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
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/HSROC.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Package suggested but not available for checking: 'hurricaneexposuredata'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/hzar.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.1Mb
    libs   1.0Mb
NB: this package is only installed for sub-architecture 'x64'
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
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  downloaded 10.3 MB
  
  1. Error: getKSJData works (@test-getData.R#4) ---------------------------------
  Cannot open data source
  1: getKSJData("http://nlftp.mlit.go.jp/ksj/gml/data/W05/W05-07/W05-07_03_GML.zip") at testthat/test-getData.R:4
  2: rgdal::ogrListLayers(data_dir)
  
  testthat results ================================================================
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: getKSJData works (@test-getData.R#4) 
  
  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/LANDD.Rcheck/00install.out' for details.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/manipulateWidget.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Running examples in 'mbclusterwise-Ex.R' failed
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/MBSGS.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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
Missing or unexported object: 'irace::removeCandidatesMetaData'
Running the tests in 'tests/run-base.R' failed.
Last 13 lines of output:
  1. Error: downsample wrapper works with xgboost, we had issue #492 (@test_base_downsample.R#38) 
  2. Failure: generateCalibrationData (@test_base_generateCalibration.R#55) 
  3. Failure: generateCalibrationData (@test_base_generateCalibration.R#57) 
  4. Failure: plotFilterValues (@test_base_generateFilterValuesData.R#72) 
  5. Failure: plotFilterValues (@test_base_generateFilterValuesData.R#74) 
  6. Failure: generateLearningCurve (@test_base_generateLearningCurve.R#46) 
  7. Failure: generateLearningCurve (@test_base_generateLearningCurve.R#48) 
  8. Failure: generatePartialDependenceData (@test_base_generatePartialDependence.R#216) 
  9. Failure: generatePartialDependenceData (@test_base_generatePartialDependence.R#219) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
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: running command 'make -f "Makevars.win" -f "D:/RCompile/recent/R-3.3.2/etc/x64/Makeconf" -f "D:/RCompile/recent/R-3.3.2/etc/x64/Makevars.site" -f "D:/RCompile/recent/R-3.3.2/share/make/winshlib.mk" SHLIB_LDFLAGS='$(SHLIB_CXXLDFLAGS)' SHLIB_LD='$(SHLIB_CXXLD)' SHLIB="MVB.dll" WIN=64 TCLBIN=64 OBJECTS="binomial.o distriFactory.o gaussian.o gme.o lps.o mvbernoulli.o mvbfit.o" symbols.rds' had status 2
See 'd:/Rcompile/CRANpkg/local/3.3/MVB.Rcheck/00install.out' for details.
Note: information on .o files for x64 is not available
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/mvst.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/nettools.Rcheck/00install.out' for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    CppCode   1.8Mb
    R         2.4Mb
    include   3.6Mb
    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
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
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: `$<-.data.table`(`*tmp*`, "id", value = 1:11)
  10: `$<-.data.frame`(x, name, value)
  11: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, nrows), domain = NA)
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: output has 17 columns (@test_tableproperties.R#27) 
  2. Error: output has the right column names (@test_tableproperties.R#31) 
  3. Error: output is of class data.frame & data.table (@test_tableproperties.R#36) 
  
  Error: testthat unit tests 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, 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.
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.
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
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/PortRisk.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/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  7.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.5Mb
    libs   2.2Mb
Found the following significant warnings:
  Warning: replacing previous import 'ape::complement' by 'Biostrings::complement' when loading 'RADami'
See 'd:/Rcompile/CRANpkg/local/3.3/RADami.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.0Mb
Running the tests in 'tests/minimalTests.R' failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > 
  > library(random)
  > 
  > X <- randomNumbers()
  Error in url(urltxt, ..., method = "libcurl") : cannot open connection
  Calls: randomNumbers -> getConnection -> url
  In addition: Warning message:
  In url(urltxt, ..., method = "libcurl") :
    URL 'https://www.random.org/integers/?num=100&min=1&max=100&col=5&base=10&format=plain&rnd=new': status was '503 Service Unavailable'
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.6Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rcplex.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    include   4.6Mb
    libs      1.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    libs      1.7Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.7Mb
    libs      2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/RcppOctave.Rcheck/00install.out' for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       8.0Mb
    libs      1.0Mb
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
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    gdal       3.0Mb
    libs      23.9Mb
    pictures   1.2Mb
    proj       4.9Mb
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rmosek.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/robustsae.Rcheck/00install.out' for details.
Running examples in 'ropenaq-Ex.R' failed
The error most likely occurred in:

> ### Name: aq_cities
> ### Title: Provides a simple listing of cities within the platform.
> ### Aliases: aq_cities
> 
> ### ** Examples
> 
> cities <- aq_cities(country = "IN")
Error in strsplit(date, ",") : non-character argument
Calls: aq_cities ... as_data_frame -> data.frame -> func_date_headers -> strsplit
Execution halted
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rpg.Rcheck/00install.out' for details.
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.
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()
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Could not guess driver for D:\temp\RtmpgzBkUE\file50903ad7918.shp
  1: st_write(x[-4], shp, quiet = TRUE) at testthat/test_tm.R:10
  2: CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options), as.character(layer_options), 
         geom, dim, quiet)
  3: guess_driver_can_write(dsn)
  4: stop("Could not guess driver for ", dns, call. = FALSE)
  
  testthat results ================================================================
  OK: 192 SKIPPED: 0 FAILED: 1
  1. Error: st_read and write handle date and time (@test_tm.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Could not guess driver for D:\temp\Rtmpmm9tTE\file4f607af0be5.shp
  1: st_write(x[-4], shp, quiet = TRUE) at testthat/test_tm.R:10
  2: CPL_write_ogr(obj, dsn, layer, driver, as.character(dataset_options), as.character(layer_options), 
         geom, dim, quiet)
  3: guess_driver_can_write(dsn)
  4: stop("Could not guess driver for ", dns, call. = FALSE)
  
  testthat results ================================================================
  OK: 192 SKIPPED: 0 FAILED: 1
  1. Error: st_read and write handle date and time (@test_tm.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 137-138 (sf2.Rmd) 
Error: processing vignette 'sf2.Rmd' failed with diagnostics:
Could not guess driver for d:\RCompile\CRANpkg\local\3.3\sf.Rcheck\vign_test\sf\vignettes\nc.shp
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    www   6.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/sizeMat.Rcheck/00install.out' for details.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    data   3.4Mb
    doc    4.6Mb
    help   5.0Mb
    libs   1.2Mb
Running the tests in 'tests/tests.R' failed.
Last 13 lines of output:
  > ## is not available
  > 
  > myurl <- "http://www.biostat.jhsph.edu/MCAPS/data_v0.3/"
  > 
  > ## create a 'remoteDB' object ##
  > db <- new("remoteDB", url= myurl, dir = dir, name= "MCAPS")
  Error in download.file(rpath, versionFile(db, where = "local"), mode = "w",  : 
    cannot open URL 'http://www.biostat.jhsph.edu/MCAPS/data_v0.3/version'
  Calls: new ... initialize -> initialize -> cacheVersionFile -> download.file
  In addition: Warning message:
  In download.file(rpath, versionFile(db, where = "local"), mode = "w",  :
    cannot open URL 'http://www.biostat.jhsph.edu/MCAPS/data_v0.3/version': HTTP status was '404 Not Found'
  Execution halted
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.
Error in re-building vignettes:
  ...
Conflicts with tidy packages ----------------------------------------------
as.difftime(): lubridate, base
date():        lubridate, base
filter():      dplyr, stats
first():       dplyr, xts
intersect():   lubridate, base
lag():         dplyr, stats
last():        dplyr, xts
setdiff():     lubridate, base
union():       lubridate, base

Attaching package: 'tidyquant'

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

    as_tibble

Warning: Removed 4160 rows containing non-finite values (stat_smooth).
Warning: Removed 4160 rows containing missing values (position_stack).
Getting data...

Quitting from lines 202-205 (tidyquant.Rmd) 
Error: processing vignette 'tidyquant.Rmd' failed with diagnostics:
Can not automatically convert from character to integer in column "Last.Trade.Size".
Execution halted
installed size is 22.4Mb
  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.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: getExportedValue(pkg, name)
  6: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  testthat results ================================================================
  OK: 132 SKIPPED: 0 FAILED: 4
  1. Error: visualization of empty automat works (@test-automat.R#131) 
  2. Error: visualization without set state works (@test-automat.R#139) 
  3. Error: visualization with implicit state works (@test-automat.R#148) 
  4. Error: visualization works (@test-automat.R#163) 
  
  Error: testthat unit tests failed
  Execution halted
newXMLDoc: no visible binding for global variable 'doc'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
[[,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/Rtmpc3WG6f/R.INSTALL3cd431882e59/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.
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.
Running examples in 'bdrift-Ex.R' failed
The error most likely occurred in:

> ### Name: BDA.loader
> ### Title: Beta Drift Anaylsis Data Loader
> ### Aliases: BDA.loader
> 
> ### ** Examples
> 
> testframe <- BDA.loader(symbol = "XOM")
Error: { "quandl_error": { "code": "QELx01", "message": "You have exceeded the anonymous user limit of 50 calls per day. To make more calls today, please register for a free Quandl account and then include your API key with your requests." } }
Execution halted
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'
Error in re-building vignettes:
  ...
Loading required package: diptest
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "Vignette.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 'Vignette.tex' failed

BibTeX errors:
I couldn't open database file Vignette.bib.bib
---line 50 of file Vignette.aux
 : \bibdata{Vignette.bib
 :                      }
I'm skipping whatever remains of this command
I found no database files---while reading file Vignette.aux
Execution halted
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'
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/birdring.Rcheck/00install.out' for details.
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.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
'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.
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/cdcsis.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: '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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/CONS.Rcheck/00install.out' for details.
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  6.0Mb
  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'
Package suggested but not available for checking: 'tidyverse'
Error in re-building vignettes:
  ...
Quitting from lines 150-160 (how_to_test_CVs.Rmd) 
Error: processing vignette 'how_to_test_CVs.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
.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'
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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/deeplearning.Rcheck/00install.out' for details.
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    1.8Mb
    help   1.2Mb
    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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/DNAtools.Rcheck/00install.out' for details.
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=0x000000000A613118, maxprocs=2, MPI_INFO_NULL, root=0, MPI_COMM_SELF, intercomm=0x00000000084E2B30, errors=0x00000000074777A0) 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.
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
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.
Running examples in 'ecb-Ex.R' failed
The error most likely occurred in:

> ### Name: convert_dates
> ### Title: Format date variable retrieved from the SDW into a proper date
> ###   variable
> ### Aliases: convert_dates
> 
> ### ** Examples
> 
> hicp <- get_data("ICP.M.U2.N.000000.4.ANR")
No encoding supplied: defaulting to UTF-8.
Error in check_status(req) : HTTP failure: 500
Error code: 3.59d77a5c.1485469520.417a517e
Calls: get_data -> make_request -> check_status
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 114-116 (ecb_sdw.Rmd) 
Error: processing vignette 'ecb_sdw.Rmd' failed with diagnostics:
HTTP failure: 500
Error code: 3.59d77a5c.1485469526.417a56c8
Execution halted
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'
plotEEG: no visible global function definition for 'tim.colors'
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'
################################################################################

Easy Microarray Analysis

EMA stable version

Current release : v1.4.4 - march 2014

################################################################################

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

Easy Microarray Analysis

EMA stable version

Current release : v1.4.4 - march 2014

################################################################################

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Found the following significant warnings:
  Warning: 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.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Type 'contributors()' for more information and
  'citation()' on how to cite R or R packages in publications.
  
  Type 'demo()' for some demos, 'help()' for on-line help, or
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > suppressMessages(library(testthat))
  > suppressMessages(library(fbar))
  > suppressMessages(library(tidyverse))
  Error in library(tidyverse) : there is no package called 'tidyverse'
  Calls: suppressMessages -> withCallingHandlers -> library
  Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

ROI: R Optimization Infrastructure
Registered solver plugins: nlminb, ecos, glpk, ipop, lpsolve, nloptr, quadprog, scs, symphony.
Default solver: auto.
Quitting from lines 19-22 (Multi-Objective_Optimization_case_study.Rmd) 
Error: processing vignette 'Multi-Objective_Optimization_case_study.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
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'
Namespace in Imports field not imported from: 'stats'
  All declared Imports should be used.
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'
Running examples in 'furniture-Ex.R' failed
The error most likely occurred in:

> ### Name: table1
> ### Title: Table 1 for Simple and Stratified Descriptive Statistics
> ### Aliases: table1
> 
> ### ** Examples
> 
> ## Ficticious Data ##
> library(furniture)
> library(tidyverse)
Error in library(tidyverse) : there is no package called 'tidyverse'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 35-40 (Furniture.Rmd) 
Error: processing vignette 'Furniture.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
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 10.4Mb
  sub-directories of 1Mb or more:
    data    3.7Mb
    doc     2.9Mb
    tests   2.6Mb
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
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
Package suggested but not available for checking: 'fontquiver'
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
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'
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'
Package suggested but not available for checking: 'vdiffr'
Namespace in Imports field not imported from: 'lazyeval'
  All declared Imports should be used.
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Error: geom_linerangeh() flips (@test-geoms.R#7) 
  2. Error: geom_pointangeh() flips (@test-geoms.R#13) 
  3. Error: geom_crossbarh() flips (@test-geoms.R#31) 
  4. Error: geom_errorbarh() flips (@test-geoms.R#37) 
  5. Error: geom_barh() flips (@test-geoms.R#45) 
  6. Error: geom_violinh() flips (@test-geoms.R#71) 
  7. Error: geom_boxploth() flips (@test-geoms.R#81) 
  8. Error: facet_grid() with free scales flips (@test-geoms.R#95) 
  9. Error: scale information is preserved (@test-geoms.R#109) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/GPareto.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/GPC.Rcheck/00install.out' for details.
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 2017-01-13 16:43:16
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 
   0.90    0.37   14.50
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: '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$resid, digits = digits, na = "",
  print.gap = 2): partial argument match of 'na' to 'na.print'
print.tsum: warning in symnum(correl, abbr.col = NULL): partial
  argument match of 'abbr.col' to 'abbr.colnames'
tlm: no visible binding for global variable 'response'
tlm: no visible binding for global variable 'dofse'
tscore: no visible binding for global variable 'response'
Btilde: no visible global function definition for 'bs'
hgam: no visible global function definition for 'LinReg'
hgam.fit: no visible global function definition for 'LinReg'
hgam.fit: no visible global function definition for 'grplasso'
hgam.fit: no visible global function definition for 'grpl.control'
hrisk: no visible binding for global variable 'mclapply'
hrisk : <anonymous>: no visible global function definition for
  'lambdamax'
plot.hrisk: no visible global function definition for 'plot3d'
plot.hrisk: no visible global function definition for 'levelplot'
gcline.fn: no visible global function definition for 'multinom'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/highriskzone.Rcheck/00install.out' for details.
hand1: no visible binding for global variable 'name1'
hotelling.stat: no visible global function definition for 'cov.shrink'
print.summary.hotspots: warning in sort(x$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'
Packages in Depends field not imported from:
  'MCMCpack' 'coda' 'foreach'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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   1.9Mb
    doc    2.2Mb
    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.
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'
Namespaces in Imports field not imported from:
  'rgeos' 'sp'
  All declared Imports should be used.
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.
.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'
Namespaces in Imports field not imported from:
  'dplyr' 'htmlwidgets'
  All declared Imports should be used.
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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/logcondens.Rcheck/00install.out' for details.
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'
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:
  
  1. Failure: Search Works (@tests.R#28) -----------------------------------------
  length(s2) not equal to 2.
  1/1 mismatches
  [1] 1 - 2 == -1
  
  
  testthat results ================================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: Search Works (@tests.R#28) 
  
  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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/manipulateWidget.Rcheck/00install.out' for details.
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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/mglmn.Rcheck/00install.out' for details.
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  6.0Mb
  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'
Running the tests in 'tests/run-base.R' failed.
Last 13 lines of output:
  1. Failure: generateCalibrationData (@test_base_generateCalibration.R#55) 
  2. Failure: generateCalibrationData (@test_base_generateCalibration.R#57) 
  3. Failure: plotFilterValues (@test_base_generateFilterValuesData.R#72) 
  4. Failure: plotFilterValues (@test_base_generateFilterValuesData.R#74) 
  5. Failure: generateLearningCurve (@test_base_generateLearningCurve.R#46) 
  6. Failure: generateLearningCurve (@test_base_generateLearningCurve.R#48) 
  7. Failure: generatePartialDependenceData (@test_base_generatePartialDependence.R#216) 
  8. Failure: generatePartialDependenceData (@test_base_generatePartialDependence.R#219) 
  9. Failure: generateThreshVsPerfData (@test_base_generateThreshVsPerf.R#119) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
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'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  14: mclapply(groundSpeedsL, getWindEstimate, phi = phi)
  15: lapply(X, FUN, ...)
  16: FUN(X[[i]], ...)
  17: FUN(X[[i]], ...)
  18: solve(optimResult$hessian/optimResult$value * n/2)
  19: solve.default(optimResult$hessian/optimResult$value * n/2)
  
  testthat results ================================================================
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: getWindEstimates (@test.getWindEstimates.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
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    2.4Mb
    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
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'
Namespace in Imports field not imported from: 'curl'
  All declared Imports should be used.
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'
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.
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."
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'
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 14.6Mb
  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'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.2Mb
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  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
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'
Error in re-building vignettes:
  ...
Quitting from lines 119-141 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Error in re-building vignettes:
  ...
Error in try(stop("this error will not appear in the document")) : 
  this error will not appear in the document
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "pkgmaker.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 in find_vignette_product(name, by = "texi2pdf", engine = engine) : 
  Failed to locate the 'texi2pdf' output file (by engine 'knitr::knitr') for vignette with name 'pkgmaker'. The following files exist in directory '.': 'pkgmaker-unitTests.R', 'pkgmaker-unitTests.Rnw', 'pkgmaker-unitTests.aux', 'pkgmaker-unitTests.log', 'pkgmaker-unitTests.out', 'pkgmaker-unitTests.pdf', 'pkgmaker-unitTests.tex', 'pkgmaker.R', 'pkgmaker.Rnw', 'pkgmaker.tex'
Calls: buildVignettes -> find_vignette_product
Execution halted
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   3.7Mb
    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  7.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    doc    2.5Mb
    libs   2.1Mb
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'
Found the following significant warnings:
  Warning: replacing previous import 'ape::complement' by 'Biostrings::complement' when loading 'RADami'
See 'd:/Rcompile/CRANpkg/local/3.2/RADami.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/rainbow.Rcheck/00install.out' for details.
.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'
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
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'
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  6.7Mb
  sub-directories of 1Mb or more:
    include   4.6Mb
    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/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 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
Namespaces in Imports field not imported from:
  'igraph' 'rJava'
  All declared Imports should be used.
REEMtree: no visible binding for global variable 'SubsetVector'
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'
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  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  7.9Mb
  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   5.9Mb
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'
Package required but not available: 'mrfDepth'

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

> ### Name: in_node
> ### Title: in_node
> ### Aliases: in_node rpms::in_node
> 
> ### ** Examples
> 
> # model linear fit between retirement contributions and amount of income 
> r1 <-rpms(FINDRETX~EDUC_REF+AGE_REF+BLS_URBN+REGION, data=CE,
+      e_equ=FINDRETX~FINCBTAX, clusters=~CID) 
> 
> summary(CE$FSALARYX[in_node(node=2, r1, data=CE)])
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
      0       0   12000   29120   44600  517500 
> 
> summary(CE$FSALARYX[in_node(node=6, r1, data=CE)])
Error in in_node(node = 6, r1, data = CE) : 
  6  is not an end-node of the tree
Calls: summary -> in_node
Execution halted
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
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/rugarch.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'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/RVPedigree.Rcheck/00install.out' for details.
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'
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.
Errors in running code in vignettes:
when running code in 'seqMeta.Rnw'
  ...
6  gene13 0.214  0.211 0.17      0.31   0.0163         22         2   600

> meta.skato.results <- skatOMeta(c1, c2, rho = seq(0, 
+     1, length = 11), burden.wts = function(maf) {
+     dbeta(maf, 1, 25)
+ }, SNPInfo = SNP .... [TRUNCATED] 

  When sourcing 'seqMeta.R':
Error: replacement has length zero
Execution halted
Error in re-building vignettes:
  ...
Loading required package: survival
Note: method with signature 'CsparseMatrix#Matrix#missing#replValue' chosen for function '[<-',
 target signature 'dsCMatrix#lsyMatrix#missing#numeric'.
 "Matrix#ldenseMatrix#missing#replValue" would also be valid

Error: processing vignette 'seqMeta.Rnw' failed with diagnostics:
 chunk 9 
Error in ps[i] <- tmpP$p : replacement has length zero
Execution halted
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.
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'
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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/SkyWatchr.Rcheck/00install.out' for details.
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'
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  6.9Mb
  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'
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  'citation()' on how to cite R or R packages in publications.
  
  Type 'demo()' for some demos, 'help()' for on-line help, or
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > library(testthat)
  > library(svglite)
  > 
  > test_check("svglite")
  Error in loadNamespace(name) : there is no package called 'fontquiver'
  Calls: test_check ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
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.
Namespace in Imports field not imported from: 'colorspace'
  All declared Imports should be used.
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
Package required but not available: 'fontquiver'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
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' 'dismo' 'dplyr' 'maptools' 'raster'
  '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.