible global function definition for 'areapl'
editLattice: no visible global function definition for 'card'
formLattice: no visible global function definition for 'dnearneigh'
makeTmatrix: no visible global function definition for 'as.spam.listw'
makeTmatrix: no visible global function definition for 'nb2listw'
makeTmatrix: no visible global function definition for 'diag.spam'
makeTmatrix: no visible global function definition for 'nb2mat'
nodeFilling: no visible global function definition for 'inout'
nodeFilling: no visible global function definition for 'as.points'
plot.formLatticeOutput: no visible global function definition for
  'card'
predict.NparRegOut: no visible global function definition for 'bbox'
predict.NparRegOut: no visible global function definition for 'as.ppp'
predict.NparRegOut: no visible global function definition for 'nncross'
removeHole: no visible global function definition for 'inout'
lbfit.par : loglogistic.fit.optim : loglik.lb.loglogis: no visible
  global function definition for 'pllogis'
optim.const.ordi: no visible binding for global variable 'k'
LD.Measures: no visible global function definition for 'mclapply'
Fisher1sided: warning in round(dp, d = 9): partial argument match of
  'd' to 'digits'
HWE2sided.table: warning in round(xtable, d = 4): partial argument
  match of 'd' to 'digits'
LD2sided.pvals: warning in round(dp, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.pvals: warning in round(LR, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.pvals: warning in round(rr, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.pvals: warning in round(dprime, d = 9): partial argument match
  of 'd' to 'digits'
LD2sided.pvals: warning in round(delta2, d = 9): partial argument match
  of 'd' to 'digits'
LD2sided.pvals: warning in round(yuleQ, d = 9): partial argument match
  of 'd' to 'digits'
LD2sided.tables: warning in round(dp, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.tables: warning in round(LR, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.tables: warning in round(rr, d = 9): partial argument match of
  'd' to 'digits'
LD2sided.tables: warning in round(dprime, d = 9): partial argument
  match of 'd' to 'digits'
LD2sided.tables: warning in round(delta2, d = 9): partial argument
  match of 'd' to 'digits'
LD2sided.tables: warning in round(yuleQ, d = 9): partial argument match
  of 'd' to 'digits'
LD2sided.tables: warning in round(xtable, d = 3): partial argument
  match of 'd' to 'digits'
LD2sided.tables: warning in round(ztable, d = 3): partial argument
  match of 'd' to 'digits'
BEAPFrOG: no visible global function definition for 'jags.model'
BEAPFrOG: no visible global function definition for 'coda.samples'
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.
File 'LeLogicielR/R/zzz.R':
  .onLoad calls:
    packageStartupMessage(utils::packageDescription("LeLogicielR",     lib.loc = libname), appendLF = TRUE)

See section 'Good practice' in '?.onAttach'.
gap.default: no visible global function definition for 'makeCluster'
gap.default: no visible global function definition for 'clusterEvalQ'
gap.default: no visible global function definition for 'clusterApply'
gap.default: no visible global function definition for 'clusterCall'
gap.default: no visible global function definition for 'stopCluster'
lga.default: no visible global function definition for 'makeCluster'
lga.default: no visible global function definition for 'clusterEvalQ'
lga.default: no visible global function definition for 'clusterApplyLB'
lga.default: no visible global function definition for 'stopCluster'
rlga.default: no visible global function definition for 'makeCluster'
rlga.default: no visible global function definition for 'clusterEvalQ'
rlga.default: no visible global function definition for
  'clusterApplyLB'
rlga.default: no visible global function definition for 'stopCluster'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.3Mb
estimate_LC_pdf_state: no visible global function definition for
  'huge.select'
estimate_LC_pdf_state: no visible global function definition for 'huge'
search_knn: no visible global function definition for 'ann'
LICurvature.default: no visible global function definition for 'ginv'
Namespaces in Imports field not imported from:
  'Rcpp' 'rgeos'
  All declared Imports should be used.
Running examples in 'lidR-Ex.R' failed
The error most likely occurred in:

> ### Name: lastrees
> ### Title: Individual tree segmentation
> ### Aliases: lastrees
> 
> ### ** Examples
> 
> LASfile <- system.file("extdata", "Tree.laz", package="lidR")
> las = readLAS(LASfile, XYZonly = TRUE, filter = "-drop_z_below 0")
> 
> # compute a canopy image
> chm = grid_canopy(las, res = 0.5, subcircle = 0.1, na.fill = "knnidw", k = 4)
[using inverse distance weighting]
> chm = as.raster(chm)
> 
> # smoothing post-process (e.g. 2x mean)
> kernel = matrix(1,3,3)
> chm = raster::focal(chm, w = kernel, fun = mean)
> chm = raster::focal(chm, w = kernel, fun = mean)
> raster::plot(chm, col = height.colors(50)) # check the image
> 
> # segmentation (default parameters but th = 4 + extra output)
> extra = lastrees(las, "dalponte2016", chm, th = 4, extra = TRUE)
Error in as.vector(data) : 
  no method for coercing this S4 class to a vector
Calls: lastrees -> dalponte2012 -> matrix -> as.vector
Execution halted
.N: no visible global function definition for 'mpfr'
LIHNPSD_prepare_data: no visible global function definition for
  'skewness'
LIHNPSD_prepare_data: no visible global function definition for
  'kurtosis'
LIHNPSD_standardfit_test: no visible global function definition for
  'skewness'
LIHNPSD_standardfit_test: no visible global function definition for
  'kurtosis'
LihnBetaPoly: no visible global function definition for 'Const'
LihnBetaPoly: no visible global function definition for 'getPrec'
LihnTildeFunction: no visible global function definition for 'Const'
LihnTildeFunction: no visible global function definition for 'getPrec'
prepare.LIHNPSD : D: no visible global function definition for 'mpfr'
prepare.LIHNPSD: no visible global function definition for 'Const'
psdunittest.LIHNPSD: no visible global function definition for
  'sintegral'
rawcdf.LIHNPSD : cdf: no visible global function definition for 'erf'
rawcdf.LIHNPSD : cdf: no visible global function definition for
  'T.Owen'
rawsn.LIHNPSD: no visible global function definition for 'erf'
standardfit.LIHNPSD: no visible global function definition for
  'skewness'
standardfit.LIHNPSD: no visible global function definition for
  'kurtosis'
standardfit.LIHNPSD: no visible global function definition for 'optimx'
Package required but not available: 'sf'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
solveLP: no visible global function definition for 'lp'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/lira.Rcheck/00install.out' for details.
ave.sorted: warning in matrix(y[lens == i], nr = i): partial argument
  match of 'nr' to 'nrow'
ave.sorted: warning in matrix(weights[lens == i], nr = i): partial
  argument match of 'nr' to 'nrow'
liso.adaptive: warning in multistep(coefc = rep(0, (nrow(x) - 1) *
  ncol(x)), x = x, intercept = sum(weights * y)/sum(weights), residual
  = y - sum(weights * y)/sum(weights), sorter = getSort(x)): partial
  argument match of 'coefc' to 'coefchain'
liso.backfit: warning in multistep(coefc = rep(0, (nrow(x) - 1) *
  ncol(x)), x = x, intercept = sum(weights * y)/sum(weights), residual
  = y - sum(weights * y)/sum(weights), sorter = getSort(x)): partial
  argument match of 'coefc' to 'coefchain'
liso.maxlamb: no visible global function definition for 'pava'
pavareg: no visible global function definition for 'pava'
pavaregorig: no visible global function definition for 'pava'
lle_sound: no visible binding for global variable 'lle_wave'
plot_lle: no visible global function definition for 'plot3d'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc        1.8Mb
    libs       2.1Mb
    testdata   1.5Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
Namespace in Imports field not imported from: 'boot'
  All declared Imports should be used.
File 'lmmlasso/R/zzz.R':
  .onAttach calls:
    cat("----------------------------------------------------------------------",     "This is a test release of the package 'lmmlasso'. If you have any questions or problems, do not hesitate to contact the author.",     "----------------------------------------------------------------------",     sep = "\n")

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

LambdaInv: no visible global function definition for 'quad.tform'
MLloglik: no visible global function definition for 'quad.form'
MLpdSym: no visible global function definition for 'triang'
MLpdSym: no visible global function definition for 'vecli'
MLpdSymLambda: no visible global function definition for 'quad.tform'
MLsigmaZPsiZt: no visible global function definition for 'quad.tform'
ObjFunction : tResLRes: no visible global function definition for
  'quad.form'
covStartingValues : optimize3: no visible global function definition
  for 'quad.form.inv'
lmmlasso.default: no visible global function definition for 'optL1'
lmmlasso.default: no visible global function definition for 'optL2'
lmmlasso.default: no visible global function definition for 'vecli'
lmmlasso.default: no visible global function definition for 'triang'
lfbas: no visible global function definition for 'basis'
EMmixlcd: no visible global function definition for 'hc'
EMmixlcd: no visible global function definition for 'hclass'
interactive2D: no visible global function definition for 'tktoplevel'
interactive2D: no visible global function definition for 'tclVar'
interactive2D : plotdens: no visible global function definition for
  'tclvalue'
interactive2D: no visible global function definition for 'tkrplot'
interactive2D : densplot: no visible global function definition for
  'tkrreplot'
interactive2D: no visible global function definition for 'tkscale'
interactive2D: no visible global function definition for 'tklabel'
interactive2D: no visible global function definition for 'tkpack'
plot.LogConcDEAD: no visible global function definition for 'open3d'
plot.LogConcDEAD: no visible global function definition for 'par3d'
plot.LogConcDEAD: no visible global function definition for 'surface3d'
plot.LogConcDEAD: no visible global function definition for
  'decorate3d'
plot.LogConcDEAD: no visible global function definition for
  'rgl.surface'
plot.LogConcDEAD: no visible global function definition for 'plot3d'
Namespace in Imports field not imported from: 'distr'
  All declared Imports should be used.
Package in Depends field not imported from: 'logcondens'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
LCLRCImode: no visible global function definition for 'preProcess'
Local_LL.mode: no visible global function definition for 'Local_LL'
MLE.mode: no visible global function definition for 'LocalNormalize'
MLE.mode: no visible global function definition for 'Local_LL'
MLE.mode: no visible global function definition for 'LocalF'
activeSetLogCon: no visible global function definition for 'preProcess'
activeSetLogCon: no visible global function definition for
  'LocalNormalize'
activeSetLogCon: no visible global function definition for 'LocalMLE'
activeSetLogCon: no visible global function definition for
  'LocalConvexity'
activeSetLogCon: no visible global function definition for 'LocalF'
activeSetLogCon : phi.f: no visible global function definition for
  'evaluateLogConDens'
activeSetLogCon : fhat.f: no visible global function definition for
  'evaluateLogConDens'
activeSetLogCon : Fhat.f: no visible global function definition for
  'evaluateLogConDens'
activeSetLogCon.mode: no visible global function definition for
  'preProcess'
activeSetLogCon.mode: no visible global function definition for
  'LocalNormalize'
activeSetLogCon.mode: no visible global function definition for
  'LocalF'
activeSetLogCon.mode : phi.f: no visible global function definition for
  'evaluateLogConDens'
activeSetLogCon.mode : fhat.f: no visible global function definition
  for 'evaluateLogConDens'
activeSetLogCon.mode : Fhat.f: no visible global function definition
  for 'evaluateLogConDens'
estimateLRdistn: no visible global function definition for 'preProcess'
intECDFfn : Y: no visible global function definition for 'intECDF'
intFfn: multiple local function definitions for 'H' with different
  formal arguments
logConDens: no visible global function definition for
  'evaluateLogConDens'
x2z: no visible global function definition for 'LocalNormalize'
LOGICOIL: no visible binding for global variable 'pssm'
LOGICOIL: no visible binding for global variable 'LOGICOILfit'
LOGICOIL: no visible binding for global variable 'Model_Parameters'
LogrankA: no visible global function definition for 'is.Surv'
predict.KernS: no visible global function definition for 'chkDots'
mipSolve.Rsymphony: no visible global function definition for
  'Rsymphony_solve_LP'
print.summary.lqa: warning in printCoefmat(coefs, P.value = FALSE,
  has.Pvalue = FALSE): partial argument match of 'P.value' to
  'P.values'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/lqr.Rcheck/00install.out' for details.
example.ls2w: no visible global function definition for 'lda'
Namespace in Imports field not imported from: 'tcltk2'
  All declared Imports should be used.
lsplsCv: no visible global function definition for 'cvsegments'
orthlspls.fit: no visible binding for global variable 'oscorespls.fit'
orthlsplsCv: no visible binding for global variable 'oscorespls.fit'
lss: no visible binding for global variable 'response'
lss.betag: no visible global function definition for 'l1fit'
gauher: no visible binding for global variable 'gh'
vcov.gpcm: no visible global function definition for 'ginv'
vcov.grm: no visible global function definition for 'ginv'
get.Z.HWP: no visible global function definition for 'is.genotype'
get.Z.HWP: no visible global function definition for 'allele.count'
get.lambda: no visible global function definition for 'is.genotype'
get.lambda: no visible global function definition for 'heterozygote'
luca: no visible global function definition for 'is.genotype'
luca: no visible global function definition for 'genotype'
luca: no visible global function definition for 'Surv'
luca: no visible global function definition for 'coxph.fit'
luca: no visible global function definition for 'coxph.control'
Error in re-building vignettes:
  ...
Loading required package: lucid
Loading required package: lattice
Loading required package: rjags
Loading required package: coda
Error : .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there

Quitting from lines 269-293 (lucid_printing.Rmd) 
Error: processing vignette 'lucid_printing.Rmd' failed with diagnostics:
could not find function "jags.model"
Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  6: request_fetch.write_memory(req$output, req$url, handle)
  7: curl::curl_fetch_memory(url, handle = handle)
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 5
  1. Error: Retrieve A Notice (@tests.R#4) 
  2. Error: Print Notice Summary (@tests.R#9) 
  3. Error: Retrieve Entities (@tests.R#14) 
  4. Error: Retrieve Topics (@tests.R#19) 
  5. Error: Search Works (@tests.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
LVMMCOR.default: no visible global function definition for 'fdHess'
LVMMCOR.default: no visible global function definition for 'ginv'
project.M3.1.to.M3.2: no visible global function definition for
  'coordinates<-'
project.M3.1.to.M3.2: no visible global function definition for
  'proj4string<-'
project.M3.1.to.M3.2: no visible global function definition for 'CRS'
project.M3.1.to.M3.2: no visible global function definition for
  'spTransform'
project.M3.1.to.M3.2: no visible global function definition for
  'coordinates'
Namespaces in Imports field not imported from:
  'Rcpp' 'cmprsk' 'colorspace' 'etm' 'fracdiff' 'gtable' 'munsell'
  'numDeriv' 'plyr' 'quadprog' 'scales' 'timeDate' 'tseries' 'zoo'
  All declared Imports should be used.
installed size is 41.0Mb
  sub-directories of 1Mb or more:
    doc    6.9Mb
    libs  34.0Mb
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
MalletLDA: no visible global function definition for '.jnew'
mallet.doc.topics: no visible global function definition for
  '.jevalArray'
mallet.import: no visible global function definition for 'J'
mallet.import: no visible global function definition for '.jnew'
mallet.import: no visible global function definition for '.jcast'
mallet.subset.topic.words: no visible global function definition for
  '.jevalArray'
mallet.topic.words: no visible global function definition for
  '.jevalArray'
mallet.word.freqs: no visible global function definition for
  '.jevalArray'
ageprofile: no visible global function definition for 'predict.gam'
ageprofile: no visible global function definition for 'summary.gam'
ageprofile: no visible global function definition for 'anova.gam'
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/3.2/maps/libs/i386/maps.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.2/maps/libs/x64/maps.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Package which this enhances but not available for checking: 'gpclib'
aa.account: no visible binding for global variable 'last'
cashflow.portfolio.bond: no visible global function definition for
  'sort.data.frame'
connectTheDots: no visible global function definition for
  'sort.data.frame'
connectTheDots: no visible global function definition for 'last'
connectTheDots: no visible global function definition for 'first'
current.market: no visible global function definition for 'last'
findMaxMat: no visible global function definition for 'lambert_W0'
market.rate: no visible global function definition for 'last'
plot.history.market: no visible global function definition for
  'sort.data.frame'
print.account: no visible binding for global variable 'last'
build.eqn.tex: no visible global function definition for 'str_detect'
build.eqn.tex: no visible global function definition for 'str_trim'
get.mat.tex : tmp.fun: no visible global function definition for
  'latexTranslate'
get.mat.tex : tmp.fun.2: no visible global function definition for
  'str_replace_all'
get.mat.tex: no visible global function definition for 'latexTabular'
get.mat.tex: no visible global function definition for
  'str_replace_all'
parameters.time.varying: no visible global function definition for
  'str_detect'
parameters.time.varying: no visible global function definition for
  'str_trim'
toLatex.marssMODEL: no visible global function definition for
  'str_detect'
toLatex.marssMODEL: no visible global function definition for
  'str_trim'
toLatex.marssMODEL: no visible global function definition for 'str_sub'
toLatex.marssMODEL: no visible global function definition for 'sys'
toLatex.marssMODEL: no visible global function definition for
  'str_replace'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   1.8Mb
discard: no visible global function definition for 'whatif'
distance2GAMcauchit: no visible global function definition for 'gam'
distance2GAMcloglog: no visible global function definition for 'gam'
distance2GAMlog: no visible global function definition for 'gam'
distance2GAMlogit: no visible global function definition for 'gam'
distance2GAMprobit: no visible global function definition for 'gam'
distance2nnet: no visible global function definition for 'nnet'
distance2rpart: no visible global function definition for 'rpart'
matchit2cem: no visible global function definition for 'cem'
matchit2full: no visible global function definition for 'fullmatch'
matchit2genetic: no visible global function definition for 'GenMatch'
matchit2optimal: no visible global function definition for 'fullmatch'
Found the following possibly unsafe calls:
File 'matlab/R/zzz.R':
  unlockBinding("savedTime", .MatlabNamespaceEnv)
fnorm2: no visible global function definition for 'sadmvn'
fnorm3: no visible global function definition for 'sadmvn'
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.
mbmdr : Regresion: no visible global function definition for 'logistf'
laugreen: no visible global function definition for 'lp'
relabel : min.perm.labels: no visible global function definition for
  'lp.transport'
mcgibbsit: no visible global function definition for 'is.mcmc.list'
mcgibbsit: no visible global function definition for 'thin'
mcgibbsit: no visible global function definition for 'nvar'
mcgibbsit: no visible global function definition for 'mcmc'
mcgibbsit: no visible global function definition for 'mcmc.list'
mcgibbsit: no visible global function definition for 'varnames'
mcgibbsit: no visible global function definition for 'niter'
read.mcmc: no visible global function definition for 'mcmc.list'
read.mcmc: no visible global function definition for 'mcmc'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/mcPAFit.Rcheck/00install.out' for details.
I2.MCPerm: no visible global function definition for 'rma'
I2.MCPerm: no visible global function definition for 'rma.mh'
I2.MCPerm: no visible global function definition for 'rma.peto'
I2.TradPerm: no visible global function definition for 'rma'
I2.TradPerm: no visible global function definition for 'rma.mh'
I2.TradPerm: no visible global function definition for 'rma.peto'
Q.MCPerm: no visible global function definition for 'rma'
Q.MCPerm: no visible global function definition for 'rma.mh'
Q.MCPerm: no visible global function definition for 'rma.peto'
Q.TradPerm: no visible global function definition for 'rma'
Q.TradPerm: no visible global function definition for 'rma.mh'
Q.TradPerm: no visible global function definition for 'rma.peto'
meta: no visible global function definition for 'rma'
meta: no visible global function definition for 'rma.mh'
meta: no visible global function definition for 'rma.peto'
meta.MCPerm: no visible global function definition for 'rma'
meta.MCPerm: no visible global function definition for 'rma.mh'
meta.MCPerm: no visible global function definition for 'rma.peto'
meta.TradPerm: no visible global function definition for 'rma'
meta.TradPerm: no visible global function definition for 'rma.mh'
meta.TradPerm: no visible global function definition for 'rma.peto'
geoshape: no visible global function definition for 'coordinates'
geoshape: no visible global function definition for 'ppp'
geoshape: no visible global function definition for 'nncross'
gmmlogit: no visible global function definition for 'poly2nb'
gmmlogit: no visible global function definition for 'nb2mat'
gmmprobit: no visible global function definition for 'poly2nb'
gmmprobit: no visible global function definition for 'nb2mat'
makew: no visible global function definition for 'coordinates'
makew: no visible global function definition for 'poly2nb'
makew: no visible global function definition for 'nb2mat'
makew: no visible global function definition for 'knearneigh'
makew: no visible global function definition for 'knn2nb'
qregsim1: no visible global function definition for 'brewer.pal'
qregspiv: no visible global function definition for 'poly2nb'
qregspiv: no visible global function definition for 'nb2mat'
sarml: no visible global function definition for 'poly2nb'
sarml: no visible global function definition for 'nb2mat'
sarml: no visible global function definition for 'nb2listw'
sarml: no visible global function definition for 'eigenw'
smooth12: no visible global function definition for 'nn2'
splogit: no visible global function definition for 'poly2nb'
splogit: no visible global function definition for 'nb2mat'
splogit: no visible global function definition for 'hccm'
spprobit: no visible global function definition for 'poly2nb'
spprobit: no visible global function definition for 'nb2mat'
spprobit: no visible global function definition for 'hccm'
spprobitml : makevar: no visible global function definition for
  'poly2nb'
spprobitml : makevar: no visible global function definition for
  'nb2mat'
File 'medSTC/libs/i386/medSTC.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'medstc/medstc.o', 'medstc/corpus.o',
      'svmlight/svm_common.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'medstc/corpus.o'
File 'medSTC/libs/x64/medSTC.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'medstc/medstc.o', 'medstc/corpus.o',
      'svmlight/svm_common.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'medstc/corpus.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.
Namespaces in Imports field not imported from:
  'RColorBrewer' 'RGtk2' 'RNifti' 'cairoDevice' 'gtools' 'jsonlite'
  All declared Imports should be used.
codomToPropShared: no visible global function definition for
  'df2genind'
codomToPropShared: no visible global function definition for
  'propShared'
mgLandscape: no visible global function definition for 'SpatialPoints'
mgQuick: no visible global function definition for 'distm'
mgQuick: no visible binding for global variable 'distMeeus'
metacor.DSL: no visible global function definition for 'metaplot'
metacor.OP: no visible global function definition for 'hyperg_2F1'
metacor.OP: no visible global function definition for 'metaplot'
CDF.rop : <anonymous> : <anonymous>: no visible global function
  definition for 'dmnom'
MetaDE.impute: no visible global function definition for 'impute.knn'
cal.logrank : get.stat: no visible global function definition for
  'coxph'
cal.p.logrank : get.p: no visible global function definition for
  'coxph'
get.RP: no visible binding for global variable 'na.rm'
get.RP: no visible global function definition for 'NaReplace2'
Error in re-building vignettes:
  ...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
unused arguments (self_contained, lib_dir, output_dir)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/metamisc.Rcheck/00install.out' for details.
.MetaSparsePCA: no visible global function definition for '%do%'
.MetaSparsePCA: no visible global function definition for 'foreach'
.MetaSparsePCA: no visible global function definition for 'iter'
DropDupGenes: no visible global function definition for 'registerDoMC'
DropDupGenes: no visible global function definition for 'startWorkers'
DropDupGenes: no visible global function definition for 'registerDoSMP'
DropDupGenes: no visible global function definition for '%dopar%'
DropDupGenes: no visible global function definition for 'foreach'
DropDupGenes: no visible global function definition for 'iter'
DropDupGenes: no visible global function definition for 'stopWorkers'
MetaPCA: no visible global function definition for 'PCAgrid'
PlotPC2D: no visible global function definition for 'cov.mve'
PlotPC2D: no visible global function definition for 'ellipse'
PreprocessMetaAnalysis: no visible global function definition for
  '%do%'
PreprocessMetaAnalysis: no visible global function definition for
  'foreach'
PreprocessMetaAnalysis: no visible global function definition for
  'iter'
PreprocessMetaAnalysis: no visible binding for global variable 'dat'
PreprocessMetaAnalysis: no visible global function definition for
  'impute.knn'
requireAll: no visible global function definition for 'biocLite'
downloadAEMETcurrentday: no visible global function definition for
  'startsWith'
downloadAEMETcurrentday: no visible global function definition for
  'endsWith'
QCRep: warning in axis(1, at = 0:axislen, lab = 0:axislen, cex.axis =
  0.7, tcl = -0.2): partial argument match of 'lab' to 'labels'
QCplot: warning in axis(1, at = 1:lenRow, lab = 1:lenRow, cex.axis =
  0.7): partial argument match of 'lab' to 'labels'
AltReg: no visible global function definition for 'lme'
BA.est: no visible global function definition for 'lmeControl'
MCmcmc: no visible global function definition for 'jags.model'
MCmcmc: no visible global function definition for 'bugs'
MCmcmc: no visible global function definition for 'read.bugs'
VC.est: no visible global function definition for 'lmeControl'
VC.est.fixed: no visible global function definition for 'lmeControl'
VC.est.fixed: no visible global function definition for 'lme'
VC.est.fixed: no visible global function definition for 'pdIdent'
VC.est.fixed: no visible global function definition for 'varIdent'
VC.est.fixed: no visible global function definition for 'pdDiag'
VC.est.fixed: no visible global function definition for 'pdSymm'
VC.est.random: no visible global function definition for 'lmeControl'
VC.est.random: no visible global function definition for 'lme'
VC.est.random: no visible global function definition for 'pdBlocked'
VC.est.random: no visible global function definition for 'pdIdent'
VC.est.random: no visible global function definition for 'varIdent'
VC.est.random: no visible global function definition for 'ranef'
VC.est.random: no visible global function definition for 'pdDiag'
find.mean: no visible global function definition for 'varnames'
find.vars: no visible global function definition for 'varnames'
pairs.MCmcmc: no visible global function definition for 'varnames'
subset.MCmcmc : char.2.num: no visible global function definition for
  'varnames'
eventpois: no visible global function definition for 'dsort'
FoM.FitBinnedSampleRepeatErrors : local.fit.function: no visible global
  function definition for 'rlm'
RevNet.JacobianMethod : RevNet.FirstEstimate: no visible global
  function definition for 'lm.ridge'
dbgpd_bilog: no visible global function definition for 'pbvevd'
dbgpd_negbilog: no visible global function definition for 'pbvevd'
dtgpd_psilog : conv: no visible global function definition for
  'is.positive.definite'
dtgpd_psilog: no visible global function definition for 'image.plot'
dtgpd_psineglog : conv: no visible global function definition for
  'is.positive.definite'
dtgpd_psineglog: no visible global function definition for 'image.plot'
mgpd_init: no visible global function definition for 'fgev'
ml_bilog: no visible global function definition for 'pbvevd'
ml_negbilog: no visible global function definition for 'pbvevd'
pbgpd_bilog: no visible global function definition for 'pbvevd'
pbgpd_ct: no visible global function definition for 'pbvevd'
pbgpd_negbilog: no visible global function definition for 'pbvevd'
ptgpd_psilog : conv: no visible global function definition for
  'is.positive.definite'
ptgpd_psilog: no visible global function definition for 'image.plot'
ptgpd_psineglog : conv: no visible global function definition for
  'is.positive.definite'
ptgpd_psineglog: no visible global function definition for 'image.plot'
inbar: no visible global function definition for 'spplot'
inbox: no visible global function definition for 'spplot'
indot: no visible global function definition for
  'SpatialPointsDataFrame'
indot: no visible global function definition for 'coordinates'
indot: no visible global function definition for 'CRS'
indot: no visible global function definition for 'bubble'
inhist: no visible global function definition for 'spplot'
inline: no visible global function definition for 'spplot'
inmap: no visible global function definition for
  'SpatialPointsDataFrame'
inmap: no visible global function definition for 'coordinates'
inmap: no visible global function definition for 'CRS'
inmap: no visible global function definition for 'bubble'
inmap: no visible global function definition for 'spplot'
inpie: no visible global function definition for 'spplot'
inscatter: no visible global function definition for 'spplot'
.onAttach: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible binding for global variable '.MGRAST'
build.MGRAST: no visible global function definition for 'fromJSON'
call.MGRAST: no visible binding for global variable '.MGRAST'
call.MGRAST: no visible global function definition for 'isValidJSON'
call.MGRAST: no visible global function definition for 'fromJSON'
doc.MGRAST: no visible binding for global variable '.MGRAST'
load.MGRAST: no visible binding for global variable '.MGRAST'
parse.MGRAST: no visible binding for global variable '.MGRAST'
this.package: no visible binding for global variable '.MGRAST'
lrtest.aidsEst: no visible binding for global variable 'lrtest.default'
quadFuncEst: no visible global function definition for 'plm'
quadFuncEst: no visible global function definition for 'fixef'
Running examples in 'micropan-Ex.R' failed
The error most likely occurred in:

> ### Name: entrezDownload
> ### Title: Downloading genome data
> ### Aliases: entrezDownload
> 
> ### ** Examples
> 
> # Accession numbers for the chromosome and plasmid of Buchnera aphidicola, strain APS
> entrezDownload( accession="BA000003.2,AP001071.1", out.file="Buchnera_aphidicola_APS.fsa" )
Downloading genome...Warning in url(adr, open = "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in url(adr, open = "rt") : cannot open the connection
Calls: entrezDownload -> url
Execution halted
MigClim.genClust: no visible global function definition for 'raster'
MigClim.migrate: no visible global function definition for 'raster'
MigClim.migrate: no visible global function definition for
  'dataframe2asc'
MigClim.migrate: no visible global function definition for
  'writeRaster'
MigClim.migrate: no visible global function definition for 'cellStats'
MigClim.plot: no visible global function definition for 'raster'
MigClim.plot: no visible global function definition for 'ymax'
MigClim.plot: no visible global function definition for 'ymin'
MigClim.plot: no visible global function definition for 'xmax'
MigClim.plot: no visible global function definition for 'xmin'
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.
summary.MImixresult: warning in qt(alpha/2, object$df, lower = FALSE):
  partial argument match of 'lower' to 'lower.tail'
Namespaces in Imports field not imported from:
  'DiceDesign' 'MaxPro' 'doSNOW'
  All declared Imports should be used.
minPtest: no visible global function definition for 'sfIsRunning'
minPtest: no visible global function definition for 'sfInit'
minPtest: no visible global function definition for 'sfLibrary'
minPtest: no visible global function definition for 'sfExport'
minPtest: no visible global function definition for 'sfClusterApplyLB'
minPtest: no visible global function definition for 'mclapply'
minPtest: no visible global function definition for 'sfStop'
Namespaces in Imports field not imported from:
  'MASS' 'cluster' 'dendextend' 'npmv' 'utils'
  All declared Imports should be used.
change_family,missing-proportion-family : .local: no visible binding
  for global variable '.identity_transformation'
fit_model,missing-multilevel_missing_data.frame : .local: no visible
  binding for global variable 'X'
image,mi : .local: no visible global function definition for 'Matrix'
image,missing_data.frame : .local: no visible global function
  definition for 'Matrix'
mi,grouped-binary-clogit : .local: no visible global function
  definition for 'untangle.specials'
drawScene.rgl: no visible global function definition for 'rgl.cur'
drawScene.rgl: no visible global function definition for 'open3d'
drawScene.rgl: no visible global function definition for 'clear3d'
drawScene.rgl: no visible global function definition for 'triangles3d'
image3d: no visible global function definition for 'clear3d'
image3d: no visible global function definition for 'sprites3d'
image3d: no visible global function definition for 'points3d'
slices3d : mkimg: no visible global function definition for 'tkrplot'
slices3d : mkscale : f: no visible global function definition for
  'tclvalue'
slices3d : mkscale : f: no visible global function definition for
  'tkrreplot'
slices3d : mkscale : f: no visible global function definition for
  'tkconfigure'
slices3d : mkscale: no visible global function definition for 'tkframe'
slices3d : mkscale: no visible global function definition for 'tkscale'
slices3d : mkscale: no visible global function definition for 'tklabel'
slices3d : mkscale: no visible global function definition for 'tkgrid'
slices3d : move: no visible global function definition for 'tkbind'
slices3d : move : <anonymous>: no visible global function definition
  for 'tkwinfo'
slices3d : move : <anonymous>: no visible global function definition
  for 'tkrreplot'
slices3d : move : <anonymous>: no visible global function definition
  for 'tclvalue<-'
slices3d: no visible global function definition for 'tktoplevel'
slices3d: no visible global function definition for 'tktitle<-'
slices3d: no visible binding for global variable 'tclVar'
slices3d: no visible global function definition for 'tkgrid'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/miscF.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'mvtnorm'
  All declared Imports should be used.
missForest: no visible global function definition for 'idiv'
dmvgt: no visible global function definition for 'dmvt'
rmvgt: no visible global function definition for 'rmvt'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
anova.mix: warning in pchisq(dchisq, ddf, low = FALSE): partial
  argument match of 'low' to 'lower.tail'
Namespace in Imports field not imported from: 'rjags'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  OK: 26 SKIPPED: 0 FAILED: 9
  1. Error: Wolves ex works (@test_ex1_wolves.R#33) 
  2. Error: Geese ex works (@test_ex2_geese.R#27) 
  3. Error: Lake ex works (@test_ex3_lake.R#27) 
  4. Error: Palmyra ex works (@test_ex4_palmyra.R#27) 
  5. Error: Killer whale ex works (@test_ex5_killerwhale.R#28) 
  6. Error: Snail ex works (@test_ex6_snail.R#27) 
  7. Error: Storm-petrel ex works (@test_ex7_stormpetrel.R#27) 
  8. Error: Cladocera ex works (@test_ex8_cladocera.R#31) 
  9. Error: Isopod ex works (@test_ex9_isopod.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
.DNA.connectivitylist : .fun_conn_idx: no visible global function
  definition for 'attach.big.matrix'
.DNA.distance: no visible global function definition for
  'as.big.matrix'
.checkadjmatrix: no visible global function definition for
  'is.big.matrix'
.filterLowCorrelation: no visible global function definition for
  'is.big.matrix'
.network.differences : .fun_distance: no visible global function
  definition for 'attach.big.matrix'
.uniqueTissues: no visible global function definition for 'str_sub'
geneRanker: no visible global function definition for 'RankingTstat'
geneRanker: no visible global function definition for 'RankingFC'
geneRanker: no visible global function definition for 'RankingWilcoxon'
geneRanker: no visible global function definition for
  'RankingBaldiLong'
geneRanker: no visible global function definition for
  'RankingShrinkageT'
geneRanker: no visible global function definition for 'RankingSam'
geneRanker: no visible global function definition for
  'RankingSoftthresholdT'
geneRanker: no visible global function definition for 'RankingLimma'
geneRanker: no visible global function definition for 'toplist'
mlegp: no visible global function definition for 'sfLapply'
mleurDiag: no visible global function definition for 'shapiroTest'
do.estimate.mlogit: no visible global function definition for 'maxLik'
get.mnl.data: no visible global function definition for 'abind'
imageplot.mlogit: no visible global function definition for
  'imageplot.bma'
listGenoToTable: no visible binding for global variable 'dummy'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/mlVAR.Rcheck/00install.out' for details.
Found the following significant warnings:
  mmap.c:223:48: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  mmap.c:226:46: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.2/mmap.Rcheck/00install.out' for details.
mmm: no visible global function definition for 'gee'
.Oarray_to_MB: no visible global function definition for 'is.Oarray'
.gunter: no visible global function definition for 'minmax'
.gunter: no visible global function definition for 'compositions'
MM: no visible global function definition for 'minmax'
MM_allsamesum: no visible global function definition for 'quad.tform'
MM_allsamesum_A: no visible global function definition for 'minmax'
MM_allsamesum_A: no visible global function definition for 'tr'
MM_allsamesum_A: no visible global function definition for 'quad.tform'
MM_differsums: no visible global function definition for 'quad.tform'
MM_single: no visible global function definition for 'quad.form'
NormC: no visible global function definition for 'compositions'
as.array.gunter_MB: no visible global function definition for 'Oarray'
expected_suffstats: no visible global function definition for
  'compositions'
optimizer: no visible global function definition for 'minmax'
optimizer_allsamesum: no visible global function definition for
  'minmax'
suffstats: no visible global function definition for 'minmax'
gunter,data.frame: no visible global function definition for 'minmax'
gunter,data.frame: no visible global function definition for
  'compositions'
gunter,matrix: no visible global function definition for 'minmax'
gunter,matrix: no visible global function definition for 'compositions'
biplot.character: no visible global function definition for 'opts'
biplot.character: no visible global function definition for
  'theme_blank'
distributionplot.factor: no visible global function definition for
  'opts'
distributionplot.factor: no visible global function definition for
  'theme_text'
scatterplot: no visible global function definition for 'opts'
scatterplot: no visible global function definition for 'theme_text'
timeplot: no visible global function definition for 'opts'
clusval: no visible global function definition for 'std.ext'
clusval: no visible global function definition for 'confusion.matrix'
clusval: no visible global function definition for 'similarity.index'
clusval: no visible global function definition for 'clv.Jaccard'
clusval: no visible global function definition for 'clv.Folkes.Mallows'
predict_baseline: no visible global function definition for 'knn1'
predict_cclust: no visible global function definition for 'cclust'
predict_kmeans: no visible global function definition for 'knn1'
predict_single: no visible global function definition for 'agnes'
predict_single: no visible global function definition for 'knn1'
contour.hmac: no visible global function definition for 'kde2d'
modalclust: no visible global function definition for 'mclapply'
phmac: no visible global function definition for 'mclapply'
File 'modeest/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("\nThis is package 'modeest' written by P. PONCET.\nFor a complete list of functions, use 'library(help = \"modeest\")' or 'help.start()'.\n")

See section 'Good practice' in '?.onAttach'.

.mlv.fisk: no visible global function definition for 'pfisk'
.mlv.frechet: no visible global function definition for 'pfrechet'
.mlv.gev: no visible global function definition for 'pgev'
.mlv.gh: no visible global function definition for 'pgh'
.mlv.gompertz: no visible global function definition for 'pgompertz'
.mlv.gpd: no visible global function definition for 'pgpd'
.mlv.gumbel: no visible global function definition for 'pgumbel'
.mlv.hyp: no visible global function definition for 'phyp'
.mlv.koenker: no visible global function definition for 'pkoenker'
.mlv.kumar: no visible global function definition for 'pkumar'
.mlv.laplace: no visible global function definition for 'plaplace'
.mlv.nig: no visible global function definition for 'pnig'
.mlv.paralogistic: no visible global function definition for
  'pparalogistic'
.mlv.pareto: no visible global function definition for 'ppareto'
.mlv.rayleigh: no visible global function definition for 'prayleigh'
.mlv.rweibull: no visible global function definition for 'prweibull'
.mlv.stable: no visible global function definition for 'pstable'
ghMode: no visible global function definition for 'qgh'
ghMode: no visible binding for global variable 'dgh'
nigMode: no visible global function definition for 'qnig'
nigMode: no visible binding for global variable 'dnig'
stableMode: no visible binding for global variable 'dstable'
Namespace in Imports field not imported from: 'broom'
  All declared Imports should be used.
byteint2bit: no visible global function definition for 'digitsBase'
extract_bit: no visible global function definition for 'digitsBase'
get_bitgrid: no visible global function definition for 'raster'
get_bitgrid: no visible global function definition for 'coordinates'
get_bitgrid: no visible global function definition for 'extract'
get_bitgrid_2bits: no visible global function definition for 'raster'
get_bitgrid_2bits: no visible global function definition for
  'coordinates'
get_bitgrid_2bits: no visible global function definition for 'extract'
make_cloudcount_product: no visible global function definition for
  'CRS'
make_cloudcount_product: no visible global function definition for
  'proj4string'
make_cloudcount_product: no visible global function definition for
  'extent'
make_cloudcount_product: no visible global function definition for
  'coordinates<-'
make_cloudcount_product: no visible global function definition for
  'SpatialPixelsDataFrame'
make_cloudcount_product: no visible global function definition for
  'coordinates'
numslist_to_grd: no visible global function definition for 'CRS'
numslist_to_grd: no visible global function definition for
  'proj4string'
numslist_to_grd: no visible global function definition for 'extent'
numslist_to_grd: no visible global function definition for
  'coordinates<-'
numslist_to_grd: no visible global function definition for
  'SpatialPixelsDataFrame'
numslist_to_grd: no visible global function definition for
  'coordinates'
yearday_to_date: no visible global function definition for 'mdy.date'
yearday_to_date: no visible global function definition for 'date.mdy'
yearmonthday_to_julianday: no visible global function definition for
  'mdy.date'
Package required and available but unsuitable version: 'graphics'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/morse.Rcheck/00install.out' for details.
mMap: no visible binding for global variable 'facet'
mScatter: no visible binding for global variable 'facet'
mUniplot: no visible binding for global variable 'facet'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'mpa/R/zzz.R':
  .First.lib calls:
    cat("\n mpa: CoWords Method")
    cat("\n ")
    cat("\n Universidad Nacional de Colombia")
    cat("\n ")
    cat("\n Elaborado por: Daniel Rodriguez <dhrodriguezt@unal.edu.co>")
    cat("\n                Campo Elias Pardo <cepardot@unal.edu.co>")
    cat("\n For help: ?mpa   \n\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
File 'mph/libs/i386/mph.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mph.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mph.o'
File 'mph/libs/x64/mph.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mph.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mph.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.
GetExampleData: no visible binding for global variable 'MPINetData'
Getenvir: no visible binding for global variable 'MPINetData'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/mpMap.Rcheck/00install.out' for details.
CR_calcLD: no visible global function definition for 'lowerTriangle'
fill: no visible global function definition for 'upperTriangle<-'
fill: no visible global function definition for 'lowerTriangle<-'
fill: no visible global function definition for 'lowerTriangle'
fill: no visible global function definition for 'upperTriangle'
findqtl2: no visible global function definition for 'dilation'
fit.mpqtl: no visible global function definition for 'wald.test'
mpIM: no visible global function definition for 'stepAIC'
mpIM: no visible global function definition for 'wald.test'
mpcalcld: no visible global function definition for 'lowerTriangle<-'
mpcalcld: no visible global function definition for 'upperTriangle<-'
mpcalcld: no visible global function definition for 'upperTriangle'
mpestrf: no visible global function definition for 'lowerTriangle<-'
mpestrf: no visible global function definition for 'upperTriangle<-'
mpestrf: no visible global function definition for 'upperTriangle'
mporder : <anonymous>: no visible global function definition for
  'seriate'
mporder: no visible binding for global variable 'get_order'
mpprob: no visible global function definition for 'happy'
mpprob: no visible global function definition for 'hdesign'
plot.mapcomp: no visible global function definition for 'xyplot'
plot.mpcross: no visible global function definition for
  'upperTriangle<-'
plot.mpcross: no visible global function definition for 'upperTriangle'
plot.mpcross: no visible global function definition for
  'lowerTriangle<-'
plot.mpcross: no visible global function definition for 'lowerTriangle'
plot.mpcross: no visible global function definition for 'heatmap_2'
mpmcorrelogram: no visible global function definition for
  'mantel.partial'
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
plot.mpm: warning in symbols(ss[isel, 1], ss[isel, 2], circle =
  sqs[isel], inches = FALSE, lwd = 3, add = TRUE, fg = colors[2]):
  partial argument match of 'circle' to 'circles'
plot.mpm: warning in symbols(ll[ii, 1], ll[ii, 2], square = sqs, inches
  = FALSE, lwd = 3, add = TRUE, fg = colors[2 + iGroup[i]]): partial
  argument match of 'square' to 'squares'
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
MRsurvival: no visible global function definition for 'rmvnorm'
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/msBP.Rcheck/00install.out' for details.
kgml_i: no visible global function definition for 'xmlTreeParse'
kgml_i: no visible global function definition for 'xmlRoot'
kgml_i: no visible global function definition for 'xmlAttrs'
list2xml: no visible global function definition for 'xmlNode'
list2xml: no visible global function definition for 'append.xmlNode'
read_pathway: no visible global function definition for 'xmlTreeParse'
read_pathway: no visible global function definition for 'xmlRoot'
read_pathway: no visible global function definition for 'xmlToList'
read_pathway: no visible global function definition for 'xmlAttrs'
Found the following significant warnings:
  Warning: 'loadRcppModules' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.2/MSeasy.Rcheck/00install.out' for details.
MS.DataCreation: no visible global function definition for 'tclvalue'
MS.DataCreation: no visible global function definition for
  'tkchooseDirectory'
MS.clust: no visible global function definition for 'tk_choose.files'
MS.test.clust: no visible global function definition for
  'tk_choose.files'
MSeasyToARISTO: no visible global function definition for
  'tk_choose.files'
MSeasyToMSP: no visible global function definition for
  'tk_choose.files'
SearchNIST: no visible global function definition for 'tclvalue'
SearchNIST: no visible global function definition for
  'tkchooseDirectory'
SearchNIST: no visible global function definition for 'tk_choose.files'
trans.ASCII: no visible global function definition for 'tclvalue'
trans.ASCII: no visible global function definition for
  'tkchooseDirectory'
Found the following significant warnings:
  Warning: 'loadRcppModules' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.2/MSeasyTkGUI.Rcheck/00install.out' for details.
dialog.MS.clust: no visible binding for global variable
  'Agilent_quantF_MSclust'
dialog.MS.test.clust: no visible binding for global variable
  'Data_testclust'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
[,MSM.fitted-character-missing-missing : .local: warning in switch(EXP
  = i, CondMean = return(x@CondMean), error = return(x@error), Likel =
  return(x@Likel), margLik = return(x@margLik), filtProb =
  return(x@filtProb), smoProb = return(x@smoProb), states =
  return(apply(x@smoProb, 1, which.max)), smoTransMat =
  return(x@smoTransMat), logLikel = return(x@logLikel), stop("Error:",
  i, "is not a MSM.fitted slot")): partial argument match of 'EXP' to
  'EXPR'
[,MSM.glm-character-missing-missing : .local: warning in switch(EXP =
  i, call = return(x@call), model = return(x@model), k = return(x@k),
  switch = return(x@switch), Coef = return(x@Coef), seCoef =
  return(x@seCoef), transMat = return(x@transMat), iniProb =
  return(x@iniProb), Fit = return(x@Fit), states =
  return(x@Fit["states"]), family = return(x@family), stop("Error:", i,
  "is not a MSM slot")): partial argument match of 'EXP' to 'EXPR'
[,MSM.lm-character-missing-missing : .local: warning in switch(EXP = i,
  call = return(x@call), model = return(x@model), k = return(x@k),
  switch = return(x@switch), Coef = return(x@Coef), seCoef =
  return(x@seCoef), std = return(x@std), transMat = return(x@transMat),
  iniProb = return(x@iniProb), Fit = return(x@Fit), states =
  return(x@Fit["states"]), stop("Error:", i, "is not a MSM slot")):
  partial argument match of 'EXP' to 'EXPR'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Error: `mapped_plot` not equal to lazyLoadDBfetch(c(36516L, 321L), datafile, compressed, envhook).
  Component "layers": Component 1: Component 3: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 3: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 7: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 7: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 9: Component 2: Modes of target, current: function, environment
  Component "layers": Component 1: Component 9: Component 2: target, current do not match when deparsed
  Component "layers": Component 1: Component 12: Modes of target, current: function, environment
  Component "layers": Component 1: Component 12: target, current do not match when deparsed
  Component "layers": Component 2: Component 3: Component 2: Modes of target, current: fun
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
plmm.mtk: no visible global function definition for 'stepAIC'
File 'mtsdi/R/zzz.R':
  .onLoad calls:
    packageStartupMessage(paste("This is 'mtsdi' library", ver, sep = " "))

See section 'Good practice' in '?.onAttach'.
getFlights: no visible binding for global variable 'htmlTreeParse'
getFlights: no visible binding for global variable 'xpathSApply'
getFlights: no visible binding for global variable 'xmlAttrs'
getFlights: no visible binding for global variable 'free'
plot.routes : a: no visible global function definition for
  'gcIntermediate'
routes: no visible global function definition for 'distHaversine'
routes: no visible global function definition for 'gcIntermediate'
CrossValidationMuFicokm: no visible global function definition for
  'covMatrix'
CrossValidationMuFicokmAll: no visible global function definition for
  'covMatrix'
MuFicokm: no visible global function definition for 'km'
computeAuxVariables: no visible global function definition for
  'covMatrix'
kmCok: no visible global function definition for 'drop.response'
kmCok: no visible global function definition for 'covStruct.create'
kmCok: no visible global function definition for 'covParametersBounds'
kmCok: no visible binding for global variable 'kmEstimate'
kmCok : cv: no visible global function definition for 'leaveOneOut.km'
predict.kmCok: no visible global function definition for 'covMat1Mat2'
predict.kmCok: no visible global function definition for 'covMatrix'
summary.MuFicokm: no visible global function definition for
  'covparam2vect'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/multinet.Rcheck/00install.out' for details.
genoudRob: no visible global function definition for 'genoud'
showmap: no visible binding for global variable 'landmask'
File 'multxpert/R/zzz.R':
  .onLoad calls:
    cat("multxpert: Implementation of commonly used p-value based and parametric\n",     "multiple testing procedures and parallel gatekeeping procedures.\n",     "For more information visit http://multxpert.com/wiki/MultXpert_package\n",     sep = "")

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

pdunnett: no visible global function definition for 'GenzBretz'
qdunnett: no visible global function definition for 'GenzBretz'
Plot.pca.score: no visible global function definition for 'dataEllipse'
Plot.plsda: no visible global function definition for 'dataEllipse'
explore.data: no visible global function definition for 'T2.test'
oplsda: no visible global function definition for 'dataEllipse'
ostocsy: no visible global function definition for 'colorpanel'
outlier: no visible global function definition for 'pdist'
plsda: no visible global function definition for 'plsr'
stocsy: no visible global function definition for 'colorpanel'
stocsy.1d: no visible global function definition for 'rich.colors'
ystand: no visible global function definition for 'spatial.signs'
ystand: no visible global function definition for 'spatial.rank'
mvtmeta_fe: no visible global function definition for 'combinations'
mvtsplot: no visible global function definition for 'brewer.pal'
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.3Mb
    libs   1.3Mb
quantile,cenmle-lognormal : .local: warning in formatC(100 * q, format
  = "fg", wid = 1): partial argument match of 'wid' to 'width'
summary,ros : .local: no visible global function definition for
  'plot.lm'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/NanoStringNorm.Rcheck/00install.out' for details.
Package required but not available: 'RcppCCTZ'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/NAPPA.Rcheck/00install.out' for details.
bcrm: no visible global function definition for 'startsWith'
getVarComponent.bcrm: no visible global function definition for
  'endsWith'
ncal.formula: no visible global function definition for 'startsWith'
plot.marginals: no visible global function definition for 'startsWith'
read.luminex.xls: no visible global function definition for
  'startsWith'
Running the tests in 'tests/doRUnit.R' failed.
Last 13 lines of output:
  Number of test functions: 3 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  nCal unit testing - 3 test functions, 1 error, 0 failures
  ERROR in test.ncal: Error in getVarComponent.bcrm(fit) : could not find function "endsWith"
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 100-102 (nCal-vignette.Rnw) 
Error: processing vignette 'nCal-vignette.Rnw' failed with diagnostics:
could not find function "endsWith"
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/ndjson.Rcheck/00install.out' for details.
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.
XH: no visible binding for global variable 'exprs'
XIs: no visible binding for global variable 'exprs'
cv.aep: no visible global function definition for 'mclapply'
cv.frsvm: no visible global function definition for 'mclapply'
cv.hubc: no visible global function definition for 'mclapply'
cv.pac: no visible global function definition for 'mclapply'
cv.stsvm: no visible global function definition for 'mclapply'
probeset2pathway: no visible binding for global variable
  'KEGGEXTID2PATHID'
probeset2pathwayTrain: no visible binding for global variable
  'KEGGEXTID2PATHID'
spanbound: no visible global function definition for 'param'
spanbound: no visible global function definition for 'error'
spanbound: no visible global function definition for 'kernelf'
spanbound: no visible global function definition for 'b'
svm.predict: no visible global function definition for 'b'
macros/struct_test.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'struct_test.Rd'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/NetRep.Rcheck/00install.out' for details.
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.
nMreg: warning in pt(tmreg[i], (length(xa) - 1) + (length(xb) - 1) - 4,
  lower = FALSE, log = TRUE): partial argument match of 'lower' to
  'lower.tail'
nMreg: warning in pt(tmreg[i], (length(xa) - 1) + (length(xb) - 1) - 4,
  lower = FALSE, log = TRUE): partial argument match of 'log' to
  'log.p'
bentlerParameters: no visible global function definition for
  'wireframe'
bentlerParameters: no visible global function definition for
  'contourplot'
bentlerParameters: no visible global function definition for
  'levelplot'
corFA: no visible global function definition for 'ginv'
iterativePrincipalAxis: no visible global function definition for
  'ginv'
parallel: no visible global function definition for 'mvrnorm'
parallel: no visible global function definition for 'ginv'
principalAxis: no visible global function definition for 'ginv'
structureSim: no visible global function definition for 'sim.structure'
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    CppCode   1.7Mb
    R         2.4Mb
    include   3.7Mb
    libs      1.3Mb
Error in re-building vignettes:
  ...
Error in deriv.default(firstd, "x") : 
  invalid expression in 'FindSubexprs'
Error : object 'x' not found
Error : object 'x' not found
Loading required package: Ryacas
d:\RCompile\CRANpkg\lib\3.2\Ryacas\yacdir\yacas.exe and/or d:\RCompile\CRANpkg\lib\3.2\Ryacas\yacdir\scripts.dat not found
run yacasInstall() without arguments to installation yacas.

Attaching package: 'Ryacas'

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

    Simplify

Quitting from lines 428-442 (nlsr-derivs.Rmd) 
Error: processing vignette 'nlsr-derivs.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
denoiseperm: no visible global function definition for 'ebayesthresh'
add.test: no visible global function definition for 'ace'
ll.order: no visible global function definition for 'locfit.raw'
ll.order: no visible global function definition for 'dat'
predict.ll.order: no visible global function definition for
  'locfit.raw'
algorithm,NMFStrategyOctave : .local: no visible global function
  definition for 'fstop'
evar,ANY : .local: no visible binding for global variable 'Biobase'
nmf,matrix-numeric-NMFStrategy : .local : run.all: no visible binding
  for global variable 'n'
nmf,matrix-numeric-NMFStrategy : .local : run.all: no visible binding
  for global variable 'RNGobj'
rss,matrix : .local: no visible binding for global variable 'Biobase'
Found the following significant warnings:
  Warning: failed to assign NativeSymbolInfo for env since env is already defined in the 'lazyeval' namespace
See 'd:/Rcompile/CRANpkg/local/3.2/nonparaeff.Rcheck/00install.out' for details.
additive: no visible global function definition for 'lp'
ar.dual.dea: no visible global function definition for 'lp'
cost.dea: no visible global function definition for 'lp'
ddf: no visible global function definition for 'lp'
dea: no visible global function definition for 'lp'
direc.dea: no visible global function definition for 'lp'
dual.dea: no visible global function definition for 'lp'
effdea.b.f: no visible global function definition for 'convhulln'
effdea.b.f: no visible global function definition for 'lp'
faremalm2: no visible binding for global variable 'Lag'
int.dea: no visible global function definition for 'lp'
lp2: no visible global function definition for 'lp'
revenue.dea: no visible global function definition for 'lp'
sbm.tone: no visible global function definition for 'lp'
sbm.vrs: no visible global function definition for 'lp'
dist.plot.bar.plot: no visible global function definition for
  'rainbow_hcl'
dist.plot.hist.plot: no visible global function definition for
  'rainbow_hcl'
plot.stdf: no visible global function definition for 'rainbow_hcl'
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.2.5/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.2.5/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

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

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

Execution halted
normgam.fit: no visible global function definition for 'optimx'
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'mclust' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'npde/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("     Loading library npde, version 2.0, August 2012\n         please direct bugs, questions and feedback to emmanuelle.comets@inserm.fr\n")

See section 'Good practice' in '?.onAttach'.

npde.binning: no visible global function definition for 'Mclust'
NPHMC: no visible global function definition for 'smcure'
NPHMC: no visible global function definition for 'coxph'
allsomv: no visible binding for global variable 'raw_data'
apsomv: no visible binding for global variable 'raw_data'
apsomv: no visible binding for '<<-' assignment to 'NAwarning'
cfuinterpolation: no visible binding for global variable
  'measured_values'
disconestep: no visible binding for global variable 'measured_values'
disconestep: no visible binding for global variable 'psteps'
makepdfoutput: no visible binding for '<<-' assignment to 'textt'
npmpm: no visible binding for '<<-' assignment to 'inputsettings'
npmpm: no visible binding for global variable 'psteps'
npmpm: no visible binding for '<<-' assignment to 'cfu'
npmpm: no visible binding for '<<-' assignment to 'countwarnings'
npmpm: no visible binding for global variable 'cfu'
onestep: no visible binding for global variable 'measured_values'
onestep: no visible binding for global variable 'psteps'
simpleinterpolation: no visible binding for global variable
  'measured_values'
npqcmstest : boot.wild: no visible global function definition for 'rq'
npqcmstest : boot.wild.rademacher: no visible global function
  definition for 'rq'
npqcmstest : boot.iid: no visible global function definition for 'rq'
File 'NPsimex/R/onload.R':
  .onLoad calls:
    packageStartupMessage("NPsimex 0.2-1 loaded")

See section 'Good practice' in '?.onAttach'.
npst: no visible global function definition for 'mclapply'
File 'nws/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Namespace in Imports field not imported from: 'methods'
  All declared Imports should be used.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'obliclus/libs/i386/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'
File 'obliclus/libs/x64/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
obliqueRF.default: no visible global function definition for
  'prediction'
obliqueRF.default: no visible global function definition for
  'performance'
pls_wrapper: no visible global function definition for 'kernelpls.fit'
ridge_slow_wrapper: no visible global function definition for
  'gen.ridge'
ridge_svd_wrapper: no visible global function definition for
  'gen.ridge'
svm_wrapper: no visible global function definition for 'svm'
File 'oblique.tree/libs/i386/oblique.tree.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'
File 'oblique.tree/libs/x64/oblique.tree.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/odbc.Rcheck/00install.out' for details.
isClosed: no visible global function definition for 'dbSendUpdate'
odb.close: no visible global function definition for 'dbSendUpdate'
odb.close: no visible global function definition for 'dbDisconnect'
odb.insert: no visible global function definition for 'dbSendQuery'
odb.insert: no visible global function definition for 'dbColumnInfo'
odb.open: no visible global function definition for 'JDBC'
odb.open: no visible global function definition for 'dbConnect'
odb.read: no visible global function definition for 'dbSendQuery'
odb.read: no visible global function definition for 'fetch'
odb.read: no visible global function definition for 'dbColumnInfo'
odb.tables: no visible global function definition for 'dbListTables'
odb.tables: no visible global function definition for 'dbSendQuery'
odb.tables: no visible global function definition for 'dbColumnInfo'
odb.write: no visible global function definition for 'dbSendUpdate'
Running examples in 'oec-Ex.R' failed
The error most likely occurred in:

> ### Name: treemap
> ### Title: Creates a treemap for a given year
> ### Aliases: treemap
> ### Keywords: functions
> 
> ### ** Examples
> 
> treemap("chl", "chn", "exports", 6, 2014)
[1] "HS92 (6 characters) files already exists. skipping."
[1] "creating treemap..."
[1] "writing html file..."
[1] "opening html files in the browser."

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
Assertion failed!

Program: D:\RCompile\recent\R-32~1.5\bin\x64\Rterm.exe
File: src/win/timer.c, Line 115

Expression: old == NULL
mapvar: no visible binding for global variable 'state.fips'
nearstn: no visible binding for global variable 'okstations'
nearstn: no visible binding for global variable 'Commissioned'
nearstn: no visible binding for global variable 'Decommissioned'
okmts: no visible binding for global variable 'okstations'
okmts: no visible binding for global variable 'TIME'
totalprecip: no visible binding for global variable 'TIME'
Packages suggested but not available for checking: 'RAppArmor' 'feather'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/OpenImageR.Rcheck/00install.out' for details.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs     5.5Mb
    models   4.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   4.8Mb
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
File 'orderbook/R/AllGenerics.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

.animate.plot : new.yscale.components: no visible global function
  definition for 'yscale.components.default'
.animate.plot: no visible global function definition for 'barchart'
.plot.ob : new.yscale.components: no visible global function definition
  for 'yscale.components.default'
.plot.ob: no visible global function definition for 'xyplot'
.plot.ob : <anonymous>: no visible global function definition for
  'panel.xyplot'
.plot.ob : <anonymous>: no visible global function definition for
  'panel.lines'
.plot.orders.ob : new.yscale.components: no visible global function
  definition for 'yscale.components.default'
.plot.orders.ob: no visible global function definition for 'xyplot'
.plot.orders.ob : <anonymous>: no visible global function definition
  for 'panel.xyplot'
.plot.orders.ob : <anonymous>: no visible global function definition
  for 'panel.lines'
.plot.side.ob : new.yscale.components: no visible global function
  definition for 'yscale.components.default'
.plot.side.ob: no visible global function definition for 'barchart'
.plot.side.ob: no visible global function definition for
  'trellis.focus'
.plot.side.ob: no visible global function definition for 'grid.text'
.plot.side.ob: no visible global function definition for
  'trellis.unfocus'
.supply.demand.plot: no visible global function definition for 'xyplot'
.supply.demand.plot : <anonymous>: no visible global function
  definition for 'panel.xyplot'
.supply.demand.plot : <anonymous>: no visible global function
  definition for 'panel.abline'
copy,orderbook : .local: no visible global function definition for
  'hash'
reset,orderbook: no visible global function definition for 'clear'
Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, xtabs

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

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

Welcome to Bioconductor

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

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
boat3d: no visible global function definition for 'rgl.cur'
boat3d: no visible global function definition for 'open3d'
boat3d: no visible global function definition for 'clear3d'
boat3d: no visible global function definition for 'bg3d'
boat3d: no visible global function definition for 'rgl.set'
boat3d: no visible global function definition for 'triangles3d'
boat3d: no visible global function definition for 'quads3d'
boat3d: no visible global function definition for 'decorate3d'
boat3d: no visible global function definition for 'scatterplot3d'
zsuml2minucminf.loca.p: no visible global function definition for
  'ucminf'
zsumlpminucminf.loca.p: no visible global function definition for
  'ucminf'
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for 'lme'
est.lme : <anonymous>: no visible global function definition for
  'VarCorr'
srt : <anonymous>: no visible global function definition for
  'rowttests'
chebyshev.c.polynomials: no visible global function definition for
  'polynomial'
chebyshev.s.polynomials: no visible global function definition for
  'polynomial'
chebyshev.t.polynomials: no visible global function definition for
  'polynomial'
chebyshev.u.polynomials: no visible global function definition for
  'polynomial'
gegenbauer.polynomials: no visible global function definition for
  'polynomial'
ghermite.h.polynomials: no visible global function definition for
  'polynomial'
glaguerre.polynomials: no visible global function definition for
  'polynomial'
hermite.h.polynomials: no visible global function definition for
  'polynomial'
hermite.he.polynomials: no visible global function definition for
  'polynomial'
jacobi.g.polynomials: no visible global function definition for
  'polynomial'
jacobi.p.polynomials: no visible global function definition for
  'polynomial'
legendre.polynomials: no visible global function definition for
  'polynomial'
monic.polynomials: no visible global function definition for
  'polynomial'
orthogonal.polynomials: no visible global function definition for
  'polynomial'
orthonormal.polynomials: no visible global function definition for
  'polynomial'
polynomial.integrals: no visible global function definition for
  'integral'
schebyshev.t.polynomials: no visible global function definition for
  'polynomial'
schebyshev.u.polynomials: no visible global function definition for
  'polynomial'
slegendre.polynomials: no visible global function definition for
  'polynomial'
as_igraph : <anonymous>: no visible global function definition for
  'distHaversine'
as_igraph: no visible global function definition for 'graph.edgelist'
as_igraph: no visible global function definition for 'E'
as_igraph: no visible global function definition for 'E<-'
as_sp_lines: no visible global function definition for 'Lines'
as_sp_points: no visible global function definition for
  'SpatialPointsDataFrame'
as_sp_polygons: no visible global function definition for 'Polygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygons'
as_sp_polygons: no visible global function definition for
  'SpatialPolygonsDataFrame'
make_SLDF: no visible global function definition for 'SpatialLines'
make_SLDF: no visible global function definition for
  'SpatialLinesDataFrame'
osm_crs: no visible global function definition for 'CRS'
ways_nodes2Line: no visible global function definition for 'Line'
ways_nodes2Polygon: no visible global function definition for 'Polygon'
Namespace in Imports field not imported from: 'bitops'
  All declared Imports should be used.
plot,OutlierDM-missing : .local: no visible binding for global variable
  'pch'
p3state: no visible global function definition for 'survfit'
p3state: no visible global function definition for 'coxph'
[,ClassW : .local: warning in switch(EXP = i, u1 = {: partial argument
  match of 'EXP' to 'EXPR'
[,ClassW : .local: warning in return(x@u1): partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in }, u2 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in return(x@u2): partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in }, w1 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in return(x@w1): partial argument match of
  'EXP' to 'EXPR'
[,ClassW : .local: warning in }): partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW : .local: warning in switch(EXP = i, u1 = {: partial
  argument match of 'EXP' to 'EXPR'
[<-,ClassW : .local: warning in x@u1 <- value: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW : .local: warning in }, u2 = {: partial argument match of
  'EXP' to 'EXPR'
[<-,ClassW : .local: warning in x@u2 <- value: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW : .local: warning in }, w1 = {: partial argument match of
  'EXP' to 'EXPR'
[<-,ClassW : .local: warning in x@w1 <- value: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW : .local: warning in }): partial argument match of 'EXP' to
  'EXPR'
CalGIF: no visible binding for global variable 'PAGIData'
CalGIF2: no visible binding for global variable 'PAGIData'
PAGI.Main: no visible binding for global variable 'PAGIData'
getclass.labels: no visible binding for global variable 'ExampleData'
getdataset: no visible binding for global variable 'ExampleData'
clapply_cluster: no visible global function definition for
  'makeCluster'
clapply_cluster: no visible global function definition for
  'clusterSetRNGStream'
clapply_cluster: no visible global function definition for
  'clusterExport'
clapply_cluster: no visible global function definition for
  'clusterApply'
clapply_cluster: no visible global function definition for
  'clusterApplyLB'
clapply_cluster: no visible global function definition for
  'stopCluster'
md5sumString: no visible global function definition for 'md5sum'
writeRdocumentationToDir: no visible global function definition for
  'list_files_with_exts'
performance.pcor: no visible global function definition for
  'ggm.test.edges'
par.nmds: no visible binding for global variable 'j'
par.spp.est: no visible binding for global variable 'i'
Namespace in Imports field not imported from: 'RSQLite'
  All declared Imports should be used.
fitOR: no visible global function definition for 'multinom'
parpdist: no visible binding for global variable 'tmpx'
cv_nfold: no visible global function definition for 'cv.glmnet'
glmcvbeta: no visible global function definition for 'cv.glmnet'
Errors in running code in vignettes:
when running code in 'pasta_intro.Rmd'
  ...

  When running vignette 'pasta_intro.Rmd':
Error: No such vignette 'pasta_intro.Rmd'
Execution halted
conch: no visible global function definition for 'read.tree'
conch: no visible global function definition for 'read.nexus'
conch: no visible global function definition for '.compressTipLabel'
conch: no visible global function definition for 'drop.tip'
conch: no visible global function definition for 'extract.clade'
conch: no visible global function definition for 'which.edge'
conch: no visible global function definition for 'write.tree'
read_input: no visible global function definition for 'read.tree'
read_input: no visible global function definition for 'read.dna'
oneway.plots: warning in dotchart(x = Y, groups = fac1, col = COL[2],
  pch = 1, xlab = deparse(substitute(Y)), xlim = YL, gdata = tapply(Y,
  fac1, mean), gpch = 17): partial argument match of 'col' to 'color'
animatePatches: no visible global function definition for
  'getTimestamp'
animatePatches: no visible global function definition for 'getElapsed'
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
'library' or 'require' call to 'ROCR' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'Biobase' 'ROCR' 'affy' 'igraph' 'kernlab' 'lpSolve' 'svmpath'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'parallel:::detectCores'
  See the note in ?`:::` about the use of this operator.
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Attaching package: 'gplots'

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

    lowess


Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
Loading required package: ROCR
Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

Loading required package: igraph

Attaching package: 'igraph'

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
draw: no visible global function definition for 'plotellipse'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.2/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.2/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  
  testthat results ================================================================
  OK: 187 SKIPPED: 15 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
pen_or1: no visible global function definition for 'multiroot'
plot.pedigree: no visible global function definition for
  'align.pedigree'
plotPed: no visible global function definition for 'pedigree'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/pbdBASE.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'pmclust'
Package required and available but unsuitable version: 'pbdBASE'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/pbdMPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/pbdSLAP.Rcheck/00install.out' for details.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
pbo: no visible global function definition for '%dopar%'
pbo: no visible global function definition for 'foreach'
xyplot.pbo: no visible global function definition for 'doubleYScale'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/pcnetmeta.Rcheck/00install.out' for details.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Namespaces in Imports field not imported from:
  'car' 'sandwich'
  All declared Imports should be used.
genomesim : extractA: no visible global function definition for
  'is.genotype'
genomesim : extractA : <anonymous>: no visible global function
  definition for 'nallele'
phensim: no visible global function definition for 'rmvnorm'
File 'pedantics/libs/i386/pedantics.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'pedantics.o'
File 'pedantics/libs/x64/pedantics.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'pedantics.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.
plot.clust: no visible global function definition for 'qplot'
plot.clust: no visible global function definition for 'geom_histogram'
plot.clust: no visible global function definition for 'aes_string'
.replaceinf: no visible global function definition for 'fcn_values<-'
complexity.LASSO: no visible global function definition for 'profL1'
complexity.ipec.CoxBoost: no visible global function definition for
  'CoxBoost'
complexity.ipec.CoxBoost: no visible global function definition for
  'locfit'
complexity.mincv.CoxBoost: no visible global function definition for
  'cv.CoxBoost'
complexity.ripec.CoxBoost: no visible global function definition for
  'CoxBoost'
complexity.ripec.CoxBoost: no visible global function definition for
  'locfit'
extract: no visible global function definition for 'findGlobals'
fit.CoxBoost: no visible global function definition for 'CoxBoost'
fit.LASSO: no visible global function definition for 'penalized'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

phantom : model: missing arguments not allowed in calls to 'c'
readData: no visible global function definition for 'read.image'
writeData: no visible global function definition for 'make.image'
writeData: no visible global function definition for 'write.image'
File 'PET/libs/i386/PET.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'art.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'art.o'
File 'PET/libs/x64/PET.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'art.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'art.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 'pgam/R/zzz.r':
  .onLoad calls:
    require("stats", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)
    require("utils", character.only = TRUE, quietly = TRUE, warn.conflicts = FALSE)
    cat("This is pgam library version", ver, "\n", sep = " ")

Package startup functions should not change the search path.
Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

This is pgam library version 0.4.12 
pgam: warning in assign("loglik", NULL, env = pgam.env): partial
  argument match of 'env' to 'envir'
pgam: warning in get("loglik", env = pgam.env): partial argument match
  of 'env' to 'envir'
pgam.likelihood: warning in assign("loglik", loglik, env = env):
  partial argument match of 'env' to 'envir'
File 'pgam/libs/i386/pgam.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'pgam.o'
File 'pgam/libs/x64/pgam.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'pgam.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.
plot.phtMCMC: no visible global function definition for 'ggplot'
plot.phtMCMC: no visible global function definition for 'melt'
plot.phtMCMC: no visible global function definition for 'geom_line'
plot.phtMCMC: no visible global function definition for 'aes_string'
plot.phtMCMC: no visible global function definition for 'geom_smooth'
plot.phtMCMC: no visible global function definition for 'facet_wrap'
plot.phtMCMC: no visible global function definition for 'ggtitle'
plot.phtMCMC: no visible global function definition for 'xlab'
plot.phtMCMC: no visible global function definition for 'ylab'
plot.phtMCMC: no visible global function definition for 'geom_density'
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.
File 'phmm/libs/i386/phmm.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'arms.o'
File 'phmm/libs/x64/phmm.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: '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.
Namespace in Imports field not imported from: 'quanteda'
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
bg.similarity.test: no visible global function definition for
  'sampleRandom'
bg.similarity.test: no visible global function definition for
  'coordinates'
bg.similarity.test: no visible global function definition for 'extract'
bg.similarity.test: no visible global function definition for
  'SpatialPoints'
bg.similarity.test : random.presence: no visible global function
  definition for 'sampleRandom'
bg.similarity.test : random.presence: no visible global function
  definition for 'coordinates'
bg.similarity.test: no visible global function definition for
  'writeRaster'
bg.similarity.test: no visible global function definition for
  'read.asciigrid'
di.enm: no visible global function definition for 'read.asciigrid'
niche.equivalency.test: no visible global function definition for
  'extract'
niche.equivalency.test: no visible global function definition for
  'SpatialPoints'
niche.equivalency.test: no visible global function definition for
  'sampleRandom'
niche.equivalency.test: no visible global function definition for
  'coordinates'
niche.equivalency.test: no visible global function definition for
  'writeRaster'
niche.equivalency.test: no visible global function definition for
  'read.asciigrid'
niche.overlap: no visible global function definition for
  'read.asciigrid'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/PhyloMeasures.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'ape'
  All declared Imports should be used.
comm.phylo.qr: no visible global function definition for 'rq'
sppregs: no visible global function definition for 'brglm'
ARTP.GE: no visible global function definition for 'ARTP_pathway'
LR.cont.surv: no visible global function definition for 'coxph'
LR.inter.cat.surv: no visible global function definition for 'coxph'
LR.inter.cont.surv: no visible global function definition for 'coxph'
permutation.snp: no visible global function definition for 'sfInit'
permutation.snp: no visible global function definition for 'sfLibrary'
permutation.snp: no visible global function definition for
  'sfExportAll'
permutation.snp: no visible global function definition for 'sfLapply'
permutation.snp: no visible global function definition for 'sfStop'
fitaci: no visible global function definition for 'chkDots'
.var.ij: no visible global function definition for 'hcv'
.var.ij: no visible global function definition for 'h.select'
.var.ij: no visible global function definition for 'sm.regression'
LiStengos: no visible global function definition for 'h.select'
LiStengos: no visible global function definition for 'hcv'
LiStengos: no visible global function definition for 'sm.regression'
cal_df_gamma1: no visible global function definition for 'binning'
cal_df_gamma2: no visible global function definition for 'binning'
iteration: no visible global function definition for 'h.select'
iteration: no visible global function definition for 'hcv'
iteration: no visible global function definition for 'sm.regression'
iteration0: no visible global function definition for 'sm.regression'
iteration0: no visible global function definition for 'h.select'
plmm: no visible global function definition for 'Formula'
plmm.bs: no visible global function definition for 'Formula'
plot.plmm: no visible global function definition for 'Formula'
plot.plmm: no visible global function definition for 'sm.regression'
predict.plmm: no visible global function definition for 'Formula'
predict.plmm: no visible global function definition for 'sm.regression'
print.summary.plmm: no visible global function definition for 'Formula'
ranef.plmm: no visible global function definition for 'Formula'
select.h0: no visible global function definition for 'Formula'
select.h0: no visible global function definition for 'h.select'
select.h0: no visible global function definition for 'hcv'
var.plot: no visible global function definition for 'Formula'
var.plot: no visible global function definition for 'sm.regression'
wplmm: no visible global function definition for 'Formula'
Namespaces in Imports field not imported from:
  'hexbin' 'quantreg'
  All declared Imports should be used.
llla.mc: no visible global function definition for 'coxph'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.4Mb
cor.xl.ImputeData: no visible global function definition for
  'impute.knn'
pnmtrem1: no visible global function definition for 'ginv'
smooth: no visible global function definition for 'genoud'
Permu.Ind: no visible global function definition for 'permn'
Permu.Ind: no visible global function definition for 'hcube'
poLCA: no visible global function definition for 'ginv'
poLCA.makeplot.dich: no visible global function definition for
  'scatterplot3d'
poLCA.makeplot.poly: no visible global function definition for
  'scatterplot3d'
poLCA.se: no visible global function definition for 'ginv'
Namespaces in Imports field not imported from:
  'jsonlite' 'readr'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'mvtnorm' 'sfsmisc'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
binBvn: no visible global function definition for 'pmvnorm'
hetcor.data.frame: no visible global function definition for 'nearcor'
Package unavailable to check Rd xrefs: 'gpclib'
plot.preplot.polywog: no visible global function definition for
  'persp3d'
siteocc: no visible global function definition for
  'is.positive.definite'
outputBottleSim: no visible binding for global variable 'final.vec'
outputBottleSim: no visible binding for global variable 'kvec'
join,Database : .local: no visible binding for global variable
  'new.ancil'
portest : OneMonteCarlo: no visible global function definition for
  'garchFit'
portest: no visible global function definition for 'makeCluster'
portest: no visible global function definition for
  'clusterSetRNGStream'
portest: no visible global function definition for 'clusterEvalQ'
portest: no visible global function definition for 'clusterExport'
portest: no visible global function definition for 'clusterCall'
portest: no visible global function definition for 'parSapply'
portest: no visible global function definition for 'stopCluster'
File 'portfolioSim/R/AllClasses.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in '?.onAttach'.

getSimTrades,stiFromSignal-orderable-portfolio-simData-logical :
  .local: no visible binding for global variable 'shares'
loadIn,simResult-character-missing : .local: no visible binding for
  global variable 'master.freq'
loadIn,simResult-character-missing : .local: no visible binding for
  global variable 'master.errors'
loadIn,simResult-character-missing : .local: no visible binding for
  global variable 'master.type'
loadIn,simResult-character-missing : .local: no visible binding for
  global variable 'master.summary.interface'
loadIn,simResultSinglePeriod-character-missing : .local: no visible
  binding for global variable 'x'
plot,simResult-missing: no visible global function definition for
  'xyplot'
runSim,portfolioSim-logical : .local: no visible binding for global
  variable 'id'
runSim,portfolioSim-logical : .local: no visible global function
  definition for 'updateSummary'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/PottsUtils.Rcheck/00install.out' for details.
File 'powell/libs/i386/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'
File 'powell/libs/x64/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
ExampleModels: no visible binding for global variable 'ExampleData'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'predmixcor/R/firstlib.r':
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
Namespace in Imports field not imported from: 'e1071'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/prevalence.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'graphics' 'stats'
  All declared Imports should be used.
cfbeta: no visible global function definition for 'kummerM'
cff: no visible global function definition for 'kummerU'
cff: no visible global function definition for 'kummerM'
permsn: no visible global function definition for 'permn'
getCandidates: no visible binding for global variable 'envData'
getGraph: no visible binding for global variable 'envData'
getProvidedDiseaseName: no visible binding for global variable
  'envData'
getSeed: no visible binding for global variable 'envData'
getTopDiseaseMetabolites: no visible binding for global variable
  'envData'
LR.pvalue: warning in matrix(c(y1, y2, (n1 - y1), (n2 - y2)), nr = 2,
  dimnames = list(c("treat", "control"), c("Success", "No success"))):
  partial argument match of 'nr' to 'nrow'
profilelike.gls: no visible global function definition for 'gls'
profilelike.lme: no visible global function definition for 'lme'
profilelike.polr: no visible global function definition for 'polr'
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    extdata  10.9Mb
    libs      1.4Mb
ggplot.profr: no visible global function definition for 'ggplot'
ggplot.profr: no visible global function definition for 'geom_rect'
ggplot.profr: no visible global function definition for 'aes'
ggplot.profr: no visible global function definition for 'geom_text'
ggplot.profr: no visible global function definition for
  'scale_y_continuous'
ggplot.profr: no visible global function definition for
  'scale_x_continuous'
IndividualPROC: no visible global function definition for 'survfit'
optim.two.stage.appr: no visible global function definition for
  'mvrnorm'
optim.two.stage.group: no visible global function definition for
  'mvrnorm'
optim.two.stage.single: no visible global function definition for
  'mvrnorm'
power.group.cost: no visible global function definition for 'mvrnorm'
power.single.cost: no visible global function definition for 'mvrnorm'
predict.protoclass: no visible global function definition for 'knn1'
Missing or unexported object: 'tools::nonS3methods'
Namespaces in Imports field not imported from:
  'forecast' 'knitr'
  All declared Imports should be used.
learnParameters: no visible global function definition for
  'coordinates'
makePrediction: no visible global function definition for 'coordinates'
spatialPredict.psgp: no visible global function definition for
  'coordinates'
spatialPredict.psgp: no visible global function definition for
  'makeCluster'
spatialPredict.psgp: no visible global function definition for
  'registerDoParallel'
spatialPredict.psgp: no visible global function definition for
  'clusterEvalQ'
spatialPredict.psgp: no visible global function definition for
  '%dopar%'
spatialPredict.psgp: no visible global function definition for
  'foreach'
spatialPredict.psgp: no visible global function definition for
  'stopCluster'
spatialPredict.psgp: no visible global function definition for
  'SpatialPointsDataFrame'
spatialPredict.psgp: no visible global function definition for 'bbox'
spatialPredict.psgp: no visible global function definition for
  'proj4string<-'
spatialPredict.psgp: no visible global function definition for
  'proj4string'
test.problem : g: no visible global function definition for 'grad'
catEffectBootAdaptor: no visible binding for global variable 'sumSqCat'
compPowerCatSelectivity: no visible binding for global variable
  'fRatioStat'
compPowerGeneralRespDetection: no visible binding for global variable
  'sumSqCat'
compPowerRespDetection: no visible binding for global variable
  'sumSqCat'
testCatEffectBoot: no visible global function definition for 'boot'
bootstrap_inference: no visible global function definition for
  'makeCluster'
bootstrap_inference: no visible global function definition for
  '%dopar%'
bootstrap_inference: no visible global function definition for
  'foreach'
bootstrap_inference: no visible global function definition for
  'stopCluster'
plot_chase_observed_expected: no visible global function definition for
  'meta.MH'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/PurBayes.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/PVAClone.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'RSVGTipsDevice'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

Calc.Expr: no visible binding for global variable 'Type'
Calc.Expr: no visible binding for global variable 'Identifier'
Calc.Expr: no visible binding for global variable 'Fluor'
GroupPlot: no visible binding for global variable 'Type'
plot.CT: no visible binding for global variable 'tr_gene_name'
plot.qrfactor : sp.label: no visible global function definition for
  'coordinates'
plot.qrfactor: no visible global function definition for 'spplot'
plot.qrfactor: no visible global function definition for 'bpy.colors'
plot.qrfactor: no visible global function definition for 'readOGR'
rq: no visible global function definition for 'readOGR'
Namespace in Imports field not imported from: 'xts'
  All declared Imports should be used.
tailprob: warning in pchisq(t, df, low = FALSE): partial argument match
  of 'low' to 'lower.tail'
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    contrib   3.6Mb
    doc       2.9Mb
plot,cvpen : .local: no visible binding for global variable 'lambda1'
plot,cvpen : .local: no visible binding for global variable 'lambda2'
plot,cvpen : .local: no visible binding for global variable 'serr'
plot,cvpen : .local: no visible binding for global variable 'xval'
plot,cvpen : .local: no visible binding for global variable
  'lambda.choice'
plot,quadrupen : .local: no visible binding for global variable
  'variables'
plot,stability.path : .local: no visible binding for global variable
  'variables'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.3Mb
    libs   2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/QuantTools.Rcheck/00install.out' for details.
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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.
Namespaces in Imports field not imported from:
  'afex' 'data.table' 'dplyr' 'lmerTest'
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      4.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/R2jags.Rcheck/00install.out' for details.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
allpossregs.formula: no visible global function definition for
  'regsubsets'
allpossregs.lm: no visible global function definition for 'regsubsets'
reg3d: no visible global function definition for 'rgl.open'
reg3d: no visible global function definition for 'rgl.bg'
reg3d: no visible global function definition for 'rgl.material'
reg3d: no visible global function definition for 'rgl.lines'
reg3d: no visible global function definition for 'rgl.spheres'
reg3d: no visible global function definition for 'rgl.surface'
reg3d: no visible global function definition for 'rgl.texts'
race : killSlaves.exit: no visible global function definition for
  '.PVM.initsend'
race : killSlaves.exit: no visible global function definition for
  '.PVM.send'
race : killSlaves.exit: no visible global function definition for
  '.PVM.exit'
race: no visible global function definition for '.PVM.mytid'
race: no visible global function definition for '.PVM.spawn'
race: no visible global function definition for '.PVM.initsend'
race: no visible global function definition for '.PVM.pkstrvec'
race: no visible global function definition for '.PVM.send'
race: no visible global function definition for '.PVM.recv'
race: no visible global function definition for '.PVM.bufinfo'
race: no visible global function definition for '.PVM.upkstrvec'
race : job.start: no visible global function definition for
  '.PVM.initsend'
race : job.start: no visible global function definition for
  '.PVM.pkint'
race : job.start: no visible global function definition for '.PVM.send'
race : job.wait: no visible global function definition for '.PVM.recv'
race : job.wait: no visible global function definition for
  '.PVM.bufinfo'
race : job.wait: no visible global function definition for
  '.PVM.upkint'
race : job.wait: no visible global function definition for
  '.PVM.upkdblvec'
.disableThreads: no visible global function definition for
  'stopCluster'
.enableThreads: no visible global function definition for 'detectCores'
.enableThreads: no visible global function definition for
  'makePSOCKcluster'
.enableThreads: no visible global function definition for
  'clusterExport'
.enableThreads: no visible global function definition for 'clusterCall'
CropSpatialPolygonsDataFrame: no visible global function definition for
  'bbox'
CropSpatialPolygonsDataFrame: no visible global function definition for
  'clipPolys'
BinBam: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
BinBam: no visible global function definition for 'seqlengths'
makeGCContentData: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
makeGCContentData: no visible global function definition for
  'seqlengths'
makeGCContentPerPos: no visible binding for global variable
  'BSgenome.Hsapiens.UCSC.hg19'
freq: no visible global function definition for 'melt'
rp.desc: no visible global function definition for 'melt.data.frame'
rp.desc: no visible global function definition for 'cast'
rp.freq: no visible global function definition for 'melt'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.7Mb
    libs   2.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.5Mb
.GCD: no visible global function definition for 'as.polynomial'
.LCM: no visible global function definition for 'as.polynomial'
rationalfun: no visible global function definition for 'polynomial'
rationalfun.poly: no visible global function definition for
  'polynomial'
rationalfun.poly: no visible global function definition for
  'is.polynomial'
rfun: no visible global function definition for 'polynomial'
rfun.poly: no visible global function definition for 'polynomial'
rfun.poly: no visible global function definition for 'is.polynomial'
simplify: no visible global function definition for 'polynomial'
bef.get.categories_for: no visible binding for global variable 'id'
bef.portal.get.categories_for: no visible binding for global variable
  'id'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/Rblpapi.Rcheck/00install.out' for details.
bn2nbn: no visible binding for global variable 'bn.fit'
nbn2bnfit: no visible global function definition for 'model2network'
nbn2bnfit: no visible global function definition for 'custom.fit'
simulate8mn: no visible global function definition for 'mvrnorm'
rbugs2coda: no visible global function definition for 'as.mcmc'
rbugs2coda: no visible global function definition for 'mcmc'
rbugs2coda: no visible global function definition for 'as.mcmc.list'
install_version: no visible global function definition for
  'install_url'
circlesSize: no visible global function definition for 'bbox'
discretVar: no visible global function definition for 'classIntervals'
discretVar: no visible global function definition for 'brewer.pal'
frameAutoSize: no visible global function definition for 'bbox'
mapChoroTypo: no visible global function definition for
  'readShapeSpatial'
mapChoropleth: no visible global function definition for
  'readShapeSpatial'
mapCircles: no visible global function definition for
  'readShapeSpatial'
mapCircles: no visible global function definition for 'coordinates'
mapCirclesChoro: no visible global function definition for
  'readShapeSpatial'
mapCirclesChoro: no visible global function definition for
  'coordinates'
mapCirclesTypo: no visible global function definition for
  'readShapeSpatial'
mapCirclesTypo: no visible global function definition for 'coordinates'
northArrowDisplay: no visible global function definition for
  'SpatialPolygonsRescale'
northArrowDisplay: no visible global function definition for
  'layout.north.arrow'
scalebarDisplay: no visible global function definition for
  'SpatialPolygonsRescale'
scalebarDisplay: no visible global function definition for
  'layout.scale.bar'
typo: no visible global function definition for 'brewer.pal'
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
Namespace in Imports field not imported from: 'dplyr'
  All declared Imports should be used.
climdex.data.frame: no visible global function definition for
  'as.PCICt'
computeMBD : OnOutput: no visible global function definition for
  'tkbutton'
computeMBD: no visible global function definition for 'tkbutton'
computeMBD : OnPlot: no visible global function definition for
  'tkcanvas'
computeMBD : OnPlot: no visible global function definition for
  'tkbutton'
computeTmean: no visible global function definition for 'tkcanvas'
computeTmean: no visible global function definition for 'tkbutton'
plotCentralCurves: no visible global function definition for 'tkcanvas'
plotCentralCurves: no visible global function definition for 'tkbutton'
.onAttach: no visible global function definition for 'getRcmdr'
.onAttach: no visible global function definition for 'closeCommander'
.onAttach: no visible global function definition for 'Commander'
mosaicMenuItem: no visible global function definition for
  'mosaicSelectDialog'
mosaicMenuItem: no visible global function definition for 'Message'
Rcmdr.new.loca.p: no visible binding for global variable 'top'
Rcmdr.new.loca.p: no visible binding for global variable 'buttonsFrame'
Rcmdr.orloca.norm: no visible binding for global variable 'top'
Rcmdr.orloca.norm : onOK: no visible binding for global variable
  'normaVariable'
Rcmdr.orloca.norm: no visible binding for global variable 'normaFrame'
Rcmdr.orloca.norm: no visible binding for global variable
  'buttonsFrame'
Rcmdr.rloca.p: no visible binding for global variable 'top'
Rcmdr.rloca.p: no visible binding for global variable 'buttonsFrame'
Rcmdr.zsum: no visible binding for global variable 'top'
Rcmdr.zsum: no visible binding for global variable 'buttonsFrame'
Rcmdr.zsummin: no visible binding for global variable 'top'
Rcmdr.zsummin : onOK: no visible binding for global variable
  'algorithmVariable'
Rcmdr.zsummin : onOK: no visible binding for global variable '.sol'
Rcmdr.zsummin: no visible binding for global variable 'algorithmFrame'
Rcmdr.zsummin: no visible binding for global variable 'buttonsFrame'
BOXWP: no visible binding for global variable 'top'
BOXWP: no visible binding for global variable 'buttonsFrame'
HIST: no visible binding for global variable 'top'
HIST: no visible binding for global variable 'buttonsFrame'
QQN: no visible binding for global variable 'top'
QQN: no visible binding for global variable 'buttonsFrame'
bigraphe0: no visible global function definition for 'qgraph'
bisummarize0: no visible global function definition for 'dudi.coa'
chalandise.DEP0: no visible global function definition for 'map'
histbackback0: no visible global function definition for 'mgp.axis'
mapAFC: no visible global function definition for 'scatter'
mapAFC: no visible global function definition for 'dudi.coa'
multivariate0: no visible global function definition for 'dudi.mix'
plotCat2: no visible global function definition for 's.class'
plotLikert1: no visible global function definition for 'trellis.device'
plotLikert1: no visible global function definition for 'dotplot'
plotLikert1: no visible global function definition for 'simpleKey'
plotMissing: no visible global function definition for 'whatis'
plotNum: no visible global function definition for 's.corcircle'
plotTabCont0: no visible global function definition for 'assoc'
plotTabCont0: no visible binding for global variable 'shading_hcl'
plotTabCont0: no visible global function definition for 'corresp'
sortAnova: no visible global function definition for 'Anova'
statMissing: no visible global function definition for 'whatis'
vpAFC: no visible global function definition for 'dudi.coa'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcmdrPlugin.RMTCJags.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    include   4.7Mb
    libs      1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcppCCTZ.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    libs      1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcppHMM.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RcppOctave.Rcheck/00install.out' for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       6.4Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    include   6.3Mb
    libs      1.9Mb
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    include   4.3Mb
    lib      21.3Mb
    libs      3.8Mb
sumry_categorical: no visible global function definition for 'freq'
prepare_Rd: Rdpack-package.Rd:154: unknown macro '\insertRef'
prepare_Rd: Rdpack-package.Rd:156: unknown macro '\insertRef'
prepare_Rd: insert_ref.Rd:89: unknown macro '\insertRef'
prepare_Rd: insert_ref.Rd:91: unknown macro '\insertRef'
macros/refmacros.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'refmacros.Rd'
Package suggested but not available for checking: 'RSelenium'
Namespaces in Imports field not imported from:
  'R6' 'hms'
  All declared Imports should be used.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.6Mb
Namespaces in Imports field not imported from:
  'devtools' 'dplyr' 'magrittr' 'plyr' 'reshape2'
  All declared Imports should be used.
Error in re-building vignettes:
  ...

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

    intersect, setdiff, setequal, union

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 47-64 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
object 'x' not found
Execution halted
mergeNamespace_roclet: no visible global function definition for
  'new_roclet'
Namespaces in Imports field not imported from:
  'igraph' 'rJava'
  All declared Imports should be used.
REEMtree: no visible binding for global variable 'SubsetVector'
Namespace in Imports field not imported from: 'curl'
  All declared Imports should be used.
macros/macros.Rd: Sections \title, and \name must exist and be unique in Rd files
problem found in 'macros.Rd'
wcr: no visible global function definition for 'ginv'
cv.alpha.relaxnet: no visible global function definition for
  'mc.reset.stream'
cv.alpha.relaxnet: no visible global function definition for 'mclapply'
cv.relaxnet: no visible global function definition for
  'mc.reset.stream'
cv.relaxnet: no visible global function definition for 'mclapply'
relaxo: no visible global function definition for 'lars'
cross: no visible binding for global variable 'is.Surv'
is.numeric.and.not.surv: no visible global function definition for
  'is.Surv'
remix: no visible global function definition for 'is.formula'
remix : <anonymous>: no visible global function definition for
  'is.Surv'
remix: no visible binding for global variable 'is.Surv'
remix: no visible global function definition for 'llply'
summarize.by: no visible global function definition for 'dlply'
summarize.by: no visible global function definition for '.'
summarize.data.frame.by: no visible global function definition for
  'dlply'
survival: no visible global function definition for 'survfit'
survival: no visible global function definition for 'daply'
survival: no visible global function definition for '.'
test.survival.logrank: no visible global function definition for
  'survdiff'
GlobTestMissing: no visible global function definition for 'lme'
TestStatSimple: no visible global function definition for 'ginv'
Running examples in 'repo-Ex.R' failed
The error most likely occurred in:

> ### Name: repo_pull
> ### Title: Download item remote content
> ### Aliases: repo_pull
> 
> ### ** Examples
> 
> ## Repository creation
> rp_path <- file.path(tempdir(), "example_repo")
> rp <- repo_open(rp_path, TRUE)
Repo root created.
Repo created.
> 
> ## The following item will have remote source
> rp$put("Local content", "item1", "Sample item 1", "tag",
+          URL="http://www.francesconapolitano.it/repo/remote")
> print(rp$get("item1"))
[1] "Local content"
> rp$pull("item1")
trying URL 'http://www.francesconapolitano.it/repo/remote'
Warning in download.file(e$URL, tf) :
  InternetOpenUrl failed: 'Die Serververbindung konnte nicht hergestellt werden.'
Error in download.file(e$URL, tf) : 
  cannot open URL 'http://www.francesconapolitano.it/repo/remote'
Calls: <Anonymous> -> download.file
Execution halted
Error in re-building vignettes:
  ...
trying URL 'http://www.francesconapolitano.it/repo/remote'
Quitting from lines 506-512 (index.Rmd) 
Error: processing vignette 'index.Rmd' failed with diagnostics:
cannot open URL 'http://www.francesconapolitano.it/repo/remote'
Execution halted
reshapeGUI: no visible global function definition for 'gwindow'
reshapeGUI: no visible global function definition for 'gnotebook'
reshapeGUI: no visible global function definition for 'size<-'
reshapeGUI: no visible global function definition for 'ggroup'
reshapeGUI: no visible global function definition for 'gtable'
reshapeGUI: no visible global function definition for 'addSpring'
reshapeGUI: no visible global function definition for 'gbutton'
reshapeGUI: no visible global function definition for 'glabel'
reshapeGUI: no visible global function definition for 'gedit'
reshapeGUI: no visible global function definition for 'gcheckbox'
reshapeGUI: no visible global function definition for 'gdf'
reshapeGUI: no visible global function definition for 'visible<-'
reshapeGUI: no visible global function definition for
  'addHandlerClicked'
reshapeGUI : <anonymous>: no visible global function definition for
  'gmessage'
reshapeGUI : <anonymous>: no visible global function definition for
  'svalue'
reshapeGUI : <anonymous>: no visible global function definition for
  'svalue<-'
reshapeGUI : <anonymous>: no visible global function definition for
  'delete'
reshapeGUI : <anonymous>: no visible global function definition for
  'add'
reshapeGUI : <anonymous>: no visible global function definition for
  'gdf'
reshapeGUI : <anonymous>: no visible global function definition for
  'visible<-'
reshapeGUI: no visible global function definition for
  'addHandlerChanged'
updateMeltCodeBox: no visible global function definition for 'svalue<-'
findCredentials: no visible global function definition for 'startsWith'
Running examples in 'restfulr-Ex.R' failed
The error most likely occurred in:

> ### Name: RestContainer-class
> ### Title: RestContainer
> ### Aliases: class:RestContainer RestContainer-class RestContainer
> ###   [,RestContainer-method [<-,RestContainer-method
> ###   $,RestContainer-method [[,RestContainer-method
> ###   $<-,RestContainer-method [[<-,RestContainer-method
> ###   show,RestContainer-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> apache <- RestContainer("http://wiki.apache.org")
Error in which(startsWith(uri, as.character(names(config)))) : 
  could not find function "startsWith"
Calls: RestContainer -> container -> RestUri -> findCredentials -> which
Execution halted
mat2coo: no visible global function definition for 'as.matrix.coo'
quoteFXTsData : function.fx: no visible global function definition for
  'xmlValue'
quoteFundTsData : function.fund: no visible global function definition
  for 'xmlValue'
quoteStockTsData : function.stock: no visible global function
  definition for 'xmlSize'
quoteStockTsData : function.stock: no visible global function
  definition for 'xmlValue'
quoteTsData: no visible global function definition for 'xmlRoot'
quoteTsData: no visible global function definition for 'htmlTreeParse'
quoteTsData: no visible global function definition for
  'xmlErrorCumulator'
quoteTsData: no visible global function definition for 'xmlSize'
toXts: no visible global function definition for 'as.xts'
Namespace in Imports field not imported from: 'RcppProgress'
  All declared Imports should be used.
gammaIntegral : <anonymous>: no visible global function definition for
  'hyperg_1F1'
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    gdal       3.0Mb
    libs      23.7Mb
    pictures   1.3Mb
    proj       4.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.5Mb
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  7: request_fetch.write_memory(req$output, req$url, handle)
  8: curl::curl_fetch_memory(url, handle = handle)
  
  testthat results ================================================================
  OK: 47 SKIPPED: 0 FAILED: 5
  1. Error: Formating via 'source' works (@test_format_gq.R#18) 
  2. Error: Formating via 'config' works (@test_format_gq.R#39) 
  3. Error: Formating via 'config' needs all parameters (@test_format_gq.R#50) 
  4. Error: Formating via named parameters works (@test_format_gq.R#60) 
  5. Error: add_flags plays well with rgbif (@test_synergies.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc     2.0Mb
    fonts   1.5Mb
    libs    1.1Mb
exprToIgraph: no visible global function definition for 'graph'
exprToIgraph: no visible global function definition for 'V'
exprToIgraph: no visible global function definition for 'V<-'
multiNicheGeneticProgramming: no visible binding for global variable
  'sfClusterApplyLB'
multiNicheGeneticProgramming: no visible binding for global variable
  'sfExport'
multiNicheSymbolicRegression: no visible binding for global variable
  'sfClusterApplyLB'
multiNicheSymbolicRegression: no visible binding for global variable
  'sfExport'
Error in re-building vignettes:
  ...
mpiler/texmf/fonts/type1/public/amsfonts/cm/cmr8.pfb><D:/Compiler/texmf/fonts/t
ype1/public/amsfonts/cm/cmr9.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts
/cm/cmsltt10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss10.pfb><
D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmss8.pfb><D:/Compiler/texmf/f
onts/type1/public/amsfonts/cm/cmss9.pfb><D:/Compiler/texmf/fonts/type1/public/a
msfonts/cm/cmsy10.pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti10.
pfb><D:/Compiler/texmf/fonts/type1/public/amsfonts/cm/cmti12.pfb><D:/Compiler/t
exmf/fonts/type1/public/amsfonts/cm/cmtt10.pfb><D:/Compiler/texmf/fonts/type1/p
ublic/amsfonts/cm/cmtt8.pfb><D:/Compiler/texmf/fonts/type1/public/mathpazo/fplm
ri.pfb><D:/Compiler/texmf/fonts/type1/public/cm-super/sfrm0900.pfb><D:/Compiler
/texmf/fonts/type1/public/cm-super/sfrm1000.pfb><D:/Compiler/texmf/fonts/type1/
urw/palatino/uplr8a.pfb><D:/Compiler/texmf/fonts/type1/urw/palatino/uplri8a.pfb
>
Output written on rgp_introduction.pdf (16 pages, 430970 bytes).
Transcript written on rgp_introduction.log.
"D:/RCompile/recent/R-32~1.5/bin/Rscript" -e "tools::compactPDF('rgp_introduction.pdf', gs_quality='ebook')"
  compacted 'rgp_introduction.pdf' from 421Kb to 205Kb
rm -f Rplots.pdf
rm: cannot remove 'Rplots.pdf': Device or resource busy
make[1]: *** [pdf] Error 1
make[1]: Leaving directory `/cygdrive/d/RCompile/CRANpkg/local/3.2/rgp.Rcheck/vign_test/rgp/vignettes'
Warning: running command 'make' had status 2
Error in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.2/rgp.Rcheck/vign_test/rgp") : 
  running 'make' failed
Execution halted
server: no visible global function definition for 'mcparallel'
Found the following significant warnings:
  gdkFuncs.c:1466:3: warning: passing argument 1 of 'gdk_drag_get_protocol' makes pointer from integer without a cast [enabled by default]
  gdkFuncs.c:1510:3: warning: passing argument 2 of 'gdk_drag_get_protocol_for_display' makes pointer from integer without a cast [enabled by default]
See 'd:/Rcompile/CRANpkg/local/3.2/RGtk2.Rcheck/00install.out' for details.
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   4.6Mb
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'Rf_EncodeInteger', 'Rf_EncodeLogical',
    'Rf_EncodeReal', 'Rf_formatInteger', 'Rf_formatLogical',
    'Rf_formatReal'
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'Rf_EncodeInteger', 'Rf_EncodeLogical',
    'Rf_EncodeReal', 'Rf_formatInteger', 'Rf_formatLogical',
    'Rf_formatReal'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
dbConnect,H2Driver : .local: no visible global function definition for
  '.jgetEx'
dbSendQuery,H2Connection-character : .local: no visible global function
  definition for '.jfield'
.quick_fetch: no visible global function definition for 'POST'
.quick_fetch: no visible global function definition for 'add_headers'
.quick_fetch: no visible global function definition for
  'stop_for_status'
.quick_fetch: no visible global function definition for 'content'
fetch_healthdata: no visible binding for global variable 'resources'
fetch_healthdata : <anonymous>: no visible binding for global variable
  'filters'
eclDirectCall: no visible global function definition for 'postForm'
parseResults: no visible global function definition for 'xmlRoot'
parseResults: no visible global function definition for 'xmlTreeParse'
parseResults: no visible global function definition for 'getNodeSet'
parseResults: no visible global function definition for 'xmlGetAttr'
parseResults: no visible global function definition for 'xmlValue'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    lib    3.2Mb
    libs   4.3Mb
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_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_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_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_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.
Package required but not available: 'feather'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
NumConv: no visible global function definition for 'pchip'
NumConv: no visible global function definition for 'cmpfun'
NumDeconv: no visible global function definition for 'pchip'
NumDeconv : error_function: no visible global function definition for
  'pchip'
NumDeconv: no visible global function definition for 'cmpfun'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/rjags.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/3.2/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.2/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.
getStatsData: no visible global function definition for 'xmlRoot'
getStatsData: no visible global function definition for 'xmlTreeParse'
getStatsData: no visible global function definition for 'xmlValue'
getStatsData: no visible global function definition for 'getNodeSet'
getStatsData: no visible global function definition for 'xmlSApply'
getStatsData: no visible binding for global variable 'xmlGetAttr'
getStatsData: no visible binding for global variable 'xmlValue'
getStatsList: no visible global function definition for 'xmlRoot'
getStatsList: no visible global function definition for 'xmlTreeParse'
getStatsList: no visible global function definition for 'xmlValue'
getStatsList: no visible binding for global variable 'xmlGetAttr'
getStatsList : <anonymous>: no visible global function definition for
  'xmlValue'
getStatsList : <anonymous>: no visible global function definition for
  'xmlGetAttr'
Namespace in Imports field not imported from: 'crul'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'Matrix' 'arules' 'pmml' 'rJava'
  All declared Imports should be used.
Package required and available but unsuitable version: 'Luminescence'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
parse_grammar : <anonymous>: no visible global function definition for
  'startsWith'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  
  Generating LALR tables 
  testthat results ================================================================
  OK: 153 SKIPPED: 0 FAILED: 5
  1. Failure: rule (@test.yacc_badrule.R#181) 
  2. Failure: rule (@test.yacc_badrule.R#183) 
  3. Failure: rule (@test.yacc_badrule.R#185) 
  4. Failure: rule (@test.yacc_badrule.R#187) 
  5. Failure: misplaced (@test.yacc_misplaced.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
PD_internal: no visible global function definition for 'qtnorm'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    rmd   5.8Mb
Namespaces in Imports field not imported from:
  'mnormt' 'pwr'
  All declared Imports should be used.
.onLoad: warning in dir(dll.path, pattern = this.ext, full = FALSE):
  partial argument match of 'full' to 'full.names'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[1], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[2], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
File 'RMC/libs/i386/RMC.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'RMC.o', 'predict.o'
  Found 'rand', possibly from 'rand' (C)
    Object: 'ap.o'
File 'RMC/libs/x64/RMC.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'RMC.o', 'predict.o'
  Found 'rand', possibly from 'rand' (C)
    Object: 'ap.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
plot.meta.cum: warning in qnorm((1 - conf.level)/2, s = ses[m]):
  partial argument match of 's' to 'sd'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/Rmixmod.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/Rmpi.Rcheck/00install.out' for details.
CoeffYWeq: no visible global function definition for 'index'
fitdistrForPrecipitation: no visible global function definition for
  'fitdistr'
DESeqWrapper: no visible global function definition for
  'newCountDataSet'
DESeqWrapper: no visible global function definition for
  'estimateSizeFactors'
DESeqWrapper: no visible global function definition for 'counts'
DESeqWrapper: no visible global function definition for
  'estimateDispersions'
DESeqWrapper: no visible global function definition for 'nbinomTest'
DESeqWrapper: no visible global function definition for
  'getVarianceStabilizedData'
DESeqWrapper: no visible global function definition for 'pData'
kaksFromVariants : <anonymous>: no visible global function definition
  for 'as.alignment'
kaksFromVariants : <anonymous>: no visible global function definition
  for 'kaks'
nSynNonSites : <anonymous>: no visible global function definition for
  'as.alignment'
nSynNonSites : <anonymous>: no visible global function definition for
  'kaks'
plotDispEsts: no visible global function definition for 'counts'
plotDispEsts: no visible global function definition for 'fitInfo'
runGOAnalysis: no visible binding for global variable 'annFUN.gene2GO'
runGOAnalysis: no visible global function definition for 'runTest'
runGOAnalysis: no visible global function definition for 'score'
runGOAnalysis: no visible global function definition for 'termStat'
runGOAnalysis: no visible global function definition for 'Term'
runGOAnalysis: no visible binding for global variable 'GOTERM'
runGOAnalysis: no visible global function definition for
  'showSigOfNodes'
RNGseq : <anonymous>: no visible global function definition for
  'nextRNGStream'
RNGseq: no visible global function definition for 'nextRNGStream'
RNGseq_seed: no visible global function definition for 'nextRNGStream'
checkRNG: no visible global function definition for 'checkTrue'
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.3Mb
psdcor: no visible global function definition for 'posdefify'
psdcor: no visible global function definition for 'nearcor'
robcor: no visible global function definition for 'covMcd'
robloxbioc,beadLevelData : .local: warning in
  packageDescription(annoPkg, field = "Version"): partial argument
  match of 'field' to 'fields'
AffySimStudy: no visible global function definition for 'estimate'
IlluminaSimStudy: no visible global function definition for 'estimate'
KolmogorovMinDist,BeadLevelList-AbscontDistribution : .local: no
  visible global function definition for 'arrayNames'
KolmogorovMinDist,BeadLevelList-AbscontDistribution : .local: no
  visible global function definition for 'getArrayData'
robloxbioc,beadLevelData : .local: no visible global function
  definition for 'mappedkeys'
robloxbioc,beadLevelData : .local: no visible global function
  definition for 'revmap'
robloxbioc,beadLevelData : .local: no visible global function
  definition for 'featureData<-'
robloxbioc,beadLevelData : .local: no visible global function
  definition for 'phenoData<-'
FaClassic.default: no visible global function definition for 'Cov'
FaClassic.default: no visible global function definition for 'getCov'
FaCov.default: no visible global function definition for
  'CovControlMcd'
FaCov.default: no visible global function definition for 'restimate'
FaCov.default: no visible global function definition for 'Cov'
FaCov.default: no visible global function definition for 'getCov'
compute_cov_cor: no visible global function definition for 'CovRobust'
compute_cov_cor: no visible global function definition for 'getCov'
compute_cov_cor: no visible global function definition for 'getCorr'
myplotDD: no visible global function definition for 'getData'
myplotDD: no visible global function definition for 'getCov'
myplotDD: no visible global function definition for 'CovClassic'
myplotDD: no visible global function definition for 'getDistance'
pred.robustgam: no visible global function definition for
  'Predict.matrix'
robustgam: no visible global function definition for 's'
robustgam: no visible global function definition for
  'smooth.construct.tp.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.cr.smooth.spec'
robustgam: no visible global function definition for
  'smooth.construct.ps.smooth.spec'
robustgam : w.fun: no visible global function definition for 'covMcd'
robustgam.crossval : w.fun: no visible global function definition for
  'covMcd'
File 'robust/libs/i386/robust.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'rb.o'
File 'robust/libs/x64/robust.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'rb.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.
boot.ROC: no visible global function definition for 'penalized'
boot.ROC: no visible global function definition for 'optL1'
boot.ROCt: no visible global function definition for 'penalized'
boot.ROCt: no visible global function definition for 'Surv'
boot.ROCt: no visible global function definition for 'survivalROC'
boot.ROCt: no visible global function definition for 'optL1'
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for 'prediction'
o.rocc: no visible global function definition for 'performance'
tr.rocc: no visible global function definition for 'prediction'
tr.rocc: no visible global function definition for 'performance'
api: no visible global function definition for 'endsWith'
P: no visible global function definition for 'has.key'
rand_partitions: no visible global function definition for 'hash'
rpart.rules.push: no visible global function definition for 'sqlSave'
GenerateData: no visible global function definition for 'mvrnorm'
GetVarImp : FitPenalizedModel: no visible global function definition
  for 'clogit'
cell.density.default: no visible binding for global variable
  'universalConstants'
conect.pdb: no visible binding for global variable 'elements'
masses.default: no visible binding for global variable 'elements'
toSymbols.character: no visible binding for global variable 'elements'
toSymbols.integer: no visible binding for global variable 'elements'
visualize.coords: no visible binding for global variable 'elements'
read.multi.dna: no visible binding for global variable 'read.dna'
read.phylip.data: no visible global function definition for 'read.dna'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
rrest: no visible binding for global variable 'glasso'
rrest: no visible global function definition for 'pcout'
rrlda : centerObservations: no visible global function definition for
  'l1median_NLM'
rrlda : df.L2glasso: no visible global function definition for
  'duplication.matrix'
rrlda : alt.df.L2glasso: no visible global function definition for
  'lower.triangle'
File 'RSAgeo/libs/i386/RSAgeo.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'RSAc.o', 'lib.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'RSAc.o'
File 'RSAgeo/libs/x64/RSAgeo.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'RSAc.o', 'lib.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'RSAc.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
File 'rscproxy/libs/i386/rscproxy.dll':
  Found non-API calls to R: 'R_DefParams', 'R_ReplDLLinit',
    'R_SetParams', 'R_set_command_line_arguments', 'Rf_endEmbeddedR',
    'getDLLVersion', 'getRUser', 'readconsolecfg', 'setup_Rmainloop'
File 'rscproxy/libs/x64/rscproxy.dll':
  Found non-API calls to R: 'R_DefParams', 'R_ReplDLLinit',
    'R_SetParams', 'R_set_command_line_arguments', 'Rf_endEmbeddedR',
    'getDLLVersion', 'getRUser', 'readconsolecfg', 'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Package required but not available: 'wdman'

Package suggested but not available for checking: 'Rcompression'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  d:\compiler\gcc-4.6.3\bin\../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/include/winsock2.h:15:2: warning: #warning Please include winsock2.h before windows.h [-Wcpp]
  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/3.2/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.2/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.2/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
rsig: no visible binding for global variable 'mclapply'
rsig.all: no visible binding for global variable 'mclapply'
Namespace in Imports field not imported from: 'parallel'
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.3Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========

Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
RStorm: no visible global function definition for 'alply'
File 'Rsundials/libs/i386/Rsundials.dll':
  Found 'printf', possibly from 'printf' (C)
    Objects: 'nvector_serial.o', 'sundials_band.o',
      'sundials_smalldense.o'
  Found 'putchar', possibly from 'putchar' (C)
    Objects: 'nvector_serial.o', 'sundials_band.o',
      'sundials_smalldense.o'
File 'Rsundials/libs/x64/Rsundials.dll':
  Found 'printf', possibly from 'printf' (C)
    Objects: 'nvector_serial.o', 'sundials_band.o',
      'sundials_smalldense.o'
  Found 'putchar', possibly from 'putchar' (C)
    Objects: 'nvector_serial.o', 'sundials_band.o',
      'sundials_smalldense.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.
Namespace in Imports field not imported from: 'mc2d'
  All declared Imports should be used.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
Math.Sym: no visible binding for global variable 'transtab'
jythonStart: no visible global function definition for '.jinit'
jythonStart: no visible global function definition for '.jnew'
jythonStart: no visible binding for global variable '.Jython'
sympy: no visible binding for global variable '.Jython'
sympy: no visible global function definition for '.jstrVal'
sympyStart: no visible binding for global variable '.Jython'
Namespaces in Imports field not imported from:
  'RSQLite' 'stats'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/rtk.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/runjags.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
rvgt.ftable : myrdist: no visible global function definition for 'ur'
uerror: no visible global function definition for 'unuran.is.inversion'
uerror : myaqdist: no visible global function definition for 'uq'
unuran.distr.class: no visible global function definition for
  'unuran.details'
xerror: no visible global function definition for 'unuran.is.inversion'
xerror : myaqdist: no visible global function definition for 'uq'
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
check_ISO_code: no visible binding for global variable 'NoAm_country'
check_ISO_code: no visible binding for global variable 'SoAm_country'
check_ISO_code: no visible binding for global variable 'Oceana_country'
check_ISO_code: no visible binding for global variable 'Africa_country'
check_ISO_code: no visible binding for global variable 'Asia_country'
check_ISO_code: no visible binding for global variable 'Eur_country'
Running examples in 'rwty-Ex.R' failed
The error most likely occurred in:

> ### Name: makeplot.splitfreq.matrix
> ### Title: Plots a matrix of split frequency comparisons between multiple
> ###   MCMC chains.
> ### Aliases: makeplot.splitfreq.matrix
> ### Keywords: ASDSF MCMC, clade consensus, convergence, frequency,
> ###   phylogenetics,
> 
> ### ** Examples
> 
> data(salamanders)
> makeplot.splitfreq.matrix(salamanders[1:4], burnin = 20)
[1] "Creating split frequency matrix and ASDSF clustering plots"
$splitfreq.matrix

$asdsf.tree
Error in .Call.graphics(C_palette2, .Call(C_palette2, NULL)) : 
  invalid graphics state
Calls: print -> print.ggplot -> grid.newpage -> <Anonymous>
Execution halted
Analyze: no visible global function definition for 'mcmc'
Analyze: no visible global function definition for 'varnames<-'
AnalyzeWithExitPoll: no visible global function definition for 'mcmc'
AnalyzeWithExitPoll: no visible global function definition for
  'varnames<-'
form.mcmc.object: no visible global function definition for
  'varnames<-'
gq.summary: no visible global function definition for 'mcmc.list'
gq.summary: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'mcmc.list'
gq_diagnostics: no visible global function definition for 'mcmc'
gq_diagnostics: no visible global function definition for 'gelman.diag'
gq_diagnostics: no visible global function definition for 'geweke.diag'
gq_diagnostics: no visible global function definition for 'heidel.diag'
gq_diagnostics: no visible global function definition for
  'autocorr.diag'
RXlarlso: no visible global function definition for 'lars'
RXuclars: no visible global function definition for 'lars'
Found the following significant warnings:
  Warning: S3 methods 'anova.merMod', 'as.data.frame.boot', 'as.data.frame.thpr', 'as.data.frame.VarCorr.merMod', 'as.function.merMod', 'coef.lmList4', 'coef.merMod', 'confint.lmList4', 'confint.merMod', 'confint.thpr', 'densityplot.thpr', 'deviance.merMod', 'df.residual.merMod', 'dotplot.coef.mer', 'dotplot.ranef.mer', 'drop1.merMod', 'extractAIC.merMod', 'family.glmResp', 'family.lmResp', 'family.merMod', 'family.nlsResp', 'fitted.merMod', 'fixef.merMod', 'formula.lmList4', 'formula.merMod', 'getME.merMod', 'hatvalues.merMod', 'isGLMM.merMod', 'isLMM.merMod', 'isNLMM.merMod', 'isREML.merMod', 'log.thpr', 'logLik.merMod', 'model.frame.merMod', 'model.matrix.merMod', 'ngrps.factor', 'ngrps.merMod', 'nobs.merMod', 'plot.coef.mer', 'plot.lmList4.confint', 'plot.merMod', 'plot.ranef.mer', 'predict.merMod', 'print.merMod', 'print.ranef.mer', 'print.summary.merMod', 'print.VarCorr.merMod', 'profile.merMod', 'qqmath.merMod', 'qqmath.ranef.mer', 'ranef.merMod', 'refit.merMod', 'refitML.merMod', 'residua [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.2/Rz.Rcheck/00install.out' for details.
gtkFileChooserDialogFilteredActivate: no visible binding for global
  variable 'theme_grey'
summary.CrossTable: no visible global function definition for
  'assocstats'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/s2.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'spanel'
  All declared Imports should be used.
Plot.ll: warning in axis(1, chpt - n * 2.5/100, tick = F, lab =
  expression(hat(k)), cex.axis = 1, col.axis = "red"): partial argument
  match of 'lab' to 'labels'
plot,SaemixSimData : .local: no visible binding for global variable
  'name.group'
separator: no visible global function definition for 'make.lp'
separator: no visible global function definition for 'set.column'
separator: no visible global function definition for 'set.rhs'
separator: no visible global function definition for 'set.constr.type'
separator: no visible global function definition for 'set.objfn'
separator: no visible global function definition for 'set.bounds'
separator: no visible global function definition for 'lp.control'
separator: no visible global function definition for 'get.variables'
separator: no visible global function definition for 'set.basis'
separator: no visible global function definition for
  'get.dual.solution'
distanceLimitedPDSIZ,downLog-perpendicularDistance-dlsNumeric : .local:
  warning in matrix(c(os.len, 0, 1), nr = 1): partial argument match of
  'nr' to 'nrow'
downLogs,numeric-missing : .local: warning in matrix(c(xlim, ylim), nr
  = 2, byrow = TRUE, dimnames = list(c("x", "y"), c("min", "max"))):
  partial argument match of 'nr' to 'nrow'
standingTrees,numeric-missing : .local: warning in matrix(c(xlim,
  ylim), nr = 2, byrow = TRUE, dimnames = list(c("x", "y"), c("min",
  "max"))): partial argument match of 'nr' to 'nrow'
clipStemsToTract,downLogs-SpatialPolygons : .local: no visible global
  function definition for 'gIntersects'
clipStemsToTract,downLogs-SpatialPolygons : .local: no visible global
  function definition for 'gIntersection'
izGrid,matrix-Tract : .local: no visible global function definition for
  'intersectExtent'
izGridMirage,InclusionZone-mirageTract : .local: no visible global
  function definition for 'gIntersects'
izGridMirage,InclusionZone-mirageTract : .local : mirageSection: no
  visible global function definition for 'gIntersection'
predict.samEL: no visible global function definition for 'ns'
predict.samHL: no visible global function definition for 'ns'
predict.samLL: no visible global function definition for 'ns'
predict.samQL: no visible global function definition for 'ns'
samEL: no visible global function definition for 'ns'
samHL: no visible global function definition for 'ns'
samLL: no visible global function definition for 'ns'
samQL: no visible global function definition for 'ns'
foldchange.seq.twoclass.paired: no visible global function definition
  for 'rowMedians'
foldchange.seq.twoclass.unpaired: no visible global function definition
  for 'rowMedians'
samr: no visible global function definition for 'impute.knn'
samr.xl.impute.data: no visible global function definition for
  'impute.knn'
samr.xl.impute.data: no visible binding for global variable
  'samr.xl.var.knn.neighbors'
my.SOnePro: missing arguments not allowed in calls to 'c'
slassoEst: no visible global function definition for 'lars'
slassoEst: no visible global function definition for 'predict.lars'
convert.infusion: no visible global function definition for 'size'
create.intervals: no visible global function definition for 'size'
create.intervals: no visible global function definition for 'transpose'
dde.model: no visible global function definition for 'size'
dde.model: no visible global function definition for 'transpose'
de.output: no visible global function definition for 'size'
explicit.model: no visible global function definition for 'size'
finalize.report: no visible global function definition for 'transpose'
finalize.report: no visible global function definition for 'size'
fitmle : obj.fun: no visible global function definition for 'size'
fitmle.cov: no visible global function definition for 'transpose'
get.cov.matrix: no visible global function definition for 'size'
get.parms.data: no visible global function definition for 'size'
get.secondary: no visible global function definition for 'transpose'
init.cond: no visible global function definition for 'size'
init.update: no visible global function definition for 'size'
input.scaling: no visible global function definition for 'size'
make.dosing: no visible global function definition for 'size'
ode.model: no visible global function definition for 'size'
ode.model: no visible global function definition for 'transpose'
problem.eval: no visible global function definition for 'size'
residual.report: no visible global function definition for 'size'
scarabee.check.model: no visible global function definition for 'size'
scarabee.gridsearch : grid.obj.fun: no visible global function
  definition for 'size'
scarabee.read.data: no visible global function definition for 'size'
scarabee.read.parms: no visible global function definition for 'size'
simulation.report: no visible global function definition for 'size'
weighting: no visible global function definition for 'size'
prime.factor: no visible binding for global variable 'primlist'
c,scidbdf : .local: warning in build_dim_schema(x, newname = j):
  partial argument match of 'newname' to 'newnames'
scio.refit: no visible global function definition for 'QUIC'
CreatePssm: no visible binding for global variable 'training'
scrape: no visible global function definition for 'getURLAsynchronous'
scrape: no visible binding for global variable 'xmlParse'
scrape: no visible binding for global variable 'htmlParse'
buildSNPannotation: no visible global function definition for 'db'
buildSNPannotation: no visible global function definition for
  'dbListFields'
buildSNPannotation: no visible global function definition for
  'dbGetQuery'
fblr: no visible global function definition for 'mvrnorm'
fblr.weight: no visible global function definition for 'mvrnorm'
Namespaces in Imports field not imported from:
  'gbm' 'graphics' 'ncdf4' 'rgdal' 'sp'
  All declared Imports should be used.
ConnCompLabel: no visible global function definition for 'setValues'
SigDiff: no visible global function definition for 'setValues'
asc.from.raster: no visible global function definition for 'getValues'
aspect: no visible global function definition for 'setValues'
grid.area: no visible global function definition for 'setValues'
grid.perimeter: no visible global function definition for 'setValues'
lcmw: no visible global function definition for 'setValues'
raster.from.asc: no visible global function definition for 'raster'
raster.from.asc: no visible global function definition for
  'projection<-'
raster.from.asc: no visible global function definition for 'setValues'
slope: no visible global function definition for 'setValues'
sp.from.asc: no visible global function definition for 'CRS'
sp.from.asc: no visible global function definition for 'GridTopology'
sp.from.asc: no visible global function definition for
  'SpatialGridDataFrame'
sealasso: no visible global function definition for 'lars'
weight.calc: no visible global function definition for 'lars'
dathomog: no visible global function definition for 'kde2d'
fitMod: no visible global function definition for 'survreg'
fitswavecav: no visible global function definition for 'year'
prepData: no visible global function definition for 'year'
prepData: no visible global function definition for 'month'
prepData: no visible global function definition for 'day'
rosBoxPlot: no visible global function definition for 'ros'
GKhat.env: no visible global function definition for 'Gest'
GKhat.env: no visible global function definition for 'rpoispp'
GKhat.env: no visible global function definition for 'Kest'
GKhat.env: no visible global function definition for 'runifpoint'
Okriging: no visible global function definition for 'point'
Okriging: no visible global function definition for 'krige'
eda6: no visible global function definition for 'qqPlot'
makeppp: no visible global function definition for 'ppp'
nnGK.ppp: no visible global function definition for 'Gest'
nnGK.ppp: no visible global function definition for 'Kest'
nnGKenv.ppp: no visible global function definition for 'Gest'
nnGKenv.ppp: no visible global function definition for 'Kest'
plotkriged: no visible global function definition for 'point'
quad.chisq.ppp: no visible global function definition for 'ppp'
quad.poisson.ppp: no visible global function definition for 'ppp'
vario: no visible global function definition for 'point'
vario: no visible global function definition for 'pair'
vario: no visible global function definition for 'est.variogram'
vario: no visible global function definition for 'plot.point'
vario: no visible global function definition for 'spacecloud'
vario: no visible global function definition for 'spacebox'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.4Mb
.use.spgrass6: no visible global function definition for 'listw2mat'
.use.spgrass6: no visible global function definition for 'sn2listw'
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
semdiag: no visible global function definition for 'sem'
semdiag.robfit.r: no visible global function definition for 'sem'
semdiag.robfit1.r: no visible global function definition for 'sem'
computeProjectionFromKernel : <anonymous>: no visible global function
  definition for 'irlba'
ChiSquaredLRTest: no visible global function definition for 'dmvnorm'
NormalTheoryLRTest: no visible global function definition for 'dmvnorm'
semPlotModel.mplus.model: no visible global function definition for
  'readModels'
plot.sempls: no visible global function definition for
  'trellis.par.get'
plot.sempls: no visible global function definition for
  'trellis.par.set'
plot.sempls: no visible global function definition for 'xyplot'
plsm2sem.plsm: no visible global function definition for 'specifyModel'
plsm2sem.plsm: no visible global function definition for
  'specify.model'
read.splsm: no visible global function definition for
  'xmlInternalTreeParse'
read.splsm: no visible global function definition for 'xpathApply'
read.splsm: no visible binding for global variable 'xmlGetAttr'
summary.bootsempls: no visible global function definition for 'boot.ci'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/semver.Rcheck/00install.out' for details.
Namespace in Imports field not imported from: 'sp'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/SeqFeatR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/seqminer.Rcheck/00install.out' for details.
capture: no visible binding for global variable 'resultText'
restore.session: no visible binding for global variable
  '.save.session.packages'
restore.session: no visible binding for global variable
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.search'
save.session: no visible binding for '<<-' assignment to
  '.save.session.packages'
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'lattice' 'betareg'
A package should be listed in only one of these fields.
Namespaces in Imports field not imported from:
  'betareg' 'lattice'
  All declared Imports should be used.
Packages in Depends field not imported from:
  'betareg' 'lattice'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
indirectCalibration: no visible global function definition for
  'betareg'
xy.plot.lat: no visible global function definition for 'xyplot'
xy.plot.lat: no visible global function definition for 'strip.custom'
xy.plot.lat : <anonymous>: no visible global function definition for
  'panel.abline'
xy.plot.lat : <anonymous>: no visible global function definition for
  'panel.xyplot'
xy.plot.lat : <anonymous>: no visible global function definition for
  'panel.text'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/sf.Rcheck/00install.out' for details.
plotBoundary: no visible global function definition for
  'scale_y_continuous'
distLaplacian: no visible global function definition for 'sparseMatrix'
laplacian: no visible global function definition for 'sparseMatrix'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/sharx.Rcheck/00install.out' for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    www   9.4Mb
Namespaces in Imports field not imported from:
  'DT' 'gridExtra' 'latticeExtra' 'msm'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'shinyBS' 'shinythemes'
  All declared Imports should be used.
Package required and available but unsuitable version: 'CompQuadForm'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
footpoint.nodes: no visible global function definition for
  'coordinates'
nt.connect: no visible global function definition for 'bbox'
nt.connect: no visible global function definition for
  'as.SpatialLines.SLDF'
nt.connect: no visible global function definition for
  'SpatialLinesDataFrame'
ptsinnt.view: no visible global function definition for 'bbox'
readshpnw: no visible global function definition for 'coordinates'
Undocumented S4 methods:
  generic '[' and siglist 'Prob0,ANY,missing,ANY'
  generic '[' and siglist 'bFdr,ANY,missing,ANY'
  generic '[' and siglist 'basicFdr,ANY,missing,ANY'
  generic '[' and siglist 'eFdr,ANY,missing,ANY'
  generic '[' and siglist 'estimate,ANY,missing,ANY'
  generic '[' and siglist 'loss,ANY,missing,ANY'
  generic '[' and siglist 'pseudoFdr,ANY,missing,ANY'
  generic '[' and siglist 'sFdr,ANY,missing,ANY'
  generic '[' and siglist 'sortableEstimate,ANY,missing,ANY'
  generic '[' and siglist 'unsortableEstimate,ANY,missing,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
bayesMVN: no visible global function definition for 'rmultireg'
bayestwoNorm: no visible global function definition for 'runireg'
overlap: no visible global function definition for 'overlap.xypolygon'
panelcontour: no visible global function definition for 'kde2d'
siardensityplot: no visible global function definition for 'hdr'
siarhdrs: no visible global function definition for 'hdr'
siarhdrs: no visible global function definition for 'geweke.diag'
siarproportionbygroupplot: no visible global function definition for
  'hdr'
siarproportionbysourceplot: no visible global function definition for
  'hdr'
Running examples in 'SIBER-Ex.R' failed
The error most likely occurred in:

> ### Name: fitEllipse
> ### Title: Fit a multivariate normal distribution to x and y data using
> ###   jags
> ### Aliases: fitEllipse
> 
> ### ** Examples
> 
> x <- stats::rnorm(50)
> y <- stats::rnorm(50)
> parms <- list()
> parms$n.iter <- 2 * 10^3
> parms$n.burnin <- 500
> parms$n.thin <- 2     
> parms$n.chains <- 2    
> priors <- list()
> priors$R <- 1 * diag(2)
> priors$k <- 2
> priors$tau.mu <- 1.0E-3
> fitEllipse(x, y, parms, priors)
Error: .onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.2/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 197-216 (Introduction-to-SIBER.Rmd) 
Error: processing vignette 'Introduction-to-SIBER.Rmd' failed with diagnostics:
.onLoad failed in loadNamespace() for 'rjags', details:
  call: fun(libname, pkgname)
  error: The environment variable JAGS_HOME is set to
c:/Program Files/JAGS/JAGS-4.0.0
but no JAGS installation can be found there
Execution halted
filter.mRMR.default: no visible global function definition for
  'discretize'
gaussian.default: no visible global function definition for
  'cov.shrink'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'is.struct'
Error in re-building vignettes:
  ...
Quitting from lines 241-246 (fitsde.Rmd) 
Error: processing vignette 'fitsde.Rmd' failed with diagnostics:
non-finite value supplied by optim
Execution halted
clusterSetup,ANY-data.frame-SampleControl : .local: no visible binding
  for global variable 'cnam'
clusterSetup,ANY-data.frame-TwoStageControl : .local: no visible
  binding for global variable 'cnam'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/simmr.Rcheck/00install.out' for details.
Simpsons: no visible global function definition for 'Mclust'
simSummary: no visible global function definition for 'abind'
simSummary_unitTests: no visible global function definition for
  'clearLog'
simSummary_unitTests: no visible global function definition for
  'runTest'
simSummary_unitTests: no visible global function definition for
  'svSuite'
simSummary_unitTests: no visible global function definition for 'Log'
simSummary_unitTests: no visible global function definition for 'stats'
simSummary_unitTests: no visible global function definition for
  'metadata'
simSummary_unitTests: no visible global function definition for
  'errorLog'
Namespace in Imports field not imported from: 'pracma'
  All declared Imports should be used.
Namespace in Imports field not imported from: 'mcmc'
  All declared Imports should be used.
prop : <anonymous>: no visible global function definition for
  'startsWith'
Running examples in 'sjstats-Ex.R' failed
The error most likely occurred in:

> ### Name: prop
> ### Title: Proportion of values in a vector
> ### Aliases: prop
> 
> ### ** Examples
> 
> data(efc)
> 
> # proportion of value 1 in e42dep
> prop(efc, e42dep == 1)
Error in FUN(X[[i]], ...) : could not find function "startsWith"
Calls: prop -> lapply -> FUN
Execution halted
cvskda: no visible global function definition for 'detectCores'
cvskda: no visible global function definition for 'makeCluster'
cvskda: no visible global function definition for 'clusterApplyLB'
cvskda: no visible global function definition for 'mclapply'
cvskda: no visible global function definition for 'stopCluster'
qskewhyp: multiple local function definitions for 'zeroFn' with
  different formal arguments
fitted.sma: no visible global function definition for 'join'
File 'smco/R/smco.R':
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
File 'SMC/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("##\n", "## Sequential Monte Carlo Package (SMC)\n",     "##\n", "## Functionality: sequential Monte Carlo (SMC) or sequential importance\n",     "## sampling (SIS) or hidden Markov models (HMM), particle filter (PF)\n",     "## and auxiliary particle filter (APF)\n", "##\n", "## Use: \"help(package = SMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

See section 'Good practice' in '?.onAttach'.
em: no visible global function definition for 'coxph'
smcure: no visible global function definition for 'coxph'
smcure: no visible global function definition for 'survreg'
simDic: no visible global function definition for 'simil'
simDoc: no visible global function definition for 'simil'
getRoughnessMatrix: no visible global function definition for 'ns'
plotSmeRaw: no visible global function definition for 'xyplot'
plotSmeRaw : <anonymous>: no visible global function definition for
  'panel.xyplot'
plotSmeRaw : <anonymous>: no visible global function definition for
  'panel.lines'
sme.default: no visible global function definition for 'ns'
sme.list: no visible binding for global variable 'ns'
sme.list : <anonymous>: no visible global function definition for 'ns'
vcov.sme: no visible global function definition for 'ns'
coxph.disparity: no visible global function definition for 'basehaz'
disparity.glm : <anonymous>: no visible global function definition for
  'gamma.shape'
Namespaces in Imports field not imported from:
  'compiler' 'lmtest'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'MASS' 'nlme' 'survival'
  All declared Imports should be used.
sfApply: no visible global function definition for 'parApply'
sfClusterApply: no visible global function definition for
  'clusterApply'
sfClusterApplyLB: no visible global function definition for
  'clusterApplyLB'
sfClusterCall: no visible global function definition for 'clusterCall'
sfClusterSetupRNG: no visible global function definition for
  'clusterSetupRNG'
sfClusterSetupRNGstream: no visible global function definition for
  'clusterSetupRNGstream'
sfClusterSetupSPRNG: no visible global function definition for
  'clusterSetupSPRNG'
sfClusterSplit: no visible global function definition for
  'clusterSplit'
sfInit: no visible global function definition for
  'setDefaultClusterOptions'
sfInit: no visible global function definition for 'makeCluster'
sfInit: no visible global function definition for 'makeNWScluster'
sfInit: no visible global function definition for 'makeMPIcluster'
sfLapply: no visible global function definition for 'parLapply'
sfMM: no visible global function definition for 'parMM'
sfSapply: no visible global function definition for 'parSapply'
sfStop: no visible global function definition for 'stopCluster'
WGassociation: no visible global function definition for 'mclapply'
interleave: no visible global function definition for 'mclapply'
setupSNP: no visible global function definition for 'mclapply'
summary.setupSNP: no visible global function definition for 'mclapply'
tableHWE: no visible global function definition for 'mclapply'
convert.genes.to.GRanges: no visible global function definition for
  'GRanges'
convert.genes.to.GRanges: no visible global function definition for
  'IRanges'
convert.genes.to.GRanges: no visible global function definition for
  'metadata<-'
convert.pos.to.GRanges: no visible global function definition for
  'GRanges'
convert.pos.to.GRanges: no visible global function definition for
  'IRanges'
convert.variants.to.GRanges: no visible global function definition for
  'GRanges'
convert.variants.to.GRanges: no visible global function definition for
  'IRanges'
convert.variants.to.GRanges: no visible global function definition for
  'metadata<-'
find.overlapping.genes: no visible global function definition for
  'findOverlaps'
find.overlapping.genes: no visible global function definition for
  'subjectHits'
get.mgi.features: no visible global function definition for 'TabixFile'
get.mgi.features: no visible global function definition for
  'headerTabix'
get.mgi.features: no visible global function definition for 'scanTabix'
get.strains: no visible global function definition for 'TabixFile'
get.strains: no visible global function definition for 'headerTabix'
get.variants: no visible global function definition for 'TabixFile'
get.variants: no visible global function definition for 'headerTabix'
get.variants: no visible global function definition for 'scanTabix'
get.hnx.B.initialW: no visible global function definition for
  'normalize.vector'
get.hnx.B.initialW: no visible global function definition for 'adiag'
my.normdata.gen: no visible global function definition for 'mvrnorm'
odc.cv: no visible global function definition for 'ginv'
odc.optimallambda2: no visible global function definition for 'tr'
odc.optimallambda2: no visible global function definition for 'ginv'
eplot: no visible global function definition for 'trellis.par.get'
eplot: no visible global function definition for 'trellis.par.set'
eplot: no visible global function definition for 'xyplot'
munsell_to_rgb: no visible global function definition for 'munsell2rgb'
roots: no visible global function definition for 'areapl'
roots: no visible global function definition for 'point.in.polygon'
skeletal: no visible global function definition for 'areapl'
skeletal: no visible global function definition for 'point.in.polygon'
turnoverFit: no visible binding for global variable 'IntCal13'
turnoverFit: no visible binding for global variable 'Hua2013'
initialize,NlModel : .local: no visible global function definition for
  'TransportDecompositionOperator.new'
plot3d: no visible global function definition for 'persp3d'
SOS: no visible global function definition for 'getCurlHandle'
Namespaces in Imports field not imported from:
  'gtools' 'hashmap' 'uuid'
  All declared Imports should be used.
mHP.b : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.c : crossingProbDiff: no visible global function definition for
  'Miwa'
glasso.miss: no visible global function definition for 'glasso'
glasso.miss: no visible global function definition for 'Solve'
space.miss: no visible global function definition for 'Solve'
SJ: no visible binding for global variable 'bs'
SJ: no visible global function definition for 'get.adjacency'
SJ : <anonymous>: no visible global function definition for
  'graph.adjacency'
SJ: no visible binding for global variable 'ecount'
SJ.dag: no visible binding for global variable 'bs'
SJ.dag : <anonymous>: no visible global function definition for
  'graph.adjacency'
SJ.dag: no visible binding for global variable 'ecount'
SJpath: no visible global function definition for 'get.adjacency'
SJpath : <anonymous>: no visible global function definition for
  'graph.adjacency'
generate.dag.data: no visible global function definition for 'vcount'
generate.dag.data: no visible global function definition for
  'topological.sort'
generate.dag.data: no visible global function definition for
  'neighbors'
grpsel: no visible global function definition for 'Matrix'
moralize: no visible global function definition for 'vcount'
moralize: no visible global function definition for 'as.undirected'
moralize: no visible global function definition for 'get.adjacency'
moralize: no visible global function definition for 'add.edges'
moralize: no visible global function definition for 'simplify'
plot.SJ: no visible global function definition for
  'layout.fruchterman.reingold'
plot.SJ.dag: no visible global function definition for
  'layout.fruchterman.reingold'
print.SJ: no visible binding for global variable 'ecount'
print.SJ: no visible global function definition for 'ecount'
print.SJ.dag: no visible binding for global variable 'ecount'
print.SJ.dag: no visible global function definition for 'ecount'
rdag: no visible global function definition for 'graph.adjacency'
cophen: no visible global function definition for 'Ntip'
get.descendants.of.node: no visible global function definition for
  'Ntip'
phy.deresolve: no visible global function definition for
  'branching.times'
phy.deresolve: no visible global function definition for 'Ntip'
phy.dotplot: no visible global function definition for 'tiplabels'
phy.nodetimes: no visible global function definition for 'Ntip'
phy.nodetimes: no visible global function definition for
  'branching.times'
reorderspacodiobj: no visible global function definition for 'drop.tip'
resamp.phy: no visible global function definition for 'Ntip'
resamp.phy: no visible global function definition for 'branching.times'
spacodi.all.nodes: no visible global function definition for 'subtrees'
spacodi.all.nodes: no visible global function definition for
  'branching.times'
spacodi.exp.nodes: no visible global function definition for 'subtrees'
spacodi.treeplot: no visible global function definition for
  'diverge_hcl'
spacodi.treeplot: no visible global function definition for
  'nodelabels'
Namespace in Imports field not imported from: 'rstudioapi'
  All declared Imports should be used.
livy_statement_parse_response : scalaTypeOfArray: possible error in
  regexec("^\\[L(.*);", scalaType, perl = TRUE): unused argument (perl
  = TRUE)
SPARQL: no visible binding for global variable 'getURL'
SPARQL: no visible binding for global variable 'xmlParse'
SPARQL: no visible global function definition for 'getNodeSet'
SPARQL: no visible global function definition for 'xpathApply'
SPARQL: no visible binding for global variable 'postForm'
get_attr: no visible global function definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'getNodeSet'
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for 'xmlDoc'
get_value: no visible global function definition for 'xmlDoc'
get_value: no visible global function definition for 'xpathSApply'
get_value: no visible binding for global variable 'xmlValue'
get_value: no visible global function definition for 'xpathApply'
get_value: no visible binding for global variable 'xmlGetAttr'
getcoef_list: no visible global function definition for 'drop0'
sparsepredict: no visible global function definition for
  'lambda.interp'
sparsepredict: no visible global function definition for 'nonzeroCoef'
bbox_to_SpatialPolygons: no visible global function definition for
  'CRS'
bbox_to_SpatialPolygons: no visible global function definition for
  'Polygon'
bbox_to_SpatialPolygons: no visible global function definition for
  'Polygons'
bbox_to_SpatialPolygons: no visible global function definition for
  'SpatialPolygons'
list.raster.files: no visible global function definition for 'CRS'
list.raster.files: no visible global function definition for
  'spTransform'
list.raster.files: no visible global function definition for
  'SpatialPolygonsDataFrame'
list.raster.files: no visible global function definition for 'spChFIDs'
projectRaster_rigorous : chunk_function: no visible global function
  definition for 'spTransform'
projectRaster_rigorous : chunk_function: no visible global function
  definition for 'CRS'
spatial_sync_raster: no visible global function definition for 'bbox'
spatial_sync_vector: no visible global function definition for
  'spTransform'
spatial_sync_vector: no visible global function definition for 'CRS'
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    data   3.4Mb
    doc    5.0Mb
    help   4.8Mb
    libs   1.2Mb
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
err.default: no visible global function definition for 'prediction'
err.default: no visible global function definition for 'performance'
rgl.sphMW: no visible global function definition for 'plot3d'
rgl.sphcirc: no visible global function definition for 'rotate3d'
rgl.sphcirc: no visible global function definition for 'lines3d'
rgl.sphgrid: no visible global function definition for 'open3d'
rgl.sphgrid: no visible global function definition for 'plot3d'
rgl.sphgrid: no visible global function definition for 'lines3d'
rgl.sphgrid: no visible global function definition for 'text3d'
rgl.sphpoints: no visible global function definition for 'points3d'
rgl.sphsun: no visible global function definition for 'plot3d'
rgl.sphtext: no visible global function definition for 'text3d'
monophyly: no visible global function definition for 'prop.part'
monophylyBoot: no visible global function definition for 'nj'
monophylyBoot: no visible global function definition for 'boot.phylo'
monophylyBoot : <anonymous>: no visible global function definition for
  'root'
monophylyBoot : <anonymous>: no visible global function definition for
  'nj'
monophylyBoot: no visible global function definition for 'prop.part'
polyBalance: no visible global function definition for 'node.depth'
read.BOLD: no visible global function definition for 'as.DNAbin'
read.GB: no visible global function definition for 'as.DNAbin'
slideAnalyses: no visible global function definition for 'nj'
slideAnalyses: no visible global function definition for 'node.depth'
slideAnalyses: no visible binding for global variable 'nj'
tree.comp: no visible global function definition for 'unroot'
tree.comp: no visible global function definition for 'prop.part'
tree.comp: no visible global function definition for 'node.depth'
cv.spikeslab: no visible global function definition for 'mclapply'
gnet.get: no visible global function definition for 'lars'
gnet.get: no visible global function definition for 'predict.lars'
plot.spikeslab: no visible global function definition for 'plot.lars'
sparsePC.spikeslab : get.pc : <anonymous>: no visible global function
  definition for 'randomForest'
sparsePC.spikeslab: no visible global function definition for
  'randomForest'
spikeslab: no visible global function definition for 'randomForest'
SPIn: no visible global function definition for 'solve.QP'
Ell.Theta: no visible global function definition for 'ell.theta'
Namespace in Imports field not imported from: 'geoR'
  All declared Imports should be used.
Errors in running code in vignettes:
when running code in 'SQUAREM.Rnw'
  ...
+     Ap <- pvec * tA
+     pnew <- colMeans(t(Ap)/colSums(Ap))
+     pnew * (pnew > 0)
+ }

> library(interval)

  When sourcing 'SQUAREM.R':
Error: there is no package called 'interval'
Execution halted
File 'sROC/R/onload.R':
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

See section 'Good practice' in '?.onAttach'.
fit.model: no visible global function definition for 'hadamard'
station: no visible binding for global variable 'WTdiff'
stkde: no visible global function definition for 'npudensbw'
stkde: no visible global function definition for 'npudens'
stkde.base: no visible global function definition for 'npudensbw'
stkde.base: no visible global function definition for 'npudens'
stkde.sig: no visible global function definition for 'SpatialPoints'
stkde.sig: no visible global function definition for 'spsample'
stkde.sig: no visible global function definition for 'bbox'
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
File 'StanHeaders/libs/i386/StanHeaders.dll':
  Found 'printf', possibly from 'printf' (C)
    Objects: 'cvodes/src/sundials/sundials_direct.o',
      'cvodes/src/nvec_ser/nvector_serial.o'
  Found 'putchar', possibly from 'putchar' (C)
    Objects: 'cvodes/src/sundials/sundials_direct.o',
      'cvodes/src/nvec_ser/nvector_serial.o'
File 'StanHeaders/libs/x64/StanHeaders.dll':
  Found 'printf', possibly from 'printf' (C)
    Objects: 'cvodes/src/sundials/sundials_direct.o',
      'cvodes/src/nvec_ser/nvector_serial.o'
  Found 'putchar', possibly from 'putchar' (C)
    Objects: 'cvodes/src/sundials/sundials_direct.o',
      'cvodes/src/nvec_ser/nvector_serial.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.
as.spikeTrain: no visible global function definition for 'spikeTimes'
gamObj.gampsth: no visible binding for global variable 'PoissonF'
gammaMLE: multiple local function definitions for 'rFct' with different
  formal arguments
gssObj.gsspsth: no visible binding for global variable 'gfit'
gssObj.gsspsth0: no visible binding for global variable 'gfit'
gsslockedTrain: no visible global function definition for 'gssanova'
gsslockedTrain0: no visible global function definition for 'gssanova0'
gsspsth: no visible global function definition for 'gssanova'
gsspsth0: no visible global function definition for 'gssanova0'
invgaussMLE: multiple local function definitions for 'rFct' with
  different formal arguments
lines.CountingProcessSamplePath: no visible binding for global variable
  'st'
mkAR: no visible binding for global variable 'lN.1'
mkM2U: no visible global function definition for 'ssden'
mkM2U : <anonymous>: no visible global function definition for 'dssden'
mkM2U : dFct: no visible global function definition for 'dssden'
mkPostSimAnalysis: no visible global function definition for
  'findGlobals'
qqDuration: no visible binding for global variable 'yi'
qqDuration: no visible binding for global variable 'si'
thinProcess: no visible binding for global variable 'targetFct'
thinProcess: no visible binding for global variable 'posMax'
rg.robmva: no visible global function definition for 'cov.mve'
Namespaces in Imports field not imported from:
  'magrittr' 'rpart'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/StatMethRank.Rcheck/00install.out' for details.
getHb: no visible binding for global variable 'masshb'
getHbgrid: no visible binding for global variable 'masshbgrid'
showComposition: no visible binding for global variable 'compositions'
testComposition: no visible binding for global variable 'compositions'
File 'stepPlr/libs/i386/stepPlr.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'cg_descent.o'
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
    Object: 'cg_descent.o'
File 'stepPlr/libs/x64/stepPlr.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'cg_descent.o'
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
    Object: 'cg_descent.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.
Namespaces in Imports field not imported from:
  'SnowballC' 'tm'
  All declared Imports should be used.
DetailOpLines: no visible global function definition for
  'tkProgressBar'
DetailOpLines: no visible global function definition for
  'setTkProgressBar'
MultiTrainWithInventory: no visible global function definition for
  'tkProgressBar'
MultiTrainWithInventory: no visible global function definition for
  'setTkProgressBar'
SimHistory: no visible global function definition for 'tkProgressBar'
SimHistory: no visible global function definition for
  'setTkProgressBar'
.rp.stan3d: no visible global function definition for 'rp.control'
.rp.stan3d: no visible global function definition for 'rp.slider'
.rp.stan3d: no visible global function definition for 'rp.button'
.rp.stan3d : <anonymous>: no visible global function definition for
  'par3d'
.rp.stan3d : <anonymous>: no visible global function definition for
  'rotationMatrix'
.rp.stan3d: no visible global function definition for 'rp.do'
.rp.stan3d: no visible global function definition for 'rp.block'
.setBG: no visible global function definition for 'surface3d'
.setPlot: no visible global function definition for 'plot3d'
.setPlot: no visible global function definition for 'axis3d'
.setPlot: no visible global function definition for 'par3d'
.setPlot: no visible global function definition for 'aspect3d'
.setPlot: no visible global function definition for 'rotationMatrix'
.stan3d.redraw: no visible global function definition for 'par3d'
.stan3d.redraw: no visible global function definition for 'rgl.pop'
.stan3d.redraw: no visible binding for global variable 'spheres3d'
rlgcp: no visible global function definition for 'bbox'
stan: no visible global function definition for 'lines3d'
stan: no visible global function definition for 'segments3d'
stan: no visible global function definition for 'points3d'
bin.info.cubature : compute.fun: no visible global function definition
  for 'adaptIntegrate'
tess.info : new.points: no visible global function definition for
  'as.points'
tess.info : new.points: no visible global function definition for 'csr'
tess.info.MISER : int.fun: no visible global function definition for
  'as.points'
tess.info.MISER : int.fun: no visible global function definition for
  'inpip'
tessdev: no visible global function definition for 'deldir'
tessdev: no visible global function definition for 'tile.list'
tessdev : sum.l: no visible global function definition for 'as.points'
tessdev : sum.l: no visible global function definition for 'inpip'
tessdev.info : all: no visible global function definition for
  'as.points'
tessdev.info : all: no visible global function definition for 'inpip'
tessresid: no visible global function definition for 'deldir'
tessresid: no visible global function definition for 'tile.list'
tessresid : num: no visible global function definition for 'as.points'
tessresid : num: no visible global function definition for 'inpip'
Namespace in Imports field not imported from: 'sna'
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  'broom' 'car' 'lmerTest' 'pbkrtest'
  All declared Imports should be used.
breakpoints.formula: no visible global function definition for
  '%dopar%'
breakpoints.formula: no visible binding for global variable 'i'
efpFunctional: multiple local function definitions for 'plotProcess'
  with different formal arguments
mefp.efp: multiple local function definitions for 'computeEmpProc' with
  different formal arguments
plot,GBH-ANY : .local: no visible binding for global variable
  'sorted.hyp'
plot,GBH-ANY : .local: no visible binding for global variable 'pval'
plot,GBH-ANY : .local: no visible binding for global variable 'group'
plot,GBH-ANY : .local: no visible binding for global variable 'type'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/subprocess.Rcheck/00install.out' for details.
Namespaces in Imports field not imported from:
  'ISwR' 'MASS' 'corpcor'
  All declared Imports should be used.
subsemble: no visible global function definition for 'detectCores'
subsemble : .make_Z_l: no visible global function definition for
  'parSapply'
subsemble : .make_Z_l: no visible global function definition for
  'makeCluster'
subsemble : .make_Z_l: no visible global function definition for
  'stopCluster'
subsemble: no visible global function definition for 'parSapply'
subsemble: no visible global function definition for 'makeCluster'
subsemble: no visible global function definition for 'stopCluster'
test_subtype_only: no visible global function definition for 'survdiff'
test_subtype_only: no visible global function definition for 'survfit'
playSudoku: no visible global function definition for 'tktoplevel'
playSudoku: no visible global function definition for 'tkwm.title'
playSudoku: no visible global function definition for 'tkrplot'
playSudoku: no visible global function definition for 'tktext'
playSudoku: no visible global function definition for 'tkscrollbar'
playSudoku : <anonymous>: no visible global function definition for
  'tkyview'
playSudoku: no visible global function definition for 'tkconfigure'
playSudoku : <anonymous>: no visible global function definition for
  'tkset'
playSudoku: no visible global function definition for 'tkpack'
playSudoku: no visible global function definition for 'tcl'
playSudoku: no visible global function definition for 'tkcget'
playSudoku : showz: no visible global function definition for
  'tkrreplot'
playSudoku : type: no visible global function definition for 'tkinsert'
playSudoku : type: no visible global function definition for 'tksee'
playSudoku : kb: no visible global function definition for 'tkdestroy'
playSudoku: no visible global function definition for 'tkbind'
playSudoku: no visible global function definition for 'tkwait.window'
.p.1gen: warning in formatC(id, wid = 6): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(s, wid = 4): partial argument match of
  'wid' to 'width'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'dig' to
  'digits'
.p.1gen: warning in formatC(format(c(round(m, digits = digits),
  0.735))[1], wid = 7, dig = 3): partial argument match of 'wid' to
  'width'
predict.pelora: warning in matrix(c((1/(1 + exp(-(X[, 1:(noc[i] + 1)]
  %*% koeff))))), nc = 1): partial argument match of 'nc' to 'ncol'
ridge.coef: warning in diag(apply(X, 2, var) * lambda * nrow(X), nr =
  ncol(X)): partial argument match of 'nr' to 'nrow'
superdiag: no visible global function definition for 'as.mcmc.list'
superdiag: no visible global function definition for 'as.mcmc'
superdiag: no visible global function definition for 'geweke.diag'
superdiag: no visible global function definition for 'heidel.diag'
superdiag: no visible global function definition for 'raftery.diag'
superdiag: no visible global function definition for 'gelman.diag'
gen.y.mat2: no visible global function definition for 'survfit'
superpc.cv: no visible global function definition for 'coxph'
superpc.cv: no visible global function definition for 'coxph.control'
superpc.fit.to.outcome: no visible global function definition for
  'coxph'
superpc.fit.to.outcome: no visible global function definition for
  'coxph.control'
superpc.lrtest.curv: no visible global function definition for 'coxph'
superpc.predictionplot: no visible binding for global variable
  'shrinkages'
superpc.predictionplot: no visible global function definition for
  'survfit'
surv.to.class2: no visible global function definition for 'survfit'
pbc.sample: no visible binding for global variable 'pbc'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

schemper: no visible global function definition for 'survfit'
Est.PH: no visible global function definition for 'coxph'
cvC: no visible global function definition for 'coxph'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   1.5Mb
AER: no visible binding for global variable 'survexp.fr'
AER: no visible global function definition for 'survexp'
LR: no visible binding for global variable 'survexp.fr'
LR: no visible global function definition for 'survexp'
SMR: no visible binding for global variable 'survexp.fr'
SMR: no visible global function definition for 'survexp'
survexp_plot: no visible binding for global variable 'survexp.fr'
survexp_plot: no visible global function definition for 'survfit'
survexp_plot: no visible global function definition for 'survexp'
Est.HR.FUN: no visible global function definition for 'coxph'
Est.HR.FUN: no visible global function definition for 'basehaz'
Ghat.FUN: no visible global function definition for 'survfit'
IDI.INF: no visible global function definition for 'kmcens'
Running examples in 'survminer-Ex.R' failed
The error most likely occurred in:

> ### Name: ggcoxdiagnostics
> ### Title: Diagnostic Plots for Cox Proportional Hazards Model with ggplot2
> ### Aliases: ggcoxdiagnostics
> 
> ### ** Examples
> 
> 
> if(require(RTCGA.clinical)){
+ # TCGA data exmaple (http://cancergenome.nih.gov/)
+ # source("https://bioconductor.org/biocLite.R")
+ # biocLite("RTCGA.clinical") # data for examples
+ # library(RTCGA.clinical) # also loads 'RTCGA' package
+ survivalTCGA(BRCA.clinical, OV.clinical,
+             extract.cols = c("admin.disease_code", "patient.days_to_birth")) -> BRCAOV.survInfo
+ BRCAOV.survInfo$age  <- round((-as.numeric(BRCAOV.survInfo$patient.days_to_birth))/365,2)
+ 
+ library(survival)
+ coxph.fit <- coxph(Surv(times, patient.vital_status) ~ admin.disease_code + age,
+               data = BRCAOV.survInfo)
+ 
+ ggcoxdiagnostics(coxph.fit, ggtheme = theme_dark(), point.col = "white", point.aplha = 0.3)
+ ggcoxdiagnostics(coxph.fit, ggtheme = theme_RTCGA(), # library(RTCGA.clinical)
+  type = "deviance") + ylab('Deviance Residuals')
+ ggcoxdiagnostics(coxph.fit, ggtheme = theme_light(), linear.predictions = FALSE)
+ # ggcoxdiagnostics(coxph.fit, ggtheme = theme_void(), type = "deviance", linear.predictions = FALSE)
+ }
Loading required package: RTCGA.clinical
Loading required package: RTCGA
Loading required package: knitr
Welcome to the RTCGA (version: 1.0.2).
Error: could not find function "survivalTCGA"
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Loading required package: RTCGA
Welcome to the RTCGA (version: 1.0.2).
Quitting from lines 55-64 (Informative_Survival_Plots.Rmd) 
Error: processing vignette 'Informative_Survival_Plots.Rmd' failed with diagnostics:
could not find function "survivalTCGA"
Execution halted
svd3dplot: no visible global function definition for 'wireframe'
svd3dplot: no visible global function definition for 'levelplot'
Namespaces in Imports field not imported from:
  'MASS' 'graphics' 'methods' 'stats'
  All declared Imports should be used.
Package in Depends field not imported from: 'kernlab'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
roccurve: warning in formatC(sum(c1 * cumsum(c2)), digit = 4): partial
  argument match of 'digit' to 'digits'
svmmajtuning: warning in .svmmaj(Z[groups != i, ], y[groups != i],
  lambda = lambda[l], w = w[groups != i], increase.step =
  increase.step, hinge = newHinge, theta = theta, check.positive =
  FALSE, convergence = convergence, ...): partial argument match of
  'hinge' to 'hingef'
auc: no visible global function definition for 'error'
getUpdate: no visible global function definition for 'vanilladot'
getUpdate: no visible global function definition for 'kernelMatrix'
qhat.theta: no visible global function definition for 'kernelMatrix'
roccurve: no visible global function definition for 'error'
svmmaj.default: no visible binding for global variable 'vanilladot'
svmmaj.default: no visible global function definition for 'kpar'
svmmaj2.default: no visible binding for global variable 'vanilladot'
svmmaj2.default: no visible global function definition for 'kpar'
svmmajtuning: no visible binding for global variable 'vanilladot'
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
protocol_junit.svSuiteData: no visible global function definition for
  'xmlNode'
protocol_junit.svSuiteData: no visible global function definition for
  'addChildren'
protocol_junit.svSuiteData: no visible global function definition for
  'saveXML'
protocol_junit.svTestData: no visible global function definition for
  'xmlNode'
protocol_junit.svTestData: no visible global function definition for
  'addChildren'
adjust.linearmodel: no visible global function definition for 'rlm'
confounding: no visible global function definition for 'heatmap.2'
hca.plot: no visible global function definition for 'colorpanel'
hca.plot: no visible global function definition for 'hcluster'
hca.test: no visible global function definition for 'hcluster'
kill.pc: no visible global function definition for 'impute.knn'
prince: no visible global function definition for 'impute.knn'
prince.plot: no visible global function definition for 'heatmap.2'
prince.var.plot: no visible global function definition for 'impute.knn'
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
fj_pl: no visible global function definition for 'getbasismatrix'
fj_pl: no visible global function definition for 'create.bspline.basis'
fj_pl: no visible global function definition for 'getbasispenalty'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/sybilSBML.Rcheck/00install.out' for details.
integrate.polynomial : f: no visible global function definition for
  'dmvnorm'
Namespaces in Imports field not imported from:
  'doParallel' 'foreach' 'parallel'
  All declared Imports should be used.
cleavogram : savecleavogram : savefic: warning in jpeg(file =
  filename): partial argument match of 'file' to 'filename'
fn.V: no visible global function definition for 'LowRankQP'
synth: no visible global function definition for 'LowRankQP'
File 'sys/libs/i386/sys.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'exec.o'
File 'sys/libs/x64/sys.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'exec.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.
Namespace in Imports field not imported from: 'shiny'
  All declared Imports should be used.
cellgram: no visible global function definition for 'grid.rect'
cellgram: no visible global function definition for 'gpar'
cellgram: no visible global function definition for 'grid.segments'
cellgram: no visible global function definition for 'grid.circle'
cellgram: no visible global function definition for 'grid.polygon'
cellgram: no visible global function definition for 'grid.text'
cellgram: no visible global function definition for 'unit'
tableplot.colldiag: no visible global function definition for
  'colldiag'
tableplot.default: no visible global function definition for
  'grid.newpage'
tableplot.default: no visible global function definition for
  'grid.layout'
tableplot.default: no visible global function definition for 'unit'
tableplot.default: no visible global function definition for
  'pushViewport'
tableplot.default: no visible global function definition for 'viewport'
tableplot.default: no visible global function definition for
  'grid.text'
tableplot.default: no visible global function definition for
  'upViewport'
tableplot.default: no visible global function definition for 'gpar'
tableplot.default: no visible global function definition for
  'grid.rect'
tableplot.default: no visible global function definition for
  'popViewport'
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.3Mb
Namespace in Imports field not imported from: 'scales'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/TDA.Rcheck/00install.out' for details.
ConvDiffCoef: no visible global function definition for 'pascal'
DeconTrace: no visible global function definition for 'as.Zpg'
DeconTrace: no visible global function definition for 'butter'
MakeDPZ: no visible global function definition for 'bilinear'
MatchCoefDPZ: no visible global function definition for 'Zpg'
PZ2Coef: no visible global function definition for 'Poly'
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B : A2.n.f: no visible binding for global variable 'ID'
TER.deesc.1.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.1.B: no visible binding for global variable 'ID'
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A1.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A3.f: no visible binding for global variable 'ID'
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : A2.f: no visible binding for global variable 'ID'
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B : B1.f: no visible binding for global variable 'ID'
TER.deesc.A.B: no visible binding for '<<-' assignment to 'ID'
TER.deesc.A.B: no visible binding for global variable 'ID'
installed size is 44.0Mb
  sub-directories of 1Mb or more:
    libs      13.0Mb
    tessdata  30.9Mb
test_pkg : <anonymous>: no visible global function definition for
  '.traceback'
Dif.Surv.Rec: no visible global function definition for 'survfitr'
Plot.Event.Rec: no visible global function definition for 'survfitr'
Plot.Surv.Rec: no visible global function definition for 'survfitr'
Plot.Surv.Rec: no visible global function definition for 'q.search'
Print.Summary: no visible global function definition for 'survfitr'
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.5Mb
    libs   2.2Mb
Namespace in Imports field not imported from: 'irlba'
  All declared Imports should be used.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/textTinyR.Rcheck/00install.out' for details.
determine_replications: no visible global function definition for
  'microbenchmark'
plot.timeit: no visible global function definition for 'ggplot'
plot.timeit: no visible global function definition for 'aes'
plot.timeit: no visible global function definition for 'geom_boxplot'
plot.timeit: no visible global function definition for 'geom_point'
plot.timeit: no visible global function definition for 'xlab'
plot.timeit: no visible global function definition for 'ylab'
plot.timeit: no visible global function definition for 'ggtitle'
plot.timeit: no visible global function definition for 'coord_flip'
timeline: no visible global function definition for 'ggplot'
timeline: no visible global function definition for 'geom_segment'
timeline: no visible global function definition for 'aes_string'
timeline: no visible global function definition for 'geom_rect'
timeline: no visible global function definition for 'geom_text'
timeline: no visible global function definition for 'theme'
timeline: no visible global function definition for 'element_blank'
timeline: no visible global function definition for 'xlab'
timeline: no visible global function definition for 'ylab'
timeline: no visible global function definition for 'xlim'
timeline: no visible global function definition for
  'scale_y_continuous'
timeline: no visible global function definition for 'geom_point'
timeline: no visible global function definition for 'scale_color_grey'
timeline: no visible global function definition for 'geom_hline'
is.Bizday: no visible global function definition for 'isWeekday'
plotCalendarHeatmap: no visible global function definition for 'ddply'
plotCalendarHeatmap: no visible global function definition for '.'
plotCalendarHeatmap: no visible binding for global variable 'year'
plotCalendarHeatmap: no visible binding for global variable 'month'
plotCalendarHeatmap: no visible binding for global variable 'week'
plotCalendarHeatmap: no visible global function definition for 'ggplot'
plotCalendarHeatmap: no visible global function definition for 'aes'
plotCalendarHeatmap: no visible binding for global variable 'monthweek'
plotCalendarHeatmap: no visible binding for global variable 'weekday'
plotCalendarHeatmap: no visible global function definition for
  'geom_tile'
plotCalendarHeatmap: no visible global function definition for
  'facet_grid'
plotCalendarHeatmap: no visible global function definition for
  'scale_fill_gradientn'
projectDate: no visible global function definition for 'holidayNYSE'
projectDate: no visible global function definition for
  'sparse.model.matrix'
boot_autocov: no visible global function definition for 'tsboot'
boot_spec: no visible global function definition for 'tsboot'
FLXmclust.Density: no visible global function definition for 'dmvnorm'
FLXmclust.Estimate: no visible global function definition for 'flexmix'
FLXmclust.Estimate: no visible global function definition for
  'FLXmclust'
coefmclust: no visible global function definition for 'parameters'
flexmix.Estimate: no visible global function definition for 'flexmix'
flexmix.Estimate: no visible global function definition for 'FLXglm'
EMN: no visible global function definition for 'dmvnorm'
EMN: no visible global function definition for 'pmvnorm'
EMT: no visible global function definition for 'GenzBretz'
EMT: no visible global function definition for 'dmvt'
EMT: no visible global function definition for 'pmvt'
MomemNT: no visible global function definition for 'pmvnorm'
MomemNT: no visible global function definition for 'dmvnorm'
TT.moment: no visible global function definition for 'GenzBretz'
TT.moment: no visible global function definition for 'pmvt'
TT.moment: no visible global function definition for 'dmvt'
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.8Mb
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: eval(code, new_test_environment)
  3: eval(expr, envir, enclos)
  4: expect_is(trakt.user.watchlist(user = sample_user, type = "movies", extended = "min"), 
         "data.frame") at test_user.R:25
  5: expect_that(object, is_a(class), info, label)
  6: condition(object)
  7: paste0(class(x), collapse = ", ")
  8: trakt.user.watchlist(user = sample_user, type = "movies", extended = "min")
  9: convert_datetime(response)
  10: stop("Object type not supported")
  
  Error: Test failures
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/TreeBUGS.Rcheck/00install.out' for details.
mytree.asymmetric.age: no visible global function definition for
  'collapse.singles'
mytree.asymmetric.age: no visible global function definition for
  'drop.fossil'
mytree.asymmetric.taxa: no visible global function definition for
  'collapse.singles'
mytree.asymmetric.taxa: no visible global function definition for
  'drop.fossil'
mytree.symmetric.age: no visible global function definition for
  'collapse.singles'
mytree.symmetric.age: no visible global function definition for
  'drop.fossil'
mytree.symmetric.taxa: no visible global function definition for
  'collapse.singles'
mytree.symmetric.taxa: no visible global function definition for
  'drop.fossil'
plot.tkm: no visible global function definition for 'plotcluster'
plot.tkm: no visible global function definition for 'discrcoord'
HtoGp: no visible global function definition for 'odd'
HtoGp: no visible global function definition for 'even'
trioGxE: no visible global function definition for 'qtnorm'
trioplot: no visible global function definition for 'gam'
sim.cont: no visible global function definition for 'lsoda'
TSget,character-TSfameLocalConnection : .local: no visible global
  function definition for 'zoo'
TSget,character-TSfameServerConnection : .local: no visible global
  function definition for 'zoo'
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for 'index.search'
plotDominationGraph: no visible global function definition for
  'graph.adjacency'
plotDominationGraph: no visible global function definition for
  'layout.norm'
sampleCombinations: no visible global function definition for
  'qrng_alloc'
sampleCombinations: no visible global function definition for
  'qrng_get'
tunePareto: no visible global function definition for 'sfLibrary'
tunePareto : <anonymous>: no visible global function definition for
  'sfLibrary'
tunePareto: no visible global function definition for 'sfExport'
tunePareto: no visible global function definition for 'sfLapply'
tunePareto.NaiveBayes: no visible binding for global variable
  'NaiveBayes'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/uaparserjs.Rcheck/00install.out' for details.
uniCoxCV: no visible global function definition for 'coxph'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/uroot.Rcheck/00install.out' for details.
File 'UScensus2010/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("\n")
    packageStartupMessage(paste("Package ", dscr$Package, ": ", dscr$Title,     "\n", "Version ", dscr$Version, " created on ", dscr$Date,     ".\n", sep = ""))
    packageStartupMessage(paste("Zack Almquist, University of California-Irvine\nne\n",     sep = ""))
    packageStartupMessage("For citation information, type citation(\"UScensus2010\").")
    packageStartupMessage("Type help(package=UScensus2010) to get started.")

See section 'Good practice' in '?.onAttach'.
File 'uuid/libs/i386/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'
File 'uuid/libs/x64/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
mcmc.estimate: no visible global function definition for '%dopar%'
mcmc.estimate: no visible global function definition for 'foreach'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/valr.Rcheck/00install.out' for details.
SVEC: no visible global function definition for 'Null'
causality: no visible global function definition for 'ginv'
stability: no visible global function definition for 'efp'
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.3Mb
Namespace in Imports field not imported from: 'nlme'
  All declared Imports should be used.
vioplot: warning in axis(1, at = at, label = label): partial argument
  match of 'label' to 'labels'
vioplot: warning in axis(2, at = at, label = label): partial argument
  match of 'label' to 'labels'
raster.proj: no visible global function definition for 'rasterFromXYZ'
.vdensecalc: no visible global function definition for 'contour3d'
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 65-67 (vtreatRareLevels.Rmd) 
Error: processing vignette 'vtreatRareLevels.Rmd' failed with diagnostics:
unused argument (left.open = TRUE)
Execution halted
ald: no visible global function definition for 'detectCores'
ald: no visible global function definition for 'mclapply'
coltheart.N: no visible global function definition for 'detectCores'
coltheart.N: no visible global function definition for 'mclapply'
hamming.distance: no visible global function definition for
  'stringdist'
ldknn: no visible global function definition for 'detectCores'
ldknn: no visible global function definition for 'mclapply'
levenshtein.damerau.distance: no visible global function definition for
  'stringdist'
levenshtein.distance: no visible global function definition for
  'stringdist'
plot.ldknn.run: no visible global function definition for 'histogram'
plot.ldknn.run: no visible global function definition for
  'theEconomist.theme'
plot.ldknn.run: no visible global function definition for 'xyplot'
plot.ldknn.run: no visible global function definition for 'as.layer'
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.
Namespaces in Imports field not imported from:
  'DT' 'ENMeval' 'RColorBrewer' 'devtools' 'dismo' 'dplyr' 'maptools'
  'raster' 'rgdal' 'rgeos' 'rmarkdown' 'shinyBS' 'shinyjs'
  'shinythemes' 'spThin' 'spocc'
  All declared Imports should be used.
color.factor: warning in rgb(red = t.rgb[1, ], green = t.rgb[2, ], blue
  = t.rgb[3, ], max = 255): partial argument match of 'max' to
  'maxColorValue'
p.flow_comp: warning in line_sumrain(xdata = xdata, cum_sum =
  cumsum(data[crain, ])/10, theMax = rain.max, col = "grey"): partial
  argument match of 'cum_sum' to 'cum_sum_rain'
Errors in running code in vignettes:
when running code in 'vignette.Rnw'
  ...

> library(waterData)

> q05054000 <- importDVs("05054000", code = "00060", 
+     stat = "00003", sdate = "2000-01-01", edate = "2010-12-31")
Unknown IO errorfailed to load external entity "http://waterservices.usgs.gov/nwis/dv?site=05054000&parameterCd=00060&statCd=00003&startDt=2000-01-01&endDt=2010-12-31"

  When sourcing 'vignette.R':
Error: 1: Unknown IO error2: failed to load external entity "http://waterservices.usgs.gov/nwis/dv?site=05054000&parameterCd=00060&statCd=00003&startDt=2000-01-01&endDt=2010-12-31"
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'vignette.Rnw' failed with diagnostics:
 chunk 1 
Error : 1: Unknown IO error2: failed to load external entity "http://waterservices.usgs.gov/nwis/dv?site=05054000&parameterCd=00060&statCd=00003&startDt=2000-01-01&endDt=2010-12-31"

Execution halted
WDI: no visible binding for global variable 'WDI_data'
WDIcache: no visible global function definition for 'fromJSON'
WDIsearch: no visible binding for global variable 'WDI_data'
Packages required but not available: 'subprocess' 'semver'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
getStationCode: no visible binding for global variable
  'USAirportWeatherStations'
getStationCode: no visible binding for global variable 'IntlWxStations'
File 'webvis/R/zzz.R':
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

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

[1] "Welcome to the webvis pacakge."
pairtest: no visible global function definition for 'p.value'
pairtest: no visible global function definition for 'single.snp.tests'
fun.load.hals.a: no visible global function definition for 'sfExport'
fun.load.hals.a: no visible global function definition for 'sfLibrary'
fun.load.hals.fill: no visible global function definition for
  'sfExport'
fun.load.hals.fill: no visible global function definition for
  'sfLibrary'
fun.load.widals.a: no visible global function definition for 'sfExport'
fun.load.widals.a: no visible global function definition for
  'sfLibrary'
fun.load.widals.fill: no visible global function definition for
  'sfExport'
fun.load.widals.fill: no visible global function definition for
  'sfLibrary'
screen.ttest: no visible global function definition for 'colttests'
widenet: no visible global function definition for 'mc.reset.stream'
widenet: no visible global function definition for 'mclapply'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
Running examples in 'wiqid-Ex.R' failed
The error most likely occurred in:

> ### Name: dippers
> ### Title: Capture-recapture data for European dippers
> ### Aliases: dippers
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(dippers)
> 
> DH <- dippers[1:7]  # Extract the detection histories
> survCJS(DH)  # the phi(.) p(.) model
Call: survCJS(DH = DH)

Real values (duplicates omitted):
        est  lowCI  uppCI
phi1 0.5602 0.5105 0.6088
p1   0.9026 0.8305 0.9460

AIC: 670.8377 
> survCJS(DH, phi ~ .time)  # the phi(t) p(.) model
Call: survCJS(DH = DH, model = phi ~ .time)

Real values (duplicates omitted):
        est  lowCI  uppCI
phi1 0.6258 0.3965 0.8098
phi2 0.4542 0.3295 0.5849
phi3 0.4784 0.3669 0.5921
phi4 0.6244 0.5079 0.7281
phi5 0.6079 0.4970 0.7088
phi6 0.5833 0.4688 0.6895
p1   0.9021 0.8286 0.9461

AIC: 673.7301 
> 
> # Floods affected the 2nd and 3rd intervals
> df <- data.frame(flood = c(FALSE, TRUE, TRUE, FALSE, FALSE, FALSE))
> survCJS(DH, phi ~ flood, data=df)
Call: survCJS(DH = DH, model = phi ~ flood, data = df)

Real values (duplicates omitted):
        est  lowCI  uppCI
phi1 0.6071 0.5451 0.6658
phi2 0.4688 0.3858 0.5537
p1   0.8998 0.8262 0.9443

AIC: 666.1028 
> 
> # Including a grouping factor:
> survCJS(DH, phi ~ flood * group, data=df, group=dippers$sex)
Call: survCJS(DH = DH, model = phi ~ flood * group, data = df, group = dippers$sex)

Real values (duplicates omitted):
          est  lowCI  uppCI
F:phi1 0.6033 0.5163 0.6842
F:phi2 0.4568 0.3468 0.5712
M:phi1 0.6108 0.5246 0.6906
M:phi2 0.4833 0.3612 0.6073
F:p1   0.8999 0.8263 0.9444

AIC: 669.9911 
> 
> # Bayesian estimation:
> 
> Bdip <- BsurvCJS(DH, parallel=FALSE)
Error: The 'rjags' package and the JAGS program are needed to run this function.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.4Mb
Namespace in Imports field not imported from: 'RMySQL'
  All declared Imports should be used.
wordcloud: no visible global function definition for 'Corpus'
wordcloud: no visible global function definition for 'VectorSource'
wordcloud: no visible global function definition for 'tm_map'
wordcloud: no visible binding for global variable 'removePunctuation'
wordcloud : <anonymous>: no visible global function definition for
  'removeWords'
wordcloud : <anonymous>: no visible global function definition for
  'stopwords'
wordcloud: no visible global function definition for
  'TermDocumentMatrix'
wordmatch: no visible global function definition for 'llply'
wordmatch : <anonymous>: no visible global function definition for
  'llply'
wordmatch: no visible global function definition for 'melt'
wordmatch: no visible global function definition for 'count'
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
simul.wsvm: no visible binding for global variable 'mixture.example'
plot,x12Batch : .local: no visible binding for global variable 'xb'
x12,ts : .local: no visible binding for global variable 'out'
x12,x12Batch : .local: no visible global function definition for
  'mclapply'
x12,x12Single : .local: no visible binding for global variable 'out'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/xgboost.Rcheck/00install.out' for details.
R5.value.default: no visible binding for global variable 'data.table'
R5.value.default: no visible global function definition for
  'as.data.table'
R5.value.parse: no visible binding for global variable 'data.table'
R5.value.parse: no visible global function definition for
  'is.data.table'
R5.value.parse: no visible global function definition for
  'as.data.table'
File 'xml2/libs/i386/xml2.dll':
  Found non-API call to R: 'getConnection'
File 'xml2/libs/x64/xml2.dll':
  Found non-API call to R: 'getConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.1Mb
newXMLDoc: no visible binding for global variable 'doc'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
[[,XMLCodeFile : .local: possible error in updateIds(doc, save = x):
  unused argument (save = x)
as.xts.ts: no visible global function definition for 'as.yearqtr'
as.xts.ts: no visible global function definition for 'as.yearmon'
rollapply.xts: no visible global function definition for 'na.fill'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'yacca/R/zzz.R':
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat("Copyright (c) 2008, Carter T. Butts, University of California-Irvine\n")
    cat("For citation information, type citation(\"yacca\").\n")
    cat("Type help(\"yacca-package\") to get started.\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
tZC_NS: no visible global function definition for 'cmpfun'
tZC_NS_extra: no visible global function definition for 'cmpfun'
tZC_SV: no visible global function definition for 'cmpfun'
tZC_SV_extra: no visible global function definition for 'cmpfun'
Namespaces in Imports field not imported from:
  'DT' 'ggplot2' 'quantmod' 'sde' 'shinyBS' 'shinydashboard' 'shinyjs'
  'yuima'
  All declared Imports should be used.
epirice.weather: no visible binding for global variable
  'weather_SouthAsia'
maize.multisy: no visible binding for global variable
  'weather_EuropeEU'
maize.multisy240 : <anonymous>: no visible binding for global variable
  'weather_EuropeEU'
maize.weather: no visible binding for global variable
  'weather_FranceWest'
param.rtriangle: no visible global function definition for 'rtriangle'
population.age.model.ode: no visible global function definition for
  'ode'
population.age.model.ode: no visible global function definition for
  'rkMethod'
predator.prey.model: no visible global function definition for 'ode'
predator.prey.model: no visible global function definition for
  'rkMethod'
watbal.weather: no visible binding for global variable
  'weather_FranceWest'
Namespaces in Imports field not imported from:
  'dplyr' 'ggplot2' 'lubridate'
  All declared Imports should be used.