installed size is 12.2Mb
  sub-directories of 1Mb or more:
    R     2.3Mb
    doc   9.4Mb
Running ‘testthat.R’ [159s/201s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library("checkmate")
  > library("testthat")
  > library("ParamHelpers")
  > library("mlr")
  'mlr' is in maintenance mode since July 2019. Future development
  efforts will go into its successor 'mlr3' (<https://mlr3.mlr-org.com>).
  > library("mlrCPO")
  > 
  > test_check("mosmafs")
  Loading required package: mosmafs
  Loading required package: ecr
  Loading required package: BBmisc
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  Loading required package: smoof
  
  Attaching package: 'ecr'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  
  Attaching package: 'mosmafs'
  
  The following objects are masked from 'package:ecr':
  
      getPopulations, getStatistics
  
  ── 1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232)  ─────────
  `slickEcr(...)` threw an error with unexpected message.
  Expected match: "Must be of type 'numeric', not 'factor'"
  Actual message: "Assertion on 'fidelity[[2]]' failed: Must be of type 'numeric', not 'character'."
  Backtrace:
    1. testthat::expect_error(...)
    6. mosmafs::slickEcr(...)
    7. mosmafs::initEcr(...)
    8. mosmafs:::checkFidelity(fidelity)
    9. checkmate::assertNumeric(fidelity[[2]], any.missing = FALSE)
   10. checkmate::makeAssertion(x, res, .var.name, add)
   11. checkmate:::mstop(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 458 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: multiFidelity with 2 columns (@test_customnsga2.R#232) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
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    extdata   4.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘msaR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘msaR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.2Mb
    libs   1.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘msir.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot697d33794fb2.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot697d33794fb2.png': No such file or directory
Quitting from lines 102-104 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/MultiBD.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘RMark’
XIO:  fatal IO error 146 (Connection refused) on X server ":5.0"
      after 0 requests (0 known processed) with 0 events remaining.
Running examples in ‘mxmmod-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxMmodModel
> ### Title: Create an MMOD
> ### Aliases: mxMmodModel
> 
> ### ** Examples
> 
> data(nlsy97depression)
> # Fit one factor MMOD
> structure <- list(
+   F1 = c('nervous', 'down', 'depressed', 'calm', 'happy')
+ )
> mmod_model <- mxMmodModel(data=nlsy97depression,
+                           modelName='1 Factor MMOD',
+                           idvar='pid', timevar='occasion', structure=structure)
Warning in mxMmodModel(data = nlsy97depression, modelName = "1 Factor MMOD",  :
  Missing values detected; omitting them.
> mmod_fit <- OpenMx::mxRun(mmod_model)
Running 1 Factor MMOD with 33 parameters
Error: C stack usage  270832788 is too close to the limit

 *** caught segfault ***
address 3000018, cause 'memory not mapped'
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    java  14.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    2.6Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata  16.3Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    doc    1.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ncmeta)
  > skip_on_os("solaris")
  Error: Reason: On Solaris
  Execution halted
Running examples in ‘NCutYX-Ex.R’ failed
The error most likely occurred in:

> ### Name: ancut
> ### Title: Cluster the Columns of Y into K Groups with the Help of External
> ###   Features X.
> ### Aliases: ancut
> 
> ### ** Examples
> 
> #This sets up the initial parameters for the simulation.
> library(MASS)#for mvrnorm
> library(fields)
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.5-1 (2019-12-12) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: ‘spam’

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

    backsolve, forwardsolve

Loading required package: maps
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
> n=30 #Sample size
> B=50 #Number of iterations in the simulated annealing algorithm.
> L=10000 #Temperature coefficient.
> p=50 #Number of columns of Y.
> q=p #Number of columns of X.
> h1=0.15
> h2=0.25
> 
> S=matrix(0.2,q,q)
> S[1:(q/2),(q/2+1):q]=0
> S[(q/2+1):q,1:(q/2)]=0
> S=S-diag(diag(S))+diag(q)
> 
> mu=rep(0,q)
> 
> W0=matrix(1,p,p)
> W0[1:(p/2),1:(p/2)]=0
> W0[(p/2+1):p,(p/2+1):p]=0
> Denum=sum(W0)
> 
> B2=matrix(0,q,p)
> for (i in 1:(p/2)){
+    B2[1:(q/2),i]=runif(q/2,h1,h2)
+    in1=sample.int(q/2,6)
+    B2[-in1,i]=0
+ }
> 
> for (i in (p/2+1):p){
+    B2[(q/2+1):q,i]=runif(q/2,h1,h2)
+    in2=sample(seq(q/2+1,q),6)
+    B2[-in2,i]=0
+ }
> 
> X=mvrnorm(n, mu, S)
> Z=X%*%B2
> Y=Z+matrix(rnorm(n*p,0,1),n,p)
> #Our method
> Res=ancut(Y=Y,X=X,B=B,L=L,alpha=0,ncv=3)
Error in if (J2 > J) { : missing value where TRUE/FALSE needed
Calls: ancut
Execution halted
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of ‘Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests-devel/NestedCategBayesImpute.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introducing_nhanesA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-98 (Introducing_nhanesA.Rmd) 
Error: processing vignette 'Introducing_nhanesA.Rmd' failed with diagnostics:
Timeout was reached: [wwwn.cdc.gov] Resolving timed out after 10002 milliseconds
--- failed re-building ‘Introducing_nhanesA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   5.9Mb
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    CppCode  10.4Mb
    R         6.3Mb
    include   5.3Mb
    libs      2.8Mb
    tests     1.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘geocode.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘geocode.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data      4.4Mb
    doc       1.2Mb
    reports   3.8Mb
Found the following significant warnings:
  WrapperNMFGPU.cpp:96:12: warning: converting ‘false’ to pointer type for argument 1 of ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests-devel/nmfgpu4R.Rcheck/00install.out’ for details.
Running examples in ‘NMF-Ex.R’ failed
The error most likely occurred in:

> ### Name: NMFfitX-class
> ### Title: Virtual Class to Handle Results from Multiple Runs of NMF
> ###   Algorithms
> ### Aliases: NMFfitX-class
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # generate a synthetic dataset with known classes
> n <- 20; counts <- c(5, 2, 3);
> V <- syntheticNMF(n, counts)
> 
> # perform multiple runs of one algorithm (default is to keep only best fit)
> res <- nmf(V, 3, nrun=3)
# NOTE - CRAN check detected: limiting maximum number of cores [2/16]
Error in big.matrix(nrow = nrow(x), ncol = ncol(x), type = type, init = NULL,  : 
  Error: memory could not be allocated for instance of type big.matrix
Calls: nmf ... gVariable -> <Anonymous> -> <Anonymous> -> big.matrix
Timing stopped at: 0.03 0.031 0.061
Execution halted
Package unavailable to check Rd xrefs: ‘redux’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    7.5Mb
    libs   1.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R            1.7Mb
    test_files   4.4Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.0Mb
    doc    2.5Mb
    help   2.8Mb
Packages suggested but not available for checking: 'RMark', 'R2ucare'
Running ‘testthat.R’ [42s/54s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OpenLand)
  > 
  > test_check("OpenLand")
  ── 1. Error: (unknown) (@test_generalfunctions.R#29)  ──────────────────────────
  package 'rgdal' is not available
  Backtrace:
    1. base::lapply(...)
    2. OpenLand:::FUN(X[[i]], ...)
    4. raster::writeRaster(...)
    5. raster:::.local(x, filename, ...)
    6. raster:::.writeGDALall(...)
    7. raster:::.startGDALwriting(...)
    8. raster:::.getGDALtransient(...)
    9. raster:::.isSupportedFormat(gdalfiletype)
   10. raster:::.isSupportedGDALFormat(dname)
   11. raster:::.requireRgdal()
  
  ── 2. Error: (unknown) (@test_inputrasters.R#5)  ───────────────────────────────
  package 'rgdal' is not available
  Backtrace:
    1. base::lapply(...)
    2. OpenLand:::FUN(X[[i]], ...)
    4. raster::writeRaster(...)
    5. raster:::.local(x, filename, ...)
    6. raster:::.writeGDALall(...)
    7. raster:::.startGDALwriting(...)
    8. raster:::.getGDALtransient(...)
    9. raster:::.isSupportedFormat(gdalfiletype)
   10. raster:::.isSupportedGDALFormat(dname)
   11. raster:::.requireRgdal()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 96 | SKIPPED: 0 | WARNINGS: 24 | FAILED: 2 ]
  1. Error: (unknown) (@test_generalfunctions.R#29) 
  2. Error: (unknown) (@test_inputrasters.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘openland_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://zenodo.org/record/3685230/files/SaoLourencoBasin.rda?download=1'
Content type 'application/octet-stream' length 5309066 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Quitting from lines 264-269 (openland_vignette.Rmd) 
Error: processing vignette 'openland_vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘openland_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    R        2.7Mb
    data     1.0Mb
    libs     4.1Mb
    models   4.4Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxModelAverage
> ### Title: Information-Theoretic Model-Averaging and Multimodel Inference
> ### Aliases: mxModelAverage omxAkaikeWeights omxAICWeights
> 
> ### ** Examples
> 
> require(OpenMx)
> data(demoOneFactor)
> factorModel1 <- mxModel(
+ 	"OneFactor1",
+ 	mxMatrix(
+ 		"Full", 5, 1, values=0.8, 
+ 		labels=paste("a",1:5,sep=""),
+ 		free=TRUE, name="A"),
+ 	mxMatrix(
+ 		"Full", 5, 1, values=1,
+ 		labels=paste("u",1:5,sep=""),
+ 		free=TRUE, name="Udiag"),
+ 	mxMatrix(
+ 		"Symm", 1, 1, values=1,
+ 		free=FALSE, name="L"),
+ 	mxAlgebra(vec2diag(Udiag),name="U"),
+ 	mxAlgebra(A %*% L %*% t(A) + U, name="R"),
+ 	mxExpectationNormal(
+ 		covariance = "R",
+ 		dimnames = names(demoOneFactor)),
+ 	mxFitFunctionML(),
+ 	mxData(cov(demoOneFactor), type="cov", numObs=500))
> factorFit1 <- mxRun(factorModel1)
Running OneFactor1 with 10 parameters
Error: C stack usage  270832788 is too close to the limit
Error: The job for model 'OneFactor1' exited abnormally with the error message: User interrupt
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    java     1.3Mb
    models   6.1Mb
Packages suggested but not available for checking:
  'gurobi', 'Rsymphony', 'lpsymphony'
Running ‘testthat.R’ [17s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(ordinalNet)
  > testthatInst <- require(testthat)
  Loading required package: testthat
  > 
  > if (testthatInst) test_check("ordinalNet")
  ── 1. Failure: Elastic net sratio matches glmnetcr::glmnet.cr (@test-ordinalNet.
  coef(o) not equal to `coefg`.
  3/7 mismatches (average diff: 0.475)
  [1] -0.572 - 0 == -0.572
  [3] -0.440 - 0 == -0.440
  [4] -0.413 - 0 == -0.413
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
  1. Failure: Elastic net sratio matches glmnetcr::glmnet.cr (@test-ordinalNet.R#213) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘OriGen/libs/OriGen.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_esfr’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Object: ‘OriGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    nifti   4.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Rcpp_API.Rmd’

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

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
sh: whoami:  not found
sh: git:  not found
sh: git:  not found
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘graph_packing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘graph_packing.Rmd’

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

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 196-217 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘progressive_packing.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Running ‘testthat.R’ [26s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(PANICr)
  > 
  > test_check("PANICr")
  ── 1. Failure: Panic 10 demeaned consistency (@test_panic_io.R#25)  ────────────
  panic10(test1, nfac = 10L, k1 = 7, criteria = "IC1", demean = TRUE) not equal to `test_10_dm`.
  Component "MP.tests": Component "pool_test": Modes: character, numeric
  Component "MP.tests": Component "pool_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "pool_test": target is character, current is factor
  Component "MP.tests": Component "mp_test": Modes: character, numeric
  Component "MP.tests": Component "mp_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "mp_test": target is character, current is factor
  
  ── 2. Failure: Panic 10 non-demeaned consistency (@test_panic_io.R#40)  ────────
  panic10(test1, nfac = 10L, k1 = 7, criteria = "IC1", demean = FALSE) not equal to `test_10_ndm`.
  Component "MP.tests": Component "mp_test": Modes: character, numeric
  Component "MP.tests": Component "mp_test": Attributes: < target is NULL, current is list >
  Component "MP.tests": Component "mp_test": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: Panic 10 demeaned consistency (@test_panic_io.R#25) 
  2. Failure: Panic 10 non-demeaned consistency (@test_panic_io.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parcoords-.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-30 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction-to-parcoords-.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc        2.3Mb
    testdata   1.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    lib   4.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.1Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   8.4Mb
Package unavailable to check Rd xrefs: ‘tesseract’
Running examples in ‘pense-Ex.R’ failed
The error most likely occurred in:

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

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

Traceback:
 1: enpy_exact(x, y, alpha, lambda, options, en_options)
 2: enpy(std_data$xs, std_data$yc, alpha, lambda, delta = pense_options$bdp,     cc = pense_options$cc, options = initest_options, en_options = en_options)
 3: pense_init_cold(x = x_train, y = y_train, lambda = job$lambda,     ...)
 4: FUN(X[[i]], ...)
 5: cluster$lapply(jobs_cold_est, get_cold_est, alpha = alpha, standardize = standardize,     pense_options = options, initest_options = init_options,     en_options = en_options)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: tryCatch({    cold_inits <- cluster$lapply(jobs_cold_est, get_cold_est,         alpha = alpha, standardize = standardize, pense_options = options,         initest_options = init_options, en_options = en_options)}, error = function(e) {    cluster$stopCluster()    stop(e)})
10: pense(x, y, alpha = 0.5, warm_reset = 1, cv_k = 3)
An irrecoverable exception occurred. R is aborting now ...
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    data   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 51-62 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data       2.4Mb
    examples   2.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   3.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘phmm_poisson_df.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: survival
Loading required package: lattice
Loading required package: Matrix
Quitting from lines 118-123 (phmm_poisson_df.Rmd) 
Error: processing vignette 'phmm_poisson_df.Rmd' failed with diagnostics:
Singular matrix in routine ludcmp
--- failed re-building ‘phmm_poisson_df.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Advanced_Usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Advanced_Usage.Rmd’

--- re-building ‘Basic_Use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 30-32 (Basic_Use.Rmd) 
Error: processing vignette 'Basic_Use.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Basic_Use.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘test-async.R’ [1m/120m]
  Running ‘testthat.R’
Running the tests in ‘tests/test-async.R’ failed.
Complete output:
  > 
  > if (file.exists("async")) {
  +   library(testthat)
  +   library(pkgcache)
  +   test <- function() {
  +     package <- "pkgcache"
  +     env_test <- asNamespace("testthat")$env_test
  +     env_test$in_test <- TRUE
  +     env_test$package <- package
  +     on.exit({
  +       env_test$in_test <- FALSE
  +       env_test$package <- NULL
  +     })
  +     test_path <- "async"
  +     asNamespace("testthat")$test_package_dir(
  +       package = package, test_path = test_path,
  +       filter = NULL, reporter = "check")
  +   }
  +   test()
  + }
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgcache)
  > 
  > test_check("pkgcache")
  ── 1. Error: load_primary_pkgs (@test-metadata-cache.R#191)  ───────────────────
  No metadata available
  Backtrace:
   1. pkgcache:::synchronise(get_private(cmc)$load_primary_pkgs(oneday()))
   2. get_private(cmc)$load_primary_pkgs(oneday())
   3. pkgcache:::cmc__load_primary_pkgs(self, private, max_age)
   4. private$update_replica_rds(alert = FALSE)
   5. pkgcache:::cmc__update_replica_rds(self, private, alert)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 305 | SKIPPED: 28 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: load_primary_pkgs (@test-metadata-cache.R#191) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [21s/92s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pkgdown)
  > 
  > test_check("pkgdown")
  ── 1. Failure: library() linked to package reference (@test-link-href.R#126)  ──
  href_expr_(library(pkgdown)) not equal to "https://pkgdown.r-lib.org/reference".
  1/1 mismatches
  x[1]: "https://rdrr.io/pkg/pkgdown/man"
  y[1]: "https://pkgdown.r-lib.org/reference"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 357 | SKIPPED: 32 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: library() linked to package reference (@test-link-href.R#126) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following files/directories:
  ‘P2Run.csv’ ‘P2Run.png’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    htmlwidgets   3.6Mb
Running ‘testthat.R’ [170s/205s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("plotly")
  Loading required package: ggplot2
  
  Attaching package: 'plotly'
  
  The following object is masked from 'package:ggplot2':
  
      last_plot
  
  The following object is masked from 'package:stats':
  
      filter
  
  The following object is masked from 'package:graphics':
  
      layout
  
  > 
  > test_check("plotly")
  Visual testing is not enabled.
  OGR: Unsupported geometry type
  ── 1. Error: (unknown) (@test-cookbook-lines.R#192)  ───────────────────────────
  arguments imply differing number of rows: 0, 2
  Backtrace:
   1. base::data.frame(cond = levels(df$cond), xval = c(10, 11.5))
  
  ── 2. Failure: paths with the same color but different groups stay together (@te
  info$data[[1]]$name not identical to "positive".
  1/1 mismatches
  x[1]: "negative"
  y[1]: "positive"
  
  ── 3. Failure: paths with the same color but different groups stay together (@te
  info$data[[2]]$name not identical to "negative".
  1/1 mismatches
  x[1]: "positive"
  y[1]: "negative"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1375 | SKIPPED: 50 | WARNINGS: 63 | FAILED: 3 ]
  1. Error: (unknown) (@test-cookbook-lines.R#192) 
  2. Failure: paths with the same color but different groups stay together (@test-ggplot-path.R#51) 
  3. Failure: paths with the same color but different groups stay together (@test-ggplot-path.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [55s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmultinom)
  > 
  > test_check("pmultinom")
  ── 1. Failure: Correct behavior when target probability is 0 or 1 (@test_invertp
  invert.pmultinom(...) not equal to 0.
  1/1 mismatches
  [1] 6 - 0 == 6
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1561 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Correct behavior when target probability is 0 or 1 (@test_invertpmultinom.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Found the following significant warnings:
  Warning: `data_frame()` is deprecated as of tibble 1.1.0.
See ‘/home/ripley/R/packages/tests-devel/poio.Rcheck/00install.out’ for details.
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘OpenCPU.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘OpenCPU.Rmd’

--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
... activating corpus: GERMAPARLMINI
... activating corpus: REUTERS
Quitting from lines 140-141 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R      6.5Mb
    data   4.0Mb
Package suggested but not available for checking: ‘ROI.plugin.symphony’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc     1.1Mb
    tests   2.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    java   5.7Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  11.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPQnote.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘PPQnote.Rmd’

--- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot5a0e6a2451c0.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot5a0e6a2451c0.png': No such file or directory
Quitting from lines 135-136 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PPQplan-vignette.Rmd’

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

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

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

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

--- re-building ‘exclusionflowcharts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 25-31 (exclusionflowcharts.Rmd) 
Error: processing vignette 'exclusionflowcharts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘exclusionflowcharts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc           9.0Mb
    htmlwidgets   2.7Mb
Running examples in ‘profile-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_rprof
> ### Title: File I/O for profiler data
> ### Aliases: read_rprof read_pprof write_rprof write_pprof
> 
> ### ** Examples
> 
> rprof_file <- system.file("samples/rprof/1.out", package = "profile")
> ds <- read_rprof(rprof_file)
> ds
Profile data: 22 samples
> pprof_file <- tempfile("profile", fileext = ".pb.gz")
> write_pprof(ds, pprof_file)
Error: Package RProtoBuf is required to read pprof files.
Backtrace:
    █
 1. └─profile::write_pprof(ds, pprof_file)
 2.   └─profile:::ds_to_msg(x)
 3.     └─profile:::provide_proto()
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    extdata   8.2Mb
Running ‘run-all.R’ [15s/28s]
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("ProjectTemplate")
  Loading required package: ProjectTemplate
  ── 1. Failure: Custom configuration is added to config (@test-add_config.R#12)  
  `load.project()` generated warnings:
  * 'options(stringsAsFactors = TRUE)' is deprecated and will be disabled
  
  ✔ |  OK F W S | Context
  
  ⠏ |   0       | Example tests
  ✔ |   1       | Example tests
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  ✔ |  OK F W S | Context
  
  ⠏ |   0       | Example tests
  ✔ |   1       | Example tests
  
  ══ Results ═════════════════════════════════════════════════════════════════════
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  [1] TRUE
  [1] FALSE
  [1] FALSE
  [1] FALSE
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 852 | SKIPPED: 4 | WARNINGS: 281 | FAILED: 1 ]
  1. Failure: Custom configuration is added to config (@test-add_config.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_start.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Rcpp
Loading required package: rlang

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 33-34 (quick_start.Rmd) 
Quitting from lines 33-34 (quick_start.Rmd) 
Error: processing vignette 'quick_start.Rmd' failed with diagnostics:
invalid connection
--- failed re-building ‘quick_start.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    extdata   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘barebones_correlation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘barebones_correlation.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 97-103 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
invalid 'row.names' length
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/psychonetrics.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    dict   5.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc        4.3Mb
    examples   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data_Model.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Data_Model.Rmd’

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

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

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

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

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

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

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

Traceback:
 1: pyinit(x = x, y = y, resid_keep_method = "proportion", psc_keep = 0.5,     resid_keep_prop = 0.5)
An irrecoverable exception occurred. R is aborting now ...
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    gui          1.6Mb
    staticdocs   3.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘orthography_processing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘orthography_processing.Rmd’

--- re-building ‘recoding_nominal_data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 49-60 (recoding_nominal_data.Rmd) 
Error: processing vignette 'recoding_nominal_data.Rmd' failed with diagnostics:
factor level [3] is duplicated
--- failed re-building ‘recoding_nominal_data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data  12.9Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R         1.9Mb
    contrib   3.7Mb
    doc       3.2Mb
    libs      1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Qtools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 124-146 (Qtools.Rmd) 
Error: processing vignette 'Qtools.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Qtools.Rmd’

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

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

--- re-building ‘topography.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 19-33 (topography.Rmd) 
Error: processing vignette 'topography.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘topography.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘wilcox1973.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Package unavailable to check Rd xrefs: ‘BRugs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘RAbHIT-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
RAbHIT version: 0.1.4
Quitting from lines 299-301 (RAbHIT-vignette.Rmd) 
Error: processing vignette 'RAbHIT-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘RAbHIT-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    app   6.0Mb
Running ‘testthat.R’ [12s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(radjust)
  > test_check("radjust")
  ── 1. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_adaptive` not equivalent to eo$mice_rv_adaptive.
  Component "results_table": Component "name": target is character, current is factor
  
  ── 2. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_non_adpt_sel` not equivalent to eo$mice_rv_non_adpt_sel.
  Component "results_table": Component "name": target is character, current is factor
  
  ── 3. Failure: The examples work and the outputs are equal to the saved copies (
  `mice_rv_non_adpt` not equivalent to eo$mice_rv_non_adpt.
  Component "results_table": Component "name": target is character, current is factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#9) 
  2. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#10) 
  3. Failure: The examples work and the outputs are equal to the saved copies (@test-radjust_sym.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.5Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    api           3.0Mb
    htmlwidgets   7.2Mb
Found the following files/directories:
  ‘blcs.dot’ ‘blcs.pdf’ ‘ex1.dot’ ‘ex1.pdf’ ‘ex1bridge1.dot’
  ‘ex1bridge1.pdf’ ‘ex1bridge2.dot’ ‘ex1bridge2.pdf’ ‘ex1bridge3.dot’
  ‘ex1bridge3.pdf’ ‘ex1effect1.dot’ ‘ex1effect1.pdf’ ‘ex1effect2.dot’
  ‘ex1effect2.pdf’ ‘gcmlinear.dot’ ‘gcmlinear.pdf’ ‘latent.dot’
  ‘latent.pdf’ ‘lcs.dot’ ‘lcs.pdf’ ‘mimic.dot’ ‘mimic.pdf’
Error(s) in re-building vignettes:
  ...
--- re-building ‘randomNames.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (randomNames.Rmd) 
Error: processing vignette 'randomNames.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘randomNames.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [192s/243s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(randomsearch)
  Loading required package: ParamHelpers
  Loading required package: smoof
  Loading required package: checkmate
  > 
  > test_check("randomsearch")
  Error : [ENOENT] Failed to stat '/tmp/RtmpLPa455/working_dir/RtmpxZa4mq/file2067591f36fd/2_10': no such file or directory
  ── 1. Error: parallel randomsearch works with parallelMap (@test_randomsearch.R#
  [ENOENT] Failed to stat '/tmp/RtmpLPa455/working_dir/RtmpxZa4mq/file2067591f36fd/2_10': no such file or directory
  
  Backtrace:
   1. randomsearch::randomsearch(...)
   2. randomsearch:::randomsearch.smoof_function(...)
   3. parallelMap::parallelMap(...)
   4. parallelMap:::checkResultsAndStopWithErrorsMessages(res)
   5. parallelMap:::stopWithJobErrorMessages(...)
   6. BBmisc::stopf(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 69 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: parallel randomsearch works with parallelMap (@test_randomsearch.R#83) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Rcpp

Attaching package: 'lubridate'

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

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

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

    date

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.5Mb
    etc    2.2Mb
    po     1.5Mb
Package suggested but not available for checking: ‘av’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   1.7Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    cont  25.9Mb
Running examples in ‘rchallenge-Ex.R’ failed
The error most likely occurred in:

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

```{r}
library(rchallenge)
```
<link rel="stylesheet" 
 href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
`r icon("fa-user")`
`r icon("fa-user fa-lg")`
`r icon("fa-user fa-2x")`
`r icon("fa-user fa-3x")`
`r icon("fa-user fa-3x fa-border")`
> rmarkdown::render(file)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rchallenge)
  > 
  > test_check("rchallenge")
  ── 1. Failure: pandoc available (@test-pandoc.R#2)  ────────────────────────────
  rmarkdown::pandoc_available("1.12.3") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: pandoc available (@test-pandoc.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘fuzzyrcmdrplugin.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 47-48 (fuzzyrcmdrplugin.Rmd) 
Error: processing vignette 'fuzzyrcmdrplugin.Rmd' failed with diagnostics:
Cluster setup failed. 1 worker of 1 failed to connect.
--- failed re-building ‘fuzzyrcmdrplugin.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.5Mb
    po    2.4Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    corpora   8.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RcppCNPy-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-104 (RcppCNPy-intro.Rmd) 
Error: processing vignette 'RcppCNPy-intro.Rmd' failed with diagnostics:
ImportError: No module named 'numpy'

Detailed traceback: 
  File "<string>", line 1, in <module>

--- failed re-building ‘RcppCNPy-intro.Rmd’

--- re-building ‘UsingReticulate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 84-94 (UsingReticulate.Rmd) 
Error: processing vignette 'UsingReticulate.Rmd' failed with diagnostics:
ImportError: No module named 'numpy'
--- failed re-building ‘UsingReticulate.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   7.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.5Mb
    lib       3.0Mb
    libs      1.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    include   5.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    include   6.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/RcppSimdJson.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [17s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RCSF)
  > 
  > test_check("RCSF")
  ── 1. Failure: csf algorithm works (@test-CSF.R#7)  ────────────────────────────
  length(id_ground) %in% c(15459L, 15453L) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: csf algorithm works (@test-CSF.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rdf_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

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

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'purrr'

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

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
Quitting from lines 183-187 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' failed with diagnostics:
Assigned data `paste(seq(as.numeric(lowerRange), as.numeric(upperRange)), collapse = ",")` must be compatible with existing data.
ℹ Error occurred for column `Indices`.
✖ No common type for `value` <character> and `x` <double>.
--- failed re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ReDaMoR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 155-161 (ReDaMoR.Rmd) 
Error: processing vignette 'ReDaMoR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ReDaMoR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [7s/20s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > # Modeled after the R6 testing structure: https://github.com/wch/R6/blob/master/tests/testthat.R
  > library(testthat)
  > library(REDCapR)
  > 
  > testthat::test_check("REDCapR")
  ── 1. Failure: validate_no_logical -concern dataset (@test-validate.R#36)  ─────
  ds$field_index not equal to 2.
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 135 | SKIPPED: 79 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: validate_no_logical -concern dataset (@test-validate.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [8s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rEDM)
  > 
  > if ("sample.kind" %in% names(formals(RNGkind)))
  + {
  +     suppressWarnings(RNGkind(sample.kind = "Rounding"))
  + }
  > 
  > test_check("rEDM")
  ── 1. Failure: multiview model_output works (@test_08_multiview.R#40)  ─────────
  digest::digest(round(model_output[, 1], 4)) not equal to "e5a987eb611ec1b250e616cb63e705e5".
  1/1 mismatches
  x[1]: "4a44297295aeb35b6fe54ef78e510397"
  y[1]: "e5a987eb611ec1b250e616cb63e705e5"
  
  ── 2. Failure: multiview model_output works (@test_08_multiview.R#42)  ─────────
  digest::digest(round(model_output[, 2], 4)) not equal to "3c35c2777121f5288749a397093b315f".
  1/1 mismatches
  x[1]: "6ce40d9c8cda41c48ab30216666c1b68"
  y[1]: "3c35c2777121f5288749a397093b315f"
  
  ── 3. Failure: multiview model_output works (@test_08_multiview.R#44)  ─────────
  digest::digest(round(model_output[, 3], 4)) not equal to "c00dbb731be86df5991ec0b46a1a5aee".
  1/1 mismatches
  x[1]: "60d6dd8107c0b095e993ba115cae9ced"
  y[1]: "c00dbb731be86df5991ec0b46a1a5aee"
  
  ── 4. Failure: beginning of range checking works (@test_11_error_checking.R#28) 
  Value hashes to e18b9aba52, not e5b3bb5459
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 190 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: multiview model_output works (@test_08_multiview.R#40) 
  2. Failure: multiview model_output works (@test_08_multiview.R#42) 
  3. Failure: multiview model_output works (@test_08_multiview.R#44) 
  4. Failure: beginning of range checking works (@test_11_error_checking.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘Rsymphony’

Package which this enhances but not available for checking: ‘Rcplex’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc   6.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'rENA'

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

    show

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

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

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


Attaching package: 'rENA'

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

    show

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

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'ssh', 'RPostgres'
Running examples in ‘respirometry-Ex.R’ failed
The error most likely occurred in:

> ### Name: calc_MO2
> ### Title: Calculate metabolic rate
> ### Aliases: calc_MO2
> 
> ### ** Examples
> 
> # get O2 data
> file <- system.file('extdata', 'witrox_file.txt', package = 'respirometry')
> o2_data <- na.omit(import_witrox(file, split_channels = TRUE)$CH_4)
Warning in strsplit(raw, split = "\r\n", fixed = T) :
  input string 1 is invalid UTF-8
Error in grep("Date &Time [", f[1:20], fixed = TRUE):length(f) : 
  argument of length 0
Calls: na.omit -> import_witrox
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [37s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("retistruct")
  Loading required package: retistruct
  ── 1. Error: IDT format is read correctly (@test-format-idt.R#9)  ──────────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(r)
  
  ── 2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8)  ───────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  ── 3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45)  
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(o)
  
  ── 4. Error: Serialisation works with a particular example (@test-reconstruct.R#
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a, error = message)
  
  ── 5. Error: No regression on Issue #21 (@test-regressions.R#5)  ───────────────
  non-numeric argument to binary operator
  Backtrace:
   1. retistruct::retistruct.read.markup(a)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 138 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 5 ]
  1. Error: IDT format is read correctly (@test-format-idt.R#9) 
  2. Error: Reconstruct SMI32 (CSV format) (@test-reconstruct.R#8) 
  3. Error: Reconstruct GMB530/R-CONTRA (IDT format) (@test-reconstruct.R#45) 
  4. Error: Serialisation works with a particular example (@test-reconstruct.R#98) 
  5. Error: No regression on Issue #21 (@test-regressions.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘revgeo-Ex.R’ failed
The error most likely occurred in:

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

Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    data   1.9Mb
    help   1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RFmerge-RainfallExample-minimal.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Linking to GEOS 3.6.3, GDAL 2.2.4, PROJ 5.2.0
Loading required package: sp
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.4, released 2018/03/19
 Path to GDAL shared files: /usr/local/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.4-1 
(C) 2019 M. Zambrano-Bigiarini and Oscar M. Baez-Villanueva (GPL >=3 license)
Type 'citation('RFmerge')' to see how to cite this package
Quitting from lines 268-274 (RFmerge-RainfallExample-minimal.Rmd) 
Error: processing vignette 'RFmerge-RainfallExample-minimal.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘RFmerge-RainfallExample-minimal.Rmd’

SUMMARY: processing the following file failed:
  ‘RFmerge-RainfallExample-minimal.Rmd’

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

Attaching package: 'dplyr'

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

    group_rows

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 230-274 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rfm-customer-level-data.Rmd’

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

Attaching package: 'dplyr'

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

    group_rows

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   2.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    doc       2.2Mb
    extdata   2.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/rGEDI.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘precipitation_stochastic_generation_v6.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: copula
Loading required package: RGENERATE
Loading required package: RMAWGEN
Loading required package: chron
NOTE: The default cutoff when expanding a 2-digit year
to a 4-digit year will change from 30 to 69 by Aug 2020
(as for Date and POSIXct in base R.)
Loading required package: date
Loading required package: vars
Loading required package: MASS
Loading required package: strucchange
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Loading required package: urca
Loading required package: lmtest

Attaching package: 'vars'

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

    A

Loading required package: blockmatrix
Loading required package: Matrix
Loading required package: stringr

Attaching package: 'stringr'

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

    boundary


Attaching package: 'lubridate'

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

    days, hours, minutes, seconds, years

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

    interval

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

    date

Quitting from lines 50-63 (precipitation_stochastic_generation_v6.Rmd) 
Error: processing vignette 'precipitation_stochastic_generation_v6.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘precipitation_stochastic_generation_v6.Rmd’

SUMMARY: processing the following file failed:
  ‘precipitation_stochastic_generation_v6.Rmd’

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘Rsymphony’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc     3.8Mb
    fonts   1.6Mb
    libs    1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘WebGL.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-19 (WebGL.Rmd) 
Error: processing vignette 'WebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘WebGL.Rmd’

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

--- re-building ‘rgl.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 16-19 (rgl.Rmd) 
Error: processing vignette 'rgl.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘rgl.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help  10.6Mb
    libs   3.1Mb
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_rhandsontable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro_rhandsontable.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [9s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(riskclustr)
  > 
  > test_check("riskclustr")
  ── 1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_message(...)
    6. riskclustr::optimal_kmeans_d(...)
    7. base::lapply(...)
    8. riskclustr:::FUN(X[[i]], ...)
    9. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   12. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   13. tibble:::tbl_subset_row(xo, i = i, i_arg)
   14. tibble:::vectbl_as_row_index(i, x, i_arg)
   15. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   22. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ── 2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_equal(...)
    4. riskclustr::optimal_kmeans_d(...)
    5. base::lapply(...)
    6. riskclustr:::FUN(X[[i]], ...)
    7. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   10. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   11. tibble:::tbl_subset_row(xo, i = i, i_arg)
   12. tibble:::vectbl_as_row_index(i, x, i_arg)
   13. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   20. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 26 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_kmeans_d.R#49) 
  2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_kmeans_d.R#65) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘calculate_d.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘calculate_d.Rmd’

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

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

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

--- re-building ‘optimal_d.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 36-46 (optimal_d.Rmd) 
Error: processing vignette 'optimal_d.Rmd' failed with diagnostics:
`i` must have one dimension, not 2.
--- failed re-building ‘optimal_d.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Note: information on .o files is not available
File ‘/home/ripley/R/Lib32-dev/rJava/libs/rJava.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    java  11.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RLumModel_-_Getting_started_with_RLumModel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Luminescence
Loading required package: magrittr
Welcome to the R package Luminescence version 0.9.7 [Built: 2020-03-28 06:17:33 UTC]
A Windows user: 'An apple a day keeps the doctor away.'
--- finished re-building ‘RLumModel_-_Getting_started_with_RLumModel.Rmd’

--- re-building ‘RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Luminescence
Loading required package: magrittr
Welcome to the R package Luminescence version 0.9.7 [Built: 2020-03-28 06:17:33 UTC]
A single grain: 'I feel so lonley.'
Quitting from lines 125-154 (RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd) 
Error: processing vignette 'RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd’

--- re-building ‘RLumModel_-_Using_own_parameter_sets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Luminescence
Loading required package: magrittr
Welcome to the R package Luminescence version 0.9.7 [Built: 2020-03-28 06:17:33 UTC]
An arctic sediment outcrop: 'Marmor, Stein und Eisen bricht...'
--- finished re-building ‘RLumModel_-_Using_own_parameter_sets.Rmd’

SUMMARY: processing the following file failed:
  ‘RLumModel_-_Simulating_luminescence_in_Al2O3.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    rmd   8.9Mb
installed size is  5.2Mb
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    java   4.4Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R  11.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘robin.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: gprege
Loading required package: gptk
Loading required package: Matrix
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.5-1 (2019-12-12) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    det

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

    backsolve, forwardsolve

Loading required package: maps
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
Quitting from lines 80-81 (robin.Rmd) 
Error: processing vignette 'robin.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘robin.Rmd’

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

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

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

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

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

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

 *** caught segfault ***
address 4, cause 'memory not mapped'

Traceback:
 1: Tabgamma(b1, b2, alpha1, alpha2, k, A, maxta, maxtc, maxit, til,     tol)
 2: gammaRob(x, ...)
 3: fitdstnRob(x = los, densfun = "gamma")
 4: eval(model.call, sys.parent())
 5: eval(model.call, sys.parent())
 6: fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"), x = los,     densfun = "gamma")
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.8Mb
    extdata   2.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   2.8Mb
Running ‘testthat.R’ [14s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rpf)
  Loading required package: parallel
  > 
  > test_check("rpf")
  ── 1. Failure: tpbw1995-table2 (@test-score.R#30)  ─────────────────────────────
  scores[, 1] not equal to c(0.084, -0.154).
  2/2 mismatches (average diff: 0.119)
  [1]  0.000 -  0.084 == -0.084
  [2] -0.307 - -0.154 == -0.153
  
  ── 2. Failure: tpbw1995-table2 (@test-score.R#31)  ─────────────────────────────
  scores[, 2] not equal to c(0.539, 0.572).
  2/2 mismatches (average diff: 0.388)
  [1] 0.000 - 0.539 == -0.539
  [2] 0.809 - 0.572 ==  0.237
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 400 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: tpbw1995-table2 (@test-score.R#30) 
  2. Failure: tpbw1995-table2 (@test-score.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/rpg.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘NEWS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘NEWS.Rmd’

--- re-building ‘rpivotTableIntroduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 51-53 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rpivotTableIntroduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/RPostgres.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rpredictit-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 54-56 (rpredictit-vignette.Rmd) 
Error: processing vignette 'rpredictit-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rpredictit-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 40-42 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
object 'warningc' not found
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following executable file:
  data/GH.RData
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/Rserve.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.8Mb
Running ‘testthat.R’ [30m/33m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(rsparse)
  > library(data.table)
  > library(Matrix)
  > options(rsparse_omp_threads = 1L)
  > logger = lgr::get_logger('rsparse')
  > logger$set_threshold('warn')
  > data("movielens100k")
  > test_check("rsparse")
Package required but not available: ‘GMMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    4.9Mb
    libs  10.9Mb
installed size is 11.6Mb
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    libs        8.5Mb
    unitTests   1.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Running examples in ‘RSuite-Ex.R’ failed
The error most likely occurred in:

> ### Name: prj_pack
> ### Title: Prepares project source pack tagged with version.
> ### Aliases: prj_pack
> 
> ### ** Examples
> 
> # create exemplary project base folder
> prj_base <- tempfile("example_")
> dir.create(prj_base, recursive = TRUE, showWarnings = FALSE)
> 
> # start project
> prj <- prj_start("my_project", skip_rc = TRUE, path = prj_base)
2020-04-02 15:49:39 INFO:rsuite:Project my_project has structure compliant with current version of RSuite(v0.37.253).
2020-04-02 15:49:39 INFO:rsuite:Project my_project started.
> 
> # create package in the project
> prj_start_package("mypackage", prj = prj, skip_rc = TRUE)
2020-04-02 15:49:39 INFO:rsuite:Package mypackage started in project my_project.
> 
> # build project source pack
> pack_fpath <- prj_pack(prj = prj, path = tempdir(), pack_ver = "1.0")
2020-04-02 15:49:39 WARNING:rsuite:Project environment is not locked!
2020-04-02 15:49:39 INFO:rsuite:Exporting project from /tmp/RtmpaTay0H/working_dir/Rtmpaua40Z/example_67a7609d3beb/my_project ...
2020-04-02 15:49:39 INFO:rsuite:Exporting project from /tmp/RtmpaTay0H/working_dir/Rtmpaua40Z/example_67a7609d3beb/my_project ... done
2020-04-02 15:49:41 WARNING:rsuite:Zip building aborted for /tmp/RtmpaTay0H/working_dir/Rtmpaua40Z/prjpack_my_project_1.0x.zip
2020-04-02 15:49:41 ERROR:rsuite:Failed to create pack file (zip returned non 0 return status).
Error: Failed to create pack file (zip returned non 0 return status).
Execution halted
installed size is  6.2Mb
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    data   5.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Skylark_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 171-172 (Skylark_example.Rmd) 
Error: processing vignette 'Skylark_example.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Skylark_example.Rmd’

--- re-building ‘rtrim_2_extensions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 261-264 (rtrim_2_extensions.Rmd) 
Error: processing vignette 'rtrim_2_extensions.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘rtrim_2_extensions.Rmd’

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

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

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

--- re-building ‘TRIM_methods_v2.pdf.asis’ using asis
--- finished re-building ‘TRIM_methods_v2.pdf.asis’

SUMMARY: processing the following files failed:
  ‘Skylark_example.Rmd’ ‘rtrim_2_extensions.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    7.9Mb
    libs   2.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     3.1Mb
    doc   1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   5.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      3.0Mb
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/s2.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc           3.3Mb
    htmlwidgets   1.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘R-versus-CPP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 63-72 (R-versus-CPP.Rmd) 
Error: processing vignette 'R-versus-CPP.Rmd' failed with diagnostics:
Package 'RcppArmadillo' referenced from LinkingTo directive is not available.
--- failed re-building ‘R-versus-CPP.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   3.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sankeywheel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-44 (sankeywheel.Rmd) 
Error: processing vignette 'sankeywheel.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sankeywheel.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 63.6Mb
  sub-directories of 1Mb or more:
    extdata  63.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.3Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'pogs'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    example   2.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data            1.5Mb
    vignette_data   2.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R   7.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Error(s) in re-building vignettes:
  ...
Cpu Limit Exceeded - core dumped
--- re-building ‘constraints.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: OpenMx
To take full advantage of multiple cores, use:
  mxOption(key='Number of Threads', value=parallel::detectCores()) #now
  Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
Warning: code chunks must not depend on the uncached chunk "difsim"
No Invariance alpha selected. alpha.invariance set to:0.05
Loading required package: ggplot2
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘getting-started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘airway’
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs   1.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data        1.7Mb
    sequences   2.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.3Mb
Packages suggested but not available for checking:
  'loomR', 'SDMTools', 'monocle'
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    doc     12.3Mb
    sqlite   1.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SGPdata.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-28 (SGPdata.Rmd) 
Error: processing vignette 'SGPdata.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGPdata.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   3.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SGP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP.Rmd) 
Error: processing vignette 'SGP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    examples           2.2Mb
    framework7-5.1.3   1.7Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    www   9.1Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    www   9.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘getting-started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Package suggested but not available for checking: ‘clipper’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘simPATHy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 263-269 (simPATHy.Rmd) 
Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
there is no package called 'clipper'
--- failed re-building ‘simPATHy.Rmd’

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

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: Ignoring unknown aesthetics: text
Warning: Ignoring unknown aesthetics: text
Warning: Ignoring unknown aesthetics: text
Warning: Ignoring unknown aesthetics: text
Warning: Removed 2 rows containing missing values (geom_col).
Warning: Ignoring unknown aesthetics: text
Quitting from lines 113-127 (simplevis.Rmd) 
Error: processing vignette 'simplevis.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘simplevis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(simrel)
  > 
  > test_check("simrel")
  ── 1. Error: Prepare Design (@test-utils.R#44)  ────────────────────────────────
  Can't join on 'q' x 'q' because of incompatible types (list / list)
  Backtrace:
   1. testthat::expect_identical(prepare_design(opts), dgn)
   3. testthat:::compare.default(act$val, exp$val)
   5. dplyr:::all.equal.tbl_df(x, y, ...)
   6. dplyr:::equal_data_frame(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 169 | SKIPPED: 21 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: Prepare Design (@test-utils.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘skm-vignettes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: magrittr
Loading required package: data.table
skm_mls: skm solver via skm_mls_cpp ...

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

skm_mls: optimizing on k <1> ...

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

skm_mls: optimizing on k <2> ...

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

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

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

skm_mls: optimizing on k <3> ...

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

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

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

skm_mls: optimizing on k <4> ...

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

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

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

skm_mls: optimizing on k <5> ...

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

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

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

skm_mls: optimizing on k <6> ...

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

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

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

skm_mls: optimizing on k <7> ...

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

skm_mls: encounter better solution at jk <7> run based on previous optim s ...

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

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

skm_mls: optimizing on k <8> ...

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

skm_mls: encounter better solution at jk <3> run based on previous optim s ...

skm_mls: encounter better solution at jk <5> run based on previous optim s ...
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   2.9Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘novel_solutions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘novel_solutions.Rmd’

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

--- re-building ‘understanding_sortable_js.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot5a5a4596592f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot5a5a4596592f.png': No such file or directory
Quitting from lines 71-72 (understanding_sortable_js.Rmd) 
Error: processing vignette 'understanding_sortable_js.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘understanding_sortable_js.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 3.43 secs
Identifing all possible orderings..
Total run time: 1.43 secs
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘SourceSet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_sparkline.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro_sparkline.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    java   3.0Mb
Running ‘testthat.R’ [12s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SpatialKDE)
  > 
  > test_check("SpatialKDE")
  ── 1. Error: (unknown) (@test-kde.R#29)  ───────────────────────────────────────
  package 'rgdal' is not available
  Backtrace:
   1. base::suppressWarnings(...)
   3. raster::projectRaster(test_raster, crs = "+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
   4. raster:::.requireRgdal()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 14 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-kde.R#29) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Running examples in ‘spatial.tools-Ex.R’ failed
The error most likely occurred in:

> ### Name: tahoe_highrez_training
> ### Title: Point and polygon files for use with spatial.tools
> ### Aliases: tahoe_highrez_training
> ### Keywords: data
> 
> ### ** Examples
> 
> library("raster")
Loading required package: sp
> library("rgdal")
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.4, released 2018/03/19
 Path to GDAL shared files: /usr/local/share/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.4-1 
> tahoe_highrez_training_polygons <- readOGR(
+ 	dsn=system.file("external", package="spatial.tools"),layer="tahoe_highrez_training")
OGR data source with driver: ESRI Shapefile 
Source: "/home/ripley/R/Lib32-dev/spatial.tools/external", layer: "tahoe_highrez_training"
with 8 features
It has 2 fields
> spplot(tahoe_highrez_training_polygons,zcol="Class")
Warning in extend.limits(range(as.numeric(z), finite = TRUE)) :
  NAs introduced by coercion
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 seq.default(zrng[1], zrng[2], length.out = cuts + 2) : 
  'from' must be a finite number
Calls: spplot ... <Anonymous> -> levelplot.formula -> seq -> seq.default
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      5.4Mb
    doc    5.1Mb
    help   5.3Mb
    libs   1.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
File ‘sqp/libs/sqp.so’:
  Found ‘__assert_c99’, possibly from ‘assert’ (C)
    Object: ‘solver_dense.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [47s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #    Copyright 2015 Province of British Columbia
  > #
  > #    Licensed under the Apache License, Version 2.0 (the "License");
  > #    you may not use this file except in compliance with the License.
  > #    You may obtain a copy of the License at
  > #
  > #       http://www.apache.org/licenses/LICENSE-2.0
  > #
  > #    Unless required by applicable law or agreed to in writing, software
  > #    distributed under the License is distributed on an "AS IS" BASIS,
  > #    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  > #    See the License for the specific language governing permissions and
  > #    limitations under the License.
  > 
  > library(testthat)
  > library(ssdtools)
  
  Attaching package: 'ssdtools'
  
  The following objects are masked from 'package:stats':
  
      dgamma, dweibull, pgamma, pweibull, qgamma, qweibull, rgamma,
      rweibull
  
  > 
  > test_check("ssdtools")
  ── 1. Failure: ssd_gof fitdistscens (@test-gof.R#46)  ──────────────────────────
  as.data.frame(ssd_gof(fluazinam_dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ── 2. Failure: manual (@test-schwarz-tillmans.R#24)  ───────────────────────────
  as.data.frame(ssd_gof(dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 269 | SKIPPED: 0 | WARNINGS: 12 | FAILED: 2 ]
  1. Failure: ssd_gof fitdistscens (@test-gof.R#46) 
  2. Failure: manual (@test-schwarz-tillmans.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lsndata   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘stacomir.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 281-303 (stacomir.Rmd) 
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
abs(round(sum(datasub$value, na.rm = TRUE), 2) - round(sum(datasub2$value,  .... is not TRUE
--- failed re-building ‘stacomir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    lib       1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘staple_example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc  10.6Mb
    nc    4.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘stars1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘stars1.Rmd’

--- re-building ‘stars2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘stars2.Rmd’

--- re-building ‘stars3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘stars3.Rmd’

--- re-building ‘stars4.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘stars4.Rmd’

--- re-building ‘stars5.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 131-134 (stars5.Rmd) 
Error: processing vignette 'stars5.Rmd' failed with diagnostics:
!is.na(st_crs(x)) is not TRUE
--- failed re-building ‘stars5.Rmd’

SUMMARY: processing the following file failed:
  ‘stars5.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R          2.3Mb
    datasets   2.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc   3.1Mb
Package suggested but not available for checking: ‘BSgenome.Ptroglodytes.UCSC.panTro5’
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘stRvignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
Process terminated
--- failed re-building ‘stRvignette.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    2.8Mb
    help   1.0Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   3.3Mb
    doc    3.9Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘survsup_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-96 (survsup_intro.Rmd) 
Error: processing vignette 'survsup_intro.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building ‘survsup_intro.Rmd’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘HTML.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

Quitting from lines 44-45 (HTML.Rmd) 
Error: processing vignette 'HTML.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘HTML.Rmd’

--- re-building ‘tables.Rnw’ using Sweave
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

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

    format.pval, units

--- finished re-building ‘tables.Rnw’

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

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

--- re-building ‘fda-example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 242-244 (fda-example.Rmd) 
Error: processing vignette 'fda-example.Rmd' failed with diagnostics:
attempt to set an attribute on NULL
--- failed re-building ‘fda-example.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [41s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(taxa)
  
  Attaching package: 'taxa'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("taxa")
  ── 1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 607 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#52) 
  2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#56) 
  3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_tbrf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 123-138 (intro_to_tbrf.Rmd) 
Error: processing vignette 'intro_to_tbrf.Rmd' failed with diagnostics:
Assigned data `as.numeric(results[1:length(results)])` must be compatible with existing data.
✖ Existing data has 1 row.
✖ Assigned data has 3 rows.
ℹ Only vectors of size 1 are recycled.
--- failed re-building ‘intro_to_tbrf.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    2.9Mb
XIO:  fatal IO error 146 (Connection refused) on X server ":5.0"
      after 0 requests (0 known processed) with 0 events remaining.
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/terra.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'lpsymphony', 'Rsymphony', 'gurobi'
Running ‘testthat.R’ [30s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(texPreview)
  > test_check("texPreview")
  ── 1. Error: (unknown) (@test-tex.R#115)  ──────────────────────────────────────
  R: delegate failed `'potrace' --svg --output '%o' '%i'' @ error/delegate.c/InvokeDelegate/1958
  Backtrace:
    1. testthat::describe(...)
    2. [ base::eval(...) ] with 1 more call
    5. texPreview:::tex_preview.xtable(...)
    7. texPreview:::tex_preview.character(...)
    8. texPreview:::tex_preview.default(...)
    9. texPreview:::tex_image(obj, stem, write_flag, overwrite)
   10. magick::image_write(imgOut, tex_path(fileDir, stem, dev = imgFormat))
   11. magick:::magick_image_write(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-tex.R#115) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.1Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   8.6Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    rda    7.7Mb
Running ‘testthat.R’ [53s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(themetagenomics)
  Loading required package: Rcpp
  > 
  > test_check("themetagenomics")
  ── 1. Failure: prepare_data works with multiclass factor (@test-prepare.R#92)  ─
  `prepare_data(...)` did not produce any warnings.
  
  ── 2. Error: prepare_data works with multiclass factor and continuous (@test-pre
  undefined columns selected
  Backtrace:
   1. testthat::expect_equal(...)
   5. base::`[.data.frame`(x$modelframe, , c("Multi1", "Multi3", "Day"))
  
  ── 3. Error: prepare_data works with multiclass factor and spline (@test-prepare
  undefined columns selected
  Backtrace:
   1. testthat::expect_equal(...)
   5. base::`[.data.frame`(x$modelframe, , c("Multi1", "Multi3", "Day"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 45 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: prepare_data works with multiclass factor (@test-prepare.R#92) 
  2. Error: prepare_data works with multiclass factor and continuous (@test-prepare.R#139) 
  3. Error: prepare_data works with multiclass factor and spline (@test-prepare.R#168) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [25s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(theseus)
  > 
  > test_check("theseus")
  ── 1. Error: rename_column_to_other returns taxa names of correct length (@test-
  attempting to coerce non-factor
  Backtrace:
   1. base::table(...)
   2. theseus:::rename_column_to_other(df, tax_level = "Phylum", top_taxa)
   3. base::as.character.factor(df[[tax_level]])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: rename_column_to_other returns taxa names of correct length (@test-helpers.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘tidydice.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 147-150 (tidydice.Rmd) 
Error: processing vignette 'tidydice.Rmd' failed with diagnostics:
Must extract column with a single valid subscript.
✖ The subscript `target_txt` can't be `NA`.
--- failed re-building ‘tidydice.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plot-smooths.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 172-177 (plot-smooths.Rmd) 
Error: processing vignette 'plot-smooths.Rmd' failed with diagnostics:
non-conformable arrays
--- failed re-building ‘plot-smooths.Rmd’

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

SUMMARY: processing the following file failed:
  ‘plot-smooths.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Rblpapi’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
Package unavailable to check Rd xrefs: ‘Rblpapi’
Running ‘testthat.R’ [34s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  ── 1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15)  ────
  paste(as.character(ovid[[1]]), collapse = " ") not equal to td$text[1].
  names for current but not for target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 297 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 1 ]
  1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Tigger-Vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: ggplot2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

sh: nproc:  not found
Quitting from lines 107-109 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command: 'Illegal seek'
--- failed re-building ‘Tigger-Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘sf::st_make_valid’ by ‘lwgeom::st_make_valid’ when loading ‘tmap’
See ‘/home/ripley/R/packages/tests-devel/tmap.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘toOrdinal.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (toOrdinal.Rmd) 
Error: processing vignette 'toOrdinal.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘toOrdinal.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Package suggested but not available for checking: ‘moveVis’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
Package unavailable to check Rd xrefs: ‘moveVis’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Source : http://tile.stamen.com/toner/13/4056/2748.png
Source : http://tile.stamen.com/toner/13/4057/2748.png
Source : http://tile.stamen.com/toner/13/4056/2749.png
Source : http://tile.stamen.com/toner/13/4057/2749.png
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘TourDetrackeR.Rmd’

--- re-building ‘trackeR.Rnw’ using Sweave
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Loading required package: splines
Loading required package: Matrix

Attaching package: 'fda'

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

    matplot

--- finished re-building 'trackeR.Rnw'

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

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

Attaching package: 'DT'

The following object is masked _by_ '.GlobalEnv':

    datatable

Quitting from lines 49-50 (basic-usage.Rmd) 
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘basic-usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [10s/119s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(traitdataform)
  > 
  > test_check("traitdataform")
  ── 1. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10)  ─────────
  Value hashes to 2448e3596a, not bc9f97d273
  
  ── 2. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#11)  ─────────
  Value hashes to 4381d5bd4d, not 74f9a02a12
  
  ── 3. Error: mapping of traits based on thesaurus works (@test.standardize.R#64)
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. traitdataform::standardize_traits(dataset2, thesaurus = traits2)
   2. base::droplevels(subset(out, traitNameStd == i)$traitUnitStd)
  
  ── 4. Error: factor level harmonizationworks (@test.standardize.R#81)  ─────────
  no applicable method for 'droplevels' applied to an object of class "character"
  Backtrace:
   1. traitdataform::standardize_traits(dd1)
   2. base::droplevels(subset(out, traitNameStd == i)$traitUnit)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 64 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#10) 
  2. Failure: gbif taxonomy reachable (@test.map_gbif_taxonomy.R#11) 
  3. Error: mapping of traits based on thesaurus works (@test.standardize.R#64) 
  4. Error: factor level harmonizationworks (@test.standardize.R#81) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘traitdataform.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 310-312 (traitdataform.Rmd) 
Error: processing vignette 'traitdataform.Rmd' failed with diagnostics:
no applicable method for 'droplevels' applied to an object of class "character"
--- failed re-building ‘traitdataform.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    fonts   5.3Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   7.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Running ‘testthat.R’ [7s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trustOptim)
  > 
  > test_check("trustOptim")
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    50       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   128       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   287       0.000000       0.000000Radius of trust region is less than stop.trust.radius
  
  ── 1. Failure: Rosenbrock (@test_rosenbrock.R#67)  ─────────────────────────────
  opt0\$status does not match "Success".
  Actual value: "Radius of trust region is less than stop\.trust\.radius"
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    65       0.000000       0.000000                    Success
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 15 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Rosenbrock (@test_rosenbrock.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc     1.5Mb
    fonts   2.9Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc     6.9Mb
    ubinc   2.2Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc         7.3Mb
    dummydata   1.5Mb
    libs        1.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.6Mb
Package suggested but not available for checking: ‘TSstudio’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-94 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.4Mb
Running examples in ‘umx-Ex.R’ failed
The error most likely occurred in:

> ### Name: RMSEA.summary.mxmodel
> ### Title: RMSEA function for MxModels
> ### Aliases: RMSEA.summary.mxmodel
> 
> ### ** Examples
> 
> require(umx)
> data(demoOneFactor)
> manifests = names(demoOneFactor)
> 
> m1 = umxRAM("One Factor", data = demoOneFactor, type = "cov",
+ 	umxPath("G", to = manifests),
+ 	umxPath(var = manifests),
+ 	umxPath(var = "G", fixedAt = 1.0)
+ )
A latent variable 'G' was created. 
Running One Factor with 10 parameters

 *** caught segfault ***
address a, cause 'memory not mapped'
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(umx)
  Loading required package: OpenMx
  To take full advantage of multiple cores, use:
    mxOption(key='Number of Threads', value=parallel::detectCores()) #now
    Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
  For an overview type '?umx'
  
  Attaching package: 'umx'
  
  The following object is masked from 'package:stats':
  
      loadings
  
  > 
  > test_check("umx")
  Error: C stack usage  276337812 is too close to the limit
  ── 1. Error: (unknown) (@test_residuals.MxModel.r#15)  ─────────────────────────
  The job for model 'test' exited abnormally with the error message: User interrupt
  Backtrace:
   1. umx::umxRAM(...)
   2. umx::xmu_safe_run_summary(...)
   3. base::tryCatch(...)
   4. base:::tryCatchList(expr, classes, parentenv, handlers)
   5. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6. value[[3L]](cond)
  
  Error: C stack usage  276337780 is too close to the limit
  Error: C stack usage  276337780 is too close to the limit
  ── 2. Error: testing umx twin models (@test_umx_ACE_etc.r#21)  ─────────────────
  The job for model 'IPa1c1e1' exited abnormally with the error message: 1:User interrupt
  2:User interrupt
  Backtrace:
   1. umx::umxIP(...)
   2. umx::xmu_safe_run_summary(model, autoRun = autoRun, tryHard = tryHard)
   3. base::tryCatch(...)
   4. base:::tryCatchList(expr, classes, parentenv, handlers)
   5. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   6. value[[3L]](cond)
  
  
   *** caught segfault ***
  address 3fea2726, cause 'memory not mapped'
Error(s) in re-building vignettes:
  ...
--- re-building ‘convexhull.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 93-98 (convexhull.Rmd) 
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘convexhull.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘upm-primer.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 70-71 (upm-primer.Rmd) 
Error: processing vignette 'upm-primer.Rmd' failed with diagnostics:
A variable(s) is listed by user as factors but data type in design matrix is not actually a factor. Reformat.
--- failed re-building ‘upm-primer.Rmd’

SUMMARY: processing the following file failed:
  ‘upm-primer.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.8Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data  14.9Mb
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    data  29.1Mb
Running ‘spelling.R’
  Running ‘testthat.R’ [36s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(usethis)
  > 
  > test_check("usethis")
  ── 1. Failure: use_logo() doesn't error (@test-use-logo.R#9)  ──────────────────
  `use_logo("logo.png")` threw an error.
  Message: R: negative or zero image size `' @ error/image.c/CloneImage/812
  Class:   Magick::ErrorCorruptImage/C++Error/error/condition
  Backtrace:
   1. usethis:::expect_error_free(use_logo("logo.png"))
   7. usethis::use_logo("logo.png")
   8. magick::image_write(img_data, logo_path)
   9. magick:::magick_image_write(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 418 | SKIPPED: 16 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: use_logo() doesn't error (@test-use-logo.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.8Mb
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    doc       1.9Mb
    extdata   6.6Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    extdata   9.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘varrank.Rmd’ using knitr
Loading required package: randomForest
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

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

    importance

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

    margin

Loading required package: parallel
Quitting from lines 122-125 (varrank.Rmd) 
Error: processing vignette 'varrank.Rmd' failed with diagnostics:
there is no package called 'FSelector'
--- failed re-building ‘varrank.Rmd’

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

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 54-55 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘basic_usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_vegalite.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro_to_vegalite.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      4.2Mb
    doc    1.3Mb
    help   3.0Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-visNetwork.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Introduction-to-visNetwork.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vortexRguide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 293-297 (vortexRguide.Rmd) 
Error: processing vignette 'vortexRguide.Rmd' failed with diagnostics:
Some items of .SDcols are not column names: [N]
--- failed re-building ‘vortexRguide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [27s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(vroom)
  > 
  > if (requireNamespace("xml2")) {
  +   test_check("vroom", reporter = MultiReporter$new(reporters = list(JunitReporter$new(file = "test-results.xml"), CheckReporter$new())))
  + } else {
  +   test_check("vroom")
  + }
  Loading required namespace: xml2
  ── 1. Error: vroom works with many connections (@test-multi-file.R#90)  ────────
  Evaluation error: cannot open the connection.
  Backtrace:
   1. vroom::vroom(files)
   2. vroom:::vroom_(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 691 | SKIPPED: 5 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: vroom works with many connections (@test-multi-file.R#90) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In as.list(attr(envir, "handlers")) :
    closing unused connection 4 (/tmp/RtmpUWaa4u/working_dir/Rtmpi1aOGI/file4505fce6b7f/133.csv.gz)
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   6.6Mb
Package suggested but not available for checking: ‘rcdk’
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    client  10.1Mb
    doc      1.1Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bn   7.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘wordcloud.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘wordcloud.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘spelling.R’
  Running ‘system-info.R’
  Running ‘testthat.R’ [68s/80s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("workflowr")
  This is workflowr version 1.6.1
  Run ?workflowr for help getting started
  > 
  > test_check("workflowr")
  ── 1. Error: check_wd_exists throws error if working directory has been deleted 
  [EINVAL] Failed to remove '/tmp/Rtmp1aaOpD/working_dir/RtmpjXaakT/file5a5063a29d0': invalid argument
  Backtrace:
   1. fs::dir_delete(path)
  
  ── 2. Error: wflow_status fails early if deleted subdirectory is current working
  [EINVAL] Failed to remove '/tmp/Rtmp1aaOpD/working_dir/RtmpjXaakT/file5a5075435bb7/sub': invalid argument
  Backtrace:
   1. fs::dir_delete(subdir)
  
  ── 3. Error: wflow_status fails early if deleted root directory is current worki
  [EINVAL] Failed to remove '/tmp/Rtmp1aaOpD/working_dir/RtmpjXaakT/file5a5063bb404': invalid argument
  Backtrace:
   1. fs::dir_delete(path)
  
  ── 4. Error: wflow_status fails early if deleted external directory is current w
  [EINVAL] Failed to remove '/tmp/Rtmp1aaOpD/working_dir/RtmpjXaakT/file5a501ba21a1': invalid argument
  Backtrace:
   1. fs::dir_delete(extdir)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1207 | SKIPPED: 165 | WARNINGS: 0 | FAILED: 4 ]
  1. Error: check_wd_exists throws error if working directory has been deleted (@test-utility.R#711) 
  2. Error: wflow_status fails early if deleted subdirectory is current working directory (@test-wflow_status.R#348) 
  3. Error: wflow_status fails early if deleted root directory is current working directory (@test-wflow_status.R#366) 
  4. Error: wflow_status fails early if deleted external directory is current working directory (@test-wflow_status.R#387) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data  13.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.9Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning: Removed 10 rows containing non-finite values (stat_smooth).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 5 row(s) containing missing values (geom_path).
Warning: Removed 10 rows containing missing values (geom_point).

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 214-234 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘x12’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/x12.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/ripley/R/packages/tests-devel/x13binary.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests-devel/XLConnect.Rcheck/00install.out’ for details.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.9Mb
Packages suggested but not available for checking: 'ChemmineR', 'fmcsR'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.1Mb
Found the following significant warnings:
  yakmo.h:184:1: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/ripley/R/packages/tests-devel/yakmoR.Rcheck/00install.out’ for details.
multiplot: no visible global function definition for ‘rainbow’
multiplot: no visible global function definition for ‘plot’
multiplot: no visible global function definition for ‘text’
multiplot: no visible global function definition for ‘lines’
multiplot: no visible global function definition for ‘par’
plot.abf2: no visible global function definition for ‘plot’
plot.abf2: no visible global function definition for ‘abline’
plot.abf2: no visible global function definition for ‘text’
plot.abf2split: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline lines par plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "plot", "text")
to your NAMESPACE file.
fillCSVData: no visible global function definition for ‘read.table’
fillData: no visible global function definition for ‘edit’
plotGraphs: no visible global function definition for ‘par’
plotGraphs: no visible global function definition for ‘plot’
plotGraphs: no visible global function definition for ‘lines’
plotGraphs: no visible global function definition for ‘legend’
plotGraphs: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  dev.new edit legend lines par plot read.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(apa)
  > 
  > test_check("apa")
  ── 1. Error: Output for anova_apa: repeated-measures ANOVA (@test-anova-apa.R#13
  Assigned data `<list>` must be compatible with existing data.
  ℹ Error occurred for column `df_n`.
  ✖ No common type for `value` <character> and `x` <double>.
  Backtrace:
    1. apa::anova_apa(...)
    2. apa:::anova_apa_afex(x, effect, sph_corr, es, format, info, print)
    7. tibble:::`[<-.tbl_df`(...)
    8. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. tibble:::tbl_subassign_row(xj, i, value, value_arg)
   10. base::tryCatch(...)
   11. base:::tryCatchList(expr, classes, parentenv, handlers)
   12. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13. value[[3L]](cond)
  
  ── 2. Error: Output for anova_apa: factorial repeated-measures ANOVA (@test-anov
  Assigned data `<list>` must be compatible with existing data.
  ℹ Error occurred for column `df_n`.
  ✖ No common type for `value` <character> and `x` <double>.
  Backtrace:
    1. apa::anova_apa(...)
    2. apa:::anova_apa_afex(x, effect, sph_corr, es, format, info, print)
    7. tibble:::`[<-.tbl_df`(...)
    8. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
    9. tibble:::tbl_subassign_row(xj, i, value, value_arg)
   10. base::tryCatch(...)
   11. base:::tryCatchList(expr, classes, parentenv, handlers)
   12. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   13. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 105 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 2 ]
  1. Error: Output for anova_apa: repeated-measures ANOVA (@test-anova-apa.R#135) 
  2. Error: Output for anova_apa: factorial repeated-measures ANOVA (@test-anova-apa.R#181) 
  
  Error: testthat unit tests failed
  Execution halted
Dependence on R version ‘3.4.2’ not with patchlevel 0
get.est.ATT: no visible global function definition for ‘tail’
get.est.MT: no visible global function definition for ‘tail’
get.est.simple: no visible global function definition for ‘tail’
newton.r: no visible global function definition for ‘tail’
plot.ATE: no visible global function definition for ‘par’
plot.ATE: no visible global function definition for ‘plot’
plot.ATE: no visible global function definition for ‘axis’
plot.ATE: no visible global function definition for ‘abline’
plot.ATE: no visible global function definition for ‘lines’
plot.ATE: no visible global function definition for ‘legend’
plot.ATE: no visible global function definition for ‘points’
print.summary.ATE: no visible global function definition for
  ‘printCoefmat’
summary.ATE: no visible global function definition for ‘qnorm’
summary.ATE: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis legend lines par plot pnorm points printCoefmat qnorm
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
atmcmc : rmvtnorm: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘rnorm’
atmcmc: no visible global function definition for ‘runif’
atmcmc: no visible global function definition for ‘par’
atmcmc: no visible global function definition for ‘lm’
atmcmc: no visible global function definition for ‘lines’
atmcmc: no visible global function definition for ‘var’
atmcmc: no visible global function definition for ‘cov’
atmcmc: no visible global function definition for ‘quantile’
atmcmc: no visible global function definition for ‘sd’
plotmcmc: no visible global function definition for ‘pdf’
plotmcmc: no visible global function definition for ‘par’
plotmcmc: no visible global function definition for ‘dev.new’
plotmcmc: no visible global function definition for ‘png’
plotmcmc: no visible global function definition for ‘hist’
plotmcmc: no visible global function definition for ‘dev.off’
plotmcmc: no visible global function definition for ‘plot’
plotmcmc: no visible global function definition for ‘lines’
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf plot png quantile rnorm
  runif sd var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
plot.AUC: no visible global function definition for ‘plot’
plot.AUC: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot
Consider adding
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: `data_frame()` is deprecated as of tibble 1.1.0.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/autocogs.Rcheck/00install.out’ for details.
BACprior.CV: no visible global function definition for ‘na.fail’
BACprior.CV: no visible global function definition for ‘plot’
BACprior.CV: no visible global function definition for ‘abline’
BACprior.boot: no visible global function definition for ‘na.fail’
BACprior.boot: no visible global function definition for ‘plot’
BACprior.boot: no visible global function definition for ‘abline’
BACprior.lm: no visible global function definition for ‘na.fail’
BACprior.lm: no visible global function definition for ‘coef’
BACprior.lm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  abline coef na.fail plot vcov
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
Dependence on R version ‘3.4.1’ not with patchlevel 0
MHratioPopPref: no visible global function definition for ‘runif’
MratioPopMult: no visible global function definition for ‘dunif’
MratioPopMult: no visible global function definition for ‘runif’
bayesPref: no visible global function definition for ‘runif’
calcP: no visible global function definition for ‘dunif’
calcP: no visible global function definition for ‘dmultinom’
calcdic: no visible global function definition for ‘median’
calcdic: no visible binding for global variable ‘median’
calcdic: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible global function definition for ‘median’
calcdicExtern: no visible global function definition for ‘dmultinom’
calcdicExtern: no visible binding for global variable ‘median’
credibleIntervals: no visible global function definition for ‘quantile’
prefPlot: no visible global function definition for ‘postscript’
prefPlot: no visible global function definition for ‘plot’
prefPlot: no visible global function definition for ‘lines’
prefPlot: no visible global function definition for ‘density’
prefPlot: no visible global function definition for ‘median’
prefPlot: no visible global function definition for ‘legend’
prefPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median plot postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
validate: no visible binding for global variable ‘qnorm’
validate: no visible global function definition for ‘pchisq’
validate: no visible global function definition for ‘qnorm’
validate: no visible global function definition for ‘plot’
validate: no visible global function definition for ‘axis’
validate: no visible global function definition for ‘points’
validate: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis pchisq plot points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
bbo: no visible global function definition for ‘runif’
bbo: no visible global function definition for ‘tail’
plot.bbo: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot runif tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
plot.cvsvd: no visible binding for global variable ‘sd’
plot.cvsvd: no visible global function definition for ‘plot’
plot.cvsvd: no visible global function definition for ‘lines’
plot.cvsvd: no visible global function definition for ‘segments’
plot.cvsvd: no visible global function definition for ‘points’
print.cvsvd: no visible binding for global variable ‘sd’
summary.cvsvd: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  lines plot points sd segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
beadtypeFilter: no visible global function definition for ‘na.omit’
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’
emCDF: no visible global function definition for ‘plot’
emCDF: no visible global function definition for ‘ecdf’
emCDF: no visible global function definition for ‘legend’
emCDF: no visible global function definition for ‘lines’
emCDF: no visible global function definition for ‘text’
emCDF: no visible global function definition for ‘reshape’
iccFun : <anonymous>: no visible global function definition for
  ‘quantile’
varianceplot: no visible global function definition for ‘reshape’
varianceplot: no visible global function definition for ‘plot’
varianceplot: no visible global function definition for ‘points’
varianceplot: no visible global function definition for ‘legend’
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit plot points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
Running ‘testthat.R’ [124s/135s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(beadplexr)
  > 
  > test_check("beadplexr")
  ── 1. Error: ident_bead_pop() works (@test_identify_assay_analyte.R#39)  ───────
  Assigned data `c("A", "B")` must be compatible with existing data.
  ✖ Existing data has 5126 rows.
  ✖ Assigned data has 2 rows.
  ℹ Only vectors of size 1 are recycled.
  Backtrace:
   1. base::`$<-`(`*tmp*`, BeadID, value = c("A", "B"))
   2. tibble:::`$<-.tbl_df`(`*tmp*`, BeadID, value = c("A", "B"))
   3. tibble:::tbl_subassign(...)
   4. tibble:::vectbl_recycle_rhs(...)
   5. base::tryCatch(...)
   6. base:::tryCatchList(expr, classes, parentenv, handlers)
   7. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 398 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: ident_bead_pop() works (@test_identify_assay_analyte.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(biscale)
  > 
  > test_check("biscale")
  ── 1. Error: sf warning is triggered (@test_bi_class.R#10)  ────────────────────
  All columns in a tibble must be vectors.
  ✖ Column `geometry` is a `sfc_POLYGON/sfc` object.
  Backtrace:
    1. testthat::expect_warning(...)
    6. biscale::bi_class(...)
    8. dplyr:::mutate.data.frame(...)
   11. dplyr::tbl_df(.data)
   13. tibble:::as_tibble.data.frame(data, .name_repair = "check_unique")
   14. tibble:::lst_to_tibble(unclass(x), .rows, .name_repair)
   15. tibble:::check_valid_cols(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 82 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: sf warning is triggered (@test_bi_class.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
BOGest: no visible global function definition for ‘read.table’
BOGstat: no visible global function definition for ‘phyper’
BOGstat: no visible global function definition for ‘wilcox.test’
BOGstat: no visible global function definition for ‘p.adjust’
gseaplot: no visible global function definition for ‘par’
gseaplot: no visible global function definition for ‘plot’
gseaplot: no visible global function definition for ‘points’
gseaplot: no visible global function definition for ‘axis’
gseaplot: no visible global function definition for ‘segments’
hgplot: no visible global function definition for ‘par’
hgplot: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  axis barplot p.adjust par phyper plot points read.table segments
  wilcox.test
Consider adding
  importFrom("graphics", "axis", "barplot", "par", "plot", "points",
             "segments")
  importFrom("stats", "p.adjust", "phyper", "wilcox.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.
bPeaksAnalysis: no visible global function definition for ‘write.table’
dataReading: no visible global function definition for ‘read.table’
dataSmoothing: no visible global function definition for ‘filter’
peakDetection: no visible global function definition for ‘quantile’
peakDetection: no visible global function definition for ‘pdf’
peakDetection: no visible global function definition for ‘par’
peakDetection: no visible global function definition for ‘plot’
peakDetection: no visible global function definition for ‘text’
peakDetection: no visible global function definition for ‘abline’
peakDetection: no visible global function definition for ‘points’
peakDetection: no visible global function definition for ‘dev.off’
peakDetection: no visible global function definition for ‘write.table’
peakDrawing: no visible global function definition for ‘par’
peakDrawing: no visible global function definition for ‘plot’
peakDrawing: no visible global function definition for ‘abline’
peakLocation: no visible global function definition for ‘read.table’
peakLocation: no visible global function definition for ‘pdf’
peakLocation: no visible global function definition for ‘barplot’
peakLocation: no visible global function definition for ‘dev.off’
peakLocation: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline barplot dev.off filter par pdf plot points quantile read.table
  text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "plot", "points",
             "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
apply.breaks: no visible binding for global variable ‘median’
break.clust: no visible global function definition for ‘plot’
break.clust: no visible global function definition for ‘median’
breakage.plot: no visible binding for global variable ‘median’
breakage.plot: no visible global function definition for ‘plot’
breakage.plot: no visible global function definition for ‘abline’
breakage.plot: no visible global function definition for ‘lm’
find.bottom: no visible global function definition for ‘filter’
fit.breakage: no visible global function definition for ‘optim’
fit.breakage: no visible global function definition for ‘plot’
fit.breakage: no visible global function definition for ‘points’
fit.sensitivity.plot: no visible global function definition for
  ‘contour’
fit.sensitivity.plot: no visible global function definition for
  ‘points’
fit.sensitivity.plot: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline contour filter lm median optim plot points text
Consider adding
  importFrom("graphics", "abline", "contour", "plot", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
plot.bspec: no visible global function definition for ‘par’
plot.bspec: no visible global function definition for ‘plot’
plot.bspec: no visible global function definition for ‘matlines’
plot.bspec: no visible global function definition for ‘points’
plot.bspec: no visible global function definition for ‘axis’
plot.bspec: no visible global function definition for ‘mtext’
plot.bspec: no visible global function definition for ‘axTicks’
plot.bspec: no visible global function definition for ‘box’
plot.bspecACF: no visible global function definition for ‘plot’
plot.bspecACF: no visible global function definition for ‘abline’
plot.bspecACF: no visible global function definition for ‘matlines’
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par plot points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "plot", "points")
to your NAMESPACE file.
plot.bursts: no visible global function definition for ‘plot’
plot.bursts: no visible global function definition for ‘axis’
plot.bursts: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis plot
Consider adding
  importFrom("graphics", "arrows", "axis", "plot")
to your NAMESPACE file.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of ‘nc’ to ‘ncol’
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘plot’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘plot’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
ccd.sequential: no visible global function definition for ‘qchisq’
dominate.random.sample: no visible global function definition for
  ‘runif’
draw.circle: no visible global function definition for ‘polygon’
juggle2: no visible global function definition for ‘rbinom’
plot.cccd: no visible global function definition for ‘gray’
plot.cccd: no visible global function definition for ‘plot’
plot.cccd: no visible global function definition for ‘points’
plot.cccdClassifier: no visible global function definition for ‘points’
plot.cccdClassifier: no visible global function definition for ‘plot’
plot.ccd: no visible global function definition for ‘plot’
Undefined global functions or variables:
  gray plot points polygon qchisq rbinom runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot", "points", "polygon")
  importFrom("stats", "qchisq", "rbinom", "runif")
to your NAMESPACE file.
p.Roy: no visible global function definition for ‘pf’
p.asym: no visible global function definition for ‘pf’
p.perm: no visible global function definition for ‘cancor’
plt.asym: no visible global function definition for ‘qf’
plt.asym: no visible global function definition for ‘plot’
plt.asym: no visible global function definition for ‘df’
plt.asym: no visible global function definition for ‘abline’
plt.perm: no visible global function definition for ‘hist’
plt.perm: no visible global function definition for ‘mtext’
plt.perm: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cancor df hist mtext pf plot qf
Consider adding
  importFrom("graphics", "abline", "hist", "mtext", "plot")
  importFrom("stats", "cancor", "df", "pf", "qf")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: `data_frame()` is deprecated as of tibble 1.1.0.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/cdcfluview.Rcheck/00install.out’ for details.
CM: no visible global function definition for ‘sd’
Erf: no visible global function definition for ‘pnorm’
Erfc: no visible global function definition for ‘pnorm’
boot.Cenarma: no visible global function definition for ‘coef’
boot.Cenarma: no visible global function definition for ‘arima.sim’
cenarma: no visible global function definition for ‘arima’
cenarma: no visible global function definition for ‘coef’
cenarma: no visible global function definition for ‘ARMAacf’
cenarma: no visible global function definition for ‘var’
plot.cents: no visible global function definition for ‘plot’
plot.cents: no visible global function definition for ‘segments’
plot.cents: no visible global function definition for ‘rgb’
plot.cents: no visible global function definition for ‘points’
rcarma: no visible global function definition for ‘arima.sim’
rcarma: no visible global function definition for ‘quantile’
scenNID: no visible global function definition for ‘sd’
se.Cenarma: no visible global function definition for ‘coef’
se.Cenarma: no visible global function definition for ‘sd’
Undefined global functions or variables:
  ARMAacf arima arima.sim coef plot pnorm points quantile rgb sd
  segments var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "ARMAacf", "arima", "arima.sim", "coef", "pnorm",
             "quantile", "sd", "var")
to your NAMESPACE file.
sw.plot : <anonymous>: no visible global function definition for
  ‘median’
sw.plot : <anonymous>: no visible global function definition for ‘mad’
sw.plot : my.line: no visible global function definition for ‘lines’
sw.plot : island.line: no visible global function definition for
  ‘lines’
sw.plot: no visible global function definition for ‘plot’
sw.plot: no visible global function definition for ‘rug’
sw.plot: no visible global function definition for ‘axis’
sw.plot: no visible global function definition for ‘mtext’
sw.plot: no visible global function definition for ‘abline’
sw.plot: no visible global function definition for ‘points’
sw.rob : <anonymous>: no visible global function definition for
  ‘median’
sw.rob : <anonymous>: no visible global function definition for ‘mad’
sw.threshold : <anonymous>: no visible global function definition for
  ‘median’
sw.threshold : <anonymous>: no visible global function definition for
  ‘mad’
Undefined global functions or variables:
  abline axis lines mad median mtext plot points rug
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "plot",
             "points", "rug")
  importFrom("stats", "mad", "median")
to your NAMESPACE file.
Running examples in ‘CGPfunctions-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chaid_table
> ### Title: Produce CHAID results tables from a partykit CHAID model
> ### Aliases: chaid_table
> 
> ### ** Examples
> 
> library(CGPfunctions)
> chaid_table(chaidUS)
Error: Assigned data `min(unlist(nodeapply(chaidobject, ids = all_nodes, FUN = function(n) n$info)[[i]]))` must be compatible with existing data.
ℹ Error occurred for column `adjustedp`.
✖ Lossy cast from `value` <double> to `x` <logical>.
* Locations: 1.
Backtrace:
    █
 1. └─CGPfunctions::chaid_table(chaidUS)
 2.   ├─base::`[<-`(`*tmp*`, split_table$nodeID == i, "adjustedp", value = 9.03286955807219e-08)
 3.   └─tibble:::`[<-.tbl_df`(...)
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::tbl_subassign_row(xj, i, value, value_arg)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
CityPlot: no visible global function definition for ‘read.table’
CityPlot: no visible global function definition for ‘tail’
CityPlot: no visible global function definition for ‘pdf’
CityPlot: no visible global function definition for ‘split.screen’
CityPlot: no visible global function definition for ‘screen’
CityPlot: no visible global function definition for ‘par’
CityPlot: no visible global function definition for ‘plot’
CityPlot: no visible global function definition for ‘rect’
CityPlot: no visible global function definition for ‘text’
CityPlot: no visible global function definition for ‘lines’
CityPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off lines par pdf plot read.table rect screen split.screen tail
  text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘getstarted.Rmd’ using rmarkdown
trying URL ‘http://weather.uwyo.edu/cgi-bin/sounding?region=europe&TYPE=TEXT%3ALIST&YEAR=2020&MONTH=03&FROM=2300&TO=2300&STNM=12120’
Quitting from lines 112-116 (getstarted.Rmd) 
Error: processing vignette 'getstarted.Rmd' failed with diagnostics:
cannot open URL ‘http://weather.uwyo.edu/cgi-bin/sounding?region=europe&TYPE=TEXT%3ALIST&YEAR=2020&MONTH=03&FROM=2300&TO=2300&STNM=12120’
--- failed re-building ‘getstarted.Rmd’

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

Error: Vignette re-building failed.
Execution halted
alpha.cronbach: no visible global function definition for ‘cov’
alpha.curve: no visible global function definition for ‘plot’
alpha.curve: no visible global function definition for ‘text’
Undefined global functions or variables:
  cov plot text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
copynumberBootstrap: no visible global function definition for
  ‘txtProgressBar’
copynumberBootstrap: no visible global function definition for
  ‘quantile’
copynumberBootstrap: no visible global function definition for
  ‘setTxtProgressBar’
gethits: no visible global function definition for ‘read.table’
normalizeGC: no visible global function definition for ‘median’
plotCNOGpro: no visible global function definition for ‘par’
plotCNOGpro: no visible global function definition for ‘plot’
plotCNOGpro: no visible global function definition for ‘rainbow’
plotCNOGpro: no visible global function definition for ‘density’
plotCNOGpro: no visible global function definition for ‘polygon’
plotCNOGpro: no visible global function definition for ‘lines’
plotCNOGpro: no visible global function definition for ‘legend’
plotCNOGpro: no visible global function definition for ‘boxplot’
sampleChromosome: no visible global function definition for ‘median’
sampleChromosome: no visible binding for global variable ‘var’
setupEmissionMatrix: no visible global function definition for ‘dgeom’
store: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  boxplot density dgeom legend lines median par plot polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "plot",
             "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
coalescentMCMC: no visible global function definition for
  ‘packageVersion’
coalescentMCMC : getparams: no visible global function definition for
  ‘nlminb’
sim.coalescent: no visible global function definition for ‘plot’
sim.coalescent: no visible global function definition for ‘segments’
sim.coalescent: no visible global function definition for ‘points’
Undefined global functions or variables:
  nlminb packageVersion plot points segments
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "nlminb")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
addxaxis: no visible global function definition for ‘par’
addxaxis: no visible global function definition for ‘axis’
addxaxis: no visible global function definition for ‘mtext’
eplot: no visible global function definition for ‘plot’
eplot: no visible global function definition for ‘par’
eplot: no visible global function definition for ‘axis’
eplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis mtext par plot
Consider adding
  importFrom("graphics", "axis", "mtext", "par", "plot")
to your NAMESPACE file.
Running ‘testthat.R’ [8s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(compstatr)
  > 
  > test_check("compstatr")
  ── 1. Failure: correct output is returned on sample data (@test_projectXY.R#36) 
  sf::st_crs(results)[[1]] not equal to 4269.
  Types not compatible: character is not double
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 225 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: correct output is returned on sample data (@test_projectXY.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
conicPlot: no visible global function definition for ‘palette’
conicPlotAsymptotes: no visible global function definition for
  ‘palette’
conicPlotAsymptotes: no visible global function definition for ‘abline’
conicPlotAxes: no visible global function definition for ‘palette’
conicPlotAxes: no visible global function definition for ‘abline’
plotDegenerateConic: no visible global function definition for ‘plot’
plotDegenerateConic: no visible global function definition for ‘points’
plotDegenerateConic: no visible global function definition for ‘abline’
plotEllipsis: no visible global function definition for ‘lines’
plotEllipsis: no visible global function definition for ‘plot’
plotEllipsis: no visible global function definition for ‘points’
plotHyperbola: no visible global function definition for ‘lines’
plotHyperbola: no visible global function definition for ‘plot’
plotHyperbola: no visible global function definition for ‘points’
plotParabola: no visible global function definition for ‘lines’
plotParabola: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline lines palette plot points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "plot", "points")
to your NAMESPACE file.
maCooperative: no visible global function definition for ‘points’
maCooperative: no visible global function definition for ‘legend’
maPessimistic: no visible global function definition for ‘combn’
maRules: no visible global function definition for ‘capture.output’
mstCooperative: no visible global function definition for ‘points’
mstCooperative: no visible global function definition for ‘legend’
mstOptimistic: no visible global function definition for ‘combn’
mstPessimistic: no visible global function definition for ‘combn’
mstRules: no visible global function definition for ‘capture.output’
plotCoreSet: no visible global function definition for ‘points’
plotCoreSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘par’
plotImputationSet: no visible global function definition for ‘plot’
plotImputationSet: no visible global function definition for ‘box’
plotImputationSet: no visible global function definition for ‘polygon’
plotImputationSet: no visible global function definition for ‘text’
shapleyValue: no visible global function definition for ‘combn’
Undefined global functions or variables:
  box capture.output combn legend par plot points polygon text
Consider adding
  importFrom("graphics", "box", "legend", "par", "plot", "points",
             "polygon", "text")
  importFrom("utils", "capture.output", "combn")
to your NAMESPACE file.
Running ‘testthat.R’ [4s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(covid19us)
  > 
  > test_check("covid19us")
  ── 1. Failure: get_states_daily works (@test-all.R#21)  ────────────────────────
  nrow(too_early) not equal to 0.
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 12 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: get_states_daily works (@test-all.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
CoxBoost: no visible global function definition for ‘Matrix’
CoxBoost: no visible binding for global variable ‘sd’
CoxBoost: no visible global function definition for ‘predict’
cv.CoxBoost : eval.fold: no visible global function definition for
  ‘predict’
cv.CoxBoost: no visible global function definition for ‘mclapply’
cv.CoxBoost: no visible binding for global variable ‘sd’
estimPVal: no visible global function definition for ‘mclapply’
iCoxBoost: no visible global function definition for ‘terms’
iCoxBoost: no visible global function definition for ‘model.response’
iCoxBoost: no visible global function definition for ‘model.frame’
iCoxBoost: no visible global function definition for ‘model.matrix’
iCoxBoost: no visible global function definition for ‘Matrix’
plot.CoxBoost: no visible global function definition for ‘plot’
plot.CoxBoost: no visible global function definition for ‘lines’
plot.CoxBoost: no visible global function definition for ‘text’
predict.iCoxBoost: no visible global function definition for
  ‘model.response’
predict.iCoxBoost: no visible global function definition for
  ‘model.frame’
predict.iCoxBoost: no visible global function definition for
  ‘model.matrix’
Undefined global functions or variables:
  Matrix lines mclapply model.frame model.matrix model.response plot
  predict sd terms text
Consider adding
  importFrom("graphics", "lines", "plot", "text")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "predict", "sd", "terms")
to your NAMESPACE file.
comp.graph: no visible global function definition for ‘qnorm’
comp.graph: no visible global function definition for ‘plot’
comp.graph: no visible global function definition for ‘polygon’
comp.graph: no visible global function definition for ‘lines’
cox.ridge: no visible global function definition for ‘terms’
cox.ridge: no visible global function definition for ‘model.extract’
cox.ridge: no visible global function definition for ‘model.matrix’
cox.ridge: no visible binding for global variable ‘hat’
Undefined global functions or variables:
  hat lines model.extract model.matrix plot polygon qnorm terms
Consider adding
  importFrom("graphics", "lines", "plot", "polygon")
  importFrom("stats", "hat", "model.extract", "model.matrix", "qnorm",
             "terms")
to your NAMESPACE file.
coxr: no visible global function definition for ‘model.extract’
coxr: no visible global function definition for ‘model.matrix’
coxr.draw: no visible global function definition for ‘plot’
coxr.draw: no visible global function definition for ‘lines’
coxr.draw: no visible global function definition for ‘points’
coxr.fit: no visible global function definition for ‘quantile’
gen_data: no visible global function definition for ‘rnorm’
gen_data: no visible global function definition for ‘rexp’
plot.coxr: no visible global function definition for ‘quantile’
plot.coxr: no visible global function definition for ‘par’
plot.coxr: no visible global function definition for ‘mtext’
plot.coxr: no visible global function definition for ‘title’
plot.coxr: no visible global function definition for ‘split.screen’
plot.coxr: no visible global function definition for ‘screen’
plot.coxr: no visible global function definition for ‘close.screen’
print.coxr: no visible global function definition for ‘pnorm’
print.coxr: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  close.screen lines model.extract model.matrix mtext par pchisq plot
  pnorm points quantile rexp rnorm screen split.screen title
Consider adding
  importFrom("graphics", "close.screen", "lines", "mtext", "par", "plot",
             "points", "screen", "split.screen", "title")
  importFrom("stats", "model.extract", "model.matrix", "pchisq", "pnorm",
             "quantile", "rexp", "rnorm")
to your NAMESPACE file.
csSAM: no visible binding for global variable ‘quantile’
csSAM: no visible global function definition for ‘median’
csfit: no visible global function definition for ‘lsfit’
csfit: no visible global function definition for ‘ls.diag’
plotCsSAM: no visible global function definition for ‘pdf’
plotCsSAM: no visible global function definition for ‘par’
plotCsSAM: no visible global function definition for ‘plot’
plotCsSAM: no visible global function definition for ‘title’
plotCsSAM: no visible global function definition for ‘dev.off’
runSAM: no visible binding for global variable ‘median’
runSAM: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  dev.off ls.diag lsfit median par pdf plot quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ctsem.Rcheck/00install.out’ for details.
cci.nostrat: no visible global function definition for ‘quantile’
cci.nostrat: no visible global function definition for ‘plot’
cci.nostrat: no visible global function definition for ‘axis’
cci.nostrat: no visible global function definition for ‘lines’
cci.nostrat: no visible global function definition for ‘legend’
cci.strat: no visible global function definition for ‘plot’
cci.strat: no visible global function definition for ‘axis’
cci.strat: no visible global function definition for ‘lines’
cci.strat: no visible global function definition for ‘legend’
clfs.nostrat: no visible global function definition for ‘quantile’
clfs.nostrat: no visible global function definition for ‘plot’
clfs.nostrat: no visible global function definition for ‘axis’
clfs.nostrat: no visible global function definition for ‘lines’
clfs.nostrat: no visible global function definition for ‘legend’
clfs.strat: no visible global function definition for ‘plot’
clfs.strat: no visible global function definition for ‘axis’
clfs.strat: no visible global function definition for ‘lines’
clfs.strat: no visible global function definition for ‘legend’
pvals.2cat: no visible global function definition for ‘pchisq’
pvals.cat: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  axis legend lines pchisq plot quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
allCombs: no visible global function definition for ‘combn’
brute.search: no visible global function definition for ‘na.omit’
dag.draw: no visible global function definition for ‘plot’
dag.draw: no visible global function definition for ‘text’
dag.init: no visible global function definition for
  ‘installed.packages’
dag.legend: no visible global function definition for ‘text’
dag.letter: no visible global function definition for ‘text’
dag.move: no visible global function definition for ‘identify’
dag.move: no visible global function definition for ‘locator’
dag.sim: no visible global function definition for ‘rnorm’
dag.sim: no visible global function definition for ‘rbinom’
dag.sim : <anonymous>: no visible global function definition for
  ‘rbinom’
garrows: no visible global function definition for ‘arrows’
smoothArc: no visible global function definition for ‘points’
summary_dagRdag: no visible global function definition for ‘na.omit’
viv: no visible global function definition for ‘na.omit’
write.paths: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows combn identify installed.packages locator na.omit plot points
  rbinom rnorm text
Consider adding
  importFrom("graphics", "arrows", "identify", "locator", "plot",
             "points", "text")
  importFrom("stats", "na.omit", "rbinom", "rnorm")
  importFrom("utils", "combn", "installed.packages")
to your NAMESPACE file.
drawAimSpot: no visible global function definition for ‘points’
drawBoard: no visible global function definition for ‘par’
drawBoard: no visible global function definition for ‘plot’
drawBoard: no visible global function definition for ‘points’
drawBoard: no visible global function definition for ‘text’
drawHeatmap: no visible global function definition for ‘heat.colors’
drawHeatmap: no visible global function definition for ‘par’
drawHeatmap: no visible global function definition for ‘image’
drawHeatmap: no visible global function definition for ‘rect’
generalExpScores: no visible global function definition for ‘fft’
simpleExpScores: no visible global function definition for ‘mvfft’
simpleExpScores: no visible global function definition for ‘fft’
Undefined global functions or variables:
  fft heat.colors image mvfft par plot points rect text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "points", "rect",
             "text")
  importFrom("stats", "fft", "mvfft")
to your NAMESPACE file.
datadict.profile: no visible global function definition for
  ‘txtProgressBar’
datadict.profile: no visible global function definition for
  ‘setTxtProgressBar’
datadict_profile: no visible global function definition for
  ‘txtProgressBar’
datadict_profile: no visible global function definition for
  ‘setTxtProgressBar’
heatmap.quality: no visible global function definition for
  ‘colorRampPalette’
heatmap.quality: no visible global function definition for ‘heatmap’
heatmap_quality: no visible global function definition for
  ‘colorRampPalette’
heatmap_quality: no visible global function definition for ‘heatmap’
is.oneOf: no visible global function definition for ‘read.csv’
is_one_of: no visible global function definition for ‘read.csv’
pkg.version: no visible global function definition for ‘citation’
pkg_version: no visible global function definition for ‘citation’
ruleCoverage: no visible global function definition for ‘dotchart’
ruleCoverage: no visible global function definition for ‘abline’
rule_coverage: no visible global function definition for ‘dotchart’
rule_coverage: no visible global function definition for ‘abline’
scoreSum: no visible global function definition for ‘plot’
score_sum: no visible global function definition for ‘plot’
shortSummary: no visible global function definition for ‘sd’
short_summary: no visible global function definition for ‘sd’
Undefined global functions or variables:
  abline citation colorRampPalette dotchart heatmap plot read.csv sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "dotchart", "plot")
  importFrom("stats", "heatmap", "sd")
  importFrom("utils", "citation", "read.csv", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
ifft: no visible global function definition for ‘fft’
lines.deamer: no visible global function definition for ‘lines’
plot.deamer: no visible global function definition for ‘plot’
rlaplace: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fft lines plot runif
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
compare.relimp: no visible global function definition for ‘qchisq’
compare.relimp: no visible global function definition for ‘pchisq’
plot_transition: no visible global function definition for ‘dnorm’
plot_transition: no visible global function definition for ‘par’
plot_transition: no visible global function definition for ‘plot’
plot_transition: no visible global function definition for ‘lines’
plot_transition: no visible global function definition for ‘plogis’
plot_transition: no visible global function definition for ‘axis’
plot_transition: no visible global function definition for ‘mtext’
relative.importance: no visible global function definition for ‘glm’
relative.importance: no visible global function definition for ‘sd’
relative.importance : tr.pr: no visible global function definition for
  ‘pnorm’
relative.importance: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  axis dnorm glm lines mtext par pchisq plogis plot pnorm qchisq sd
  vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DeLorean.Rcheck/00install.out’ for details.
bootbagg: no visible global function definition for ‘runif’
bootworpl: no visible global function definition for ‘runif’
des12: no visible global function definition for ‘rnorm’
des12: no visible global function definition for ‘runif’
eval.stage.gauss: no visible global function definition for ‘var’
plotparti: no visible global function definition for ‘plot’
plotparti: no visible global function definition for ‘lines’
plotpartilev: no visible global function definition for ‘plot’
plotpartilev: no visible global function definition for ‘polygon’
plotpartilev: no visible global function definition for ‘points’
simesi: no visible global function definition for ‘runif’
simesi3d: no visible global function definition for ‘runif’
simfssk: no visible global function definition for ‘rnorm’
simfssk: no visible global function definition for ‘runif’
simmix.delt: no visible global function definition for ‘rnorm’
simmix.delt: no visible global function definition for ‘runif’
simpp: no visible global function definition for ‘rnorm’
simpp: no visible global function definition for ‘runif’
simutree: no visible global function definition for ‘runif’
stage.gaussR: no visible global function definition for ‘var’
unidis: no visible global function definition for ‘runif’
Undefined global functions or variables:
  lines plot points polygon rnorm runif var
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
MBD: no visible global function definition for ‘par’
MBD: no visible global function definition for ‘gray’
MBD: no visible global function definition for ‘matplot’
MBD: no visible global function definition for ‘polygon’
MBD: no visible global function definition for ‘lines’
MBD: no visible global function definition for ‘legend’
MBD: no visible global function definition for ‘matlines’
R.test: no visible global function definition for ‘runif’
R.test: no visible global function definition for ‘wilcox.test’
centralPlot: no visible global function definition for ‘par’
centralPlot: no visible global function definition for
  ‘colorRampPalette’
centralPlot: no visible global function definition for ‘matplot’
centralPlot: no visible global function definition for ‘matlines’
centralPlot: no visible global function definition for ‘legend’
scalecurve: no visible global function definition for ‘plot’
scalecurve: no visible global function definition for ‘lines’
scalecurve: no visible global function definition for ‘legend’
tmean: no visible global function definition for ‘matplot’
tmean: no visible global function definition for ‘matlines’
tmean: no visible global function definition for ‘lines’
tmean: no visible global function definition for ‘legend’
tmean: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette gray legend lines matlines matplot par plot polygon
  runif wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "legend", "lines", "matlines", "matplot", "par",
             "plot", "polygon")
  importFrom("stats", "runif", "wilcox.test")
to your NAMESPACE file.
arrayUpdate : pairUpdate: no visible global function definition for
  ‘runif’
conditionUpdate: no visible global function definition for ‘runif’
designGG: no visible global function definition for ‘runif’
experimentDesignTable: no visible global function definition for
  ‘write.csv’
plotAllScores: no visible global function definition for ‘png’
plotAllScores: no visible global function definition for ‘par’
plotAllScores: no visible global function definition for ‘plot’
plotAllScores: no visible global function definition for ‘text’
plotAllScores: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off par plot png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
fs.agreement.part: no visible global function definition for ‘as.dist’
fs.agreement.part: no visible global function definition for ‘cor’
fs.leave.k.out.combn: no visible global function definition for ‘sd’
fs.leave.k.out.sample: no visible global function definition for ‘sd’
fs.rd: no visible global function definition for ‘pchisq’
fs.selection: no visible global function definition for ‘p.adjust’
plot.FIT: no visible global function definition for ‘qchisq’
plot.FIT: no visible global function definition for ‘ppoints’
plot.FIT: no visible global function definition for ‘plot’
plot.FIT: no visible global function definition for ‘points’
plot.FIT: no visible global function definition for ‘abline’
plotJn: no visible global function definition for ‘plot’
plotJn: no visible global function definition for ‘points’
robust.distance.signed: no visible global function definition for
  ‘mahalanobis’
snowball: no visible global function definition for ‘is’
snowball: no visible global function definition for ‘median’
weight.sd: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline as.dist cor is mahalanobis median p.adjust pchisq plot points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "mahalanobis", "median",
             "p.adjust", "pchisq", "ppoints", "qchisq", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error(s) in re-building vignettes:
  ...
--- re-building ‘DIF_vignette.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

no column `person_id` provided, automatically generating unique person id's
--- finished re-building ‘DIF_vignette.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building ‘Dexter.Rmd’

--- re-building ‘Equating.Rmd’ using rmarkdown
no column `person_id` provided, automatically generating unique person id's
no column `person_id` provided, automatically generating unique person id's
no column `person_id` provided, automatically generating unique person id's
--- finished re-building ‘Equating.Rmd’

--- re-building ‘Plausible_Values.Rmd’ using rmarkdown
Quitting from lines 142-169 (Plausible_Values.Rmd) 
Error: processing vignette 'Plausible_Values.Rmd' failed with diagnostics:
malformed factor
--- failed re-building ‘Plausible_Values.Rmd’

--- re-building ‘Profile-plots.Rmd’ using rmarkdown
no column `person_id` provided, automatically generating unique person id's
--- finished re-building ‘Profile-plots.Rmd’

--- re-building ‘Test_Individual_differences.Rmd’ using rmarkdown
no column `person_id` provided, automatically generating unique person id's
--- finished re-building ‘Test_Individual_differences.Rmd’

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

Error: Vignette re-building failed.
Execution halted
makeAdjMatrix: no visible global function definition for ‘combn’
plotPosteriorN: no visible global function definition for ‘plot’
plotPosteriorN: no visible global function definition for ‘title’
plotPosteriorN: no visible global function definition for ‘lines’
plotPosteriorN: no visible global function definition for ‘legend’
venn3: no visible global function definition for ‘plot’
venn3: no visible global function definition for ‘runif’
venn3: no visible global function definition for ‘points’
venn3: no visible global function definition for ‘lines’
venn3: no visible global function definition for ‘text’
venn4: no visible global function definition for ‘plot’
venn4: no visible global function definition for ‘lines’
venn4: no visible global function definition for ‘runif’
venn4: no visible global function definition for ‘points’
Undefined global functions or variables:
  combn legend lines plot points runif text title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text",
             "title")
  importFrom("stats", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
aLine: no visible global function definition for ‘lines’
aLine: no visible global function definition for ‘ecdf’
dip.test: no visible global function definition for ‘complete.cases’
dip.test: no visible global function definition for ‘runif’
dip.test: no visible global function definition for ‘approx’
plot.dip: no visible global function definition for ‘par’
plot.dip: no visible global function definition for ‘ecdf’
plot.dip: no visible global function definition for ‘plot’
plot.dip: no visible global function definition for ‘title’
plot.dip: no visible global function definition for ‘abline’
plot.dip: no visible global function definition for ‘axis’
plot.dip: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline approx axis complete.cases ecdf legend lines par plot runif
  title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "approx", "complete.cases", "ecdf", "runif")
to your NAMESPACE file.
dist.multiPhylo: no visible global function definition for ‘as.dist’
gromov.hyperbolicity: no visible global function definition for
  ‘as.dist’
mcmc.target.seq: no visible global function definition for ‘runif’
phylo.diff: no visible global function definition for ‘par’
phylo.diff: no visible global function definition for ‘plot’
Undefined global functions or variables:
  as.dist par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.dist", "runif")
to your NAMESPACE file.
DStree: no visible global function definition for ‘model.frame’
DStree: no visible global function definition for ‘model.matrix’
DStree: no visible global function definition for ‘model.response’
DStree: no visible global function definition for ‘as.formula’
bag: no visible global function definition for ‘model.frame’
bag: no visible global function definition for ‘model.response’
plot.DStree: no visible global function definition for ‘par’
plot.DStree: no visible global function definition for ‘plot’
plot.DStree: no visible global function definition for ‘rainbow’
plot.DStree: no visible global function definition for ‘lines’
plot.DStree: no visible global function definition for ‘legend’
predict.DStree: no visible global function definition for ‘predict’
print.DStree: no visible global function definition for ‘naprint’
prune.DStree: no visible global function definition for ‘median’
prune.DStree: no visible global function definition for ‘predict’
prune.DStree: no visible binding for global variable ‘var’
summ.MAE: no visible global function definition for ‘predict’
summary.DStree: no visible global function definition for ‘naprint’
Undefined global functions or variables:
  as.formula legend lines median model.frame model.matrix
  model.response naprint par plot predict rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("stats", "as.formula", "median", "model.frame",
             "model.matrix", "model.response", "naprint", "predict",
             "var")
to your NAMESPACE file.
DCEA: no visible global function definition for ‘p.adjust’
DS: no visible global function definition for ‘p.adjust’
DS: no visible global function definition for ‘pdf’
DS: no visible global function definition for ‘plot’
DS: no visible global function definition for ‘dev.off’
LFC: no visible global function definition for ‘glm’
LFC: no visible global function definition for ‘predict’
PartialCor: no visible global function definition for ‘na.omit’
comDCGLplot: no visible global function definition for ‘pdf’
comDCGLplot: no visible global function definition for ‘plot’
comDCGLplot: no visible global function definition for ‘dev.off’
percentLinkfilter: no visible global function definition for ‘cor’
qLinkfilter: no visible global function definition for ‘cor’
qLinkfilter: no visible global function definition for ‘pt’
qLinkfilter: no visible global function definition for ‘p.adjust’
rLinkfilter: no visible global function definition for ‘cor’
varianceBasedfilter: no visible binding for global variable ‘var’
varianceBasedfilter: no visible global function definition for ‘median’
varianceBasedfilter: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor dev.off glm median na.omit p.adjust pchisq pdf plot predict pt
  var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "glm", "median", "na.omit", "p.adjust",
             "pchisq", "predict", "pt", "var")
to your NAMESPACE file.
DTK.plot: no visible global function definition for ‘plot’
DTK.plot: no visible global function definition for ‘axis’
DTK.plot: no visible global function definition for ‘title’
DTK.plot: no visible global function definition for ‘lines’
DTK.plot: no visible global function definition for ‘points’
DTK.test: no visible binding for global variable ‘sd’
DTK.test: no visible global function definition for ‘qtukey’
TK.test: no visible global function definition for ‘TukeyHSD’
TK.test: no visible global function definition for ‘aov’
Undefined global functions or variables:
  TukeyHSD aov axis lines plot points qtukey sd title
Consider adding
  importFrom("graphics", "axis", "lines", "plot", "points", "title")
  importFrom("stats", "TukeyHSD", "aov", "qtukey", "sd")
to your NAMESPACE file.
DTMC: no visible global function definition for ‘runif’
DTMC: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘ebirdst-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stixelize
> ### Title: Generate stixel polygons from PI data
> ### Aliases: stixelize stixelize.data.frame stixelize.sf
> 
> ### ** Examples
> 
> # download example data
> sp_path <- ebirdst_download("example_data", tifs_only = FALSE)
Error in open.connection(x, "rb") : 
  Timeout was reached: [ebirdst-data.s3.amazonaws.com] Connection timed out after 10001 milliseconds
Calls: ebirdst_download ... read_xml.character -> read_xml.connection -> open -> open.connection
Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘sf::st_make_valid’ by ‘lwgeom::st_make_valid’ when loading ‘edbuildmapr’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/edbuildmapr.Rcheck/00install.out’ for details.
comPlot: no visible global function definition for ‘plot’
comPlot: no visible global function definition for ‘lines’
convertEiData: no visible global function definition for ‘model.frame’
plot.eiwild: no visible global function definition for ‘plot’
plot.eiwild: no visible global function definition for ‘par’
plotResult: no visible global function definition for ‘grey’
plotResult: no visible global function definition for
  ‘colorRampPalette’
plotResult: no visible global function definition for ‘plot.new’
plotResult: no visible global function definition for ‘plot.window’
prioriPlot: no visible global function definition for ‘par’
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for ‘rgamma’
prioriPlot : <anonymous>: no visible global function definition for
  ‘rbeta’
prioriPlot: no visible global function definition for ‘hist’
prioriPlot : <anonymous>: no visible global function definition for
  ‘rgamma’
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for ‘rexp’
prioriPlot : <anonymous>: no visible global function definition for
  ‘rexp’
runMBayes: no visible global function definition for ‘runif’
runMBayes: no visible global function definition for ‘rgamma’
runMBayes: no visible global function definition for ‘rexp’
str0: no visible global function definition for ‘str’
tuneVars: no visible global function definition for ‘sd’
Undefined global functions or variables:
  colorRampPalette grey hist lines model.frame par plot plot.new
  plot.window rbeta rexp rgamma runif sd str
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey")
  importFrom("graphics", "hist", "lines", "par", "plot", "plot.new",
             "plot.window")
  importFrom("stats", "model.frame", "rbeta", "rexp", "rgamma", "runif",
             "sd")
  importFrom("utils", "str")
to your NAMESPACE file.
empiricalFDR: no visible global function definition for ‘axis’
empiricalFDR: no visible global function definition for ‘loess’
empiricalFDR: no visible global function definition for ‘predict’
empiricalFDR: no visible global function definition for ‘lines’
empiricalFDR: no visible global function definition for ‘abline’
fdrBiCurve: no visible global function definition for ‘plot’
fdrBiCurve: no visible global function definition for ‘axis’
fdrBiCurve: no visible global function definition for ‘lines’
fdrBiCurve: no visible global function definition for ‘abline’
fdrBiCurve: no visible global function definition for ‘legend’
simulateCounts: no visible global function definition for
  ‘txtProgressBar’
simulateCounts: no visible global function definition for
  ‘setTxtProgressBar’
simulateCounts: no visible global function definition for ‘rnorm’
simulateCounts: no visible global function definition for ‘hist’
simulateCounts: no visible global function definition for ‘colData’
Undefined global functions or variables:
  abline axis colData hist legend lines loess plot predict rnorm
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "plot")
  importFrom("stats", "loess", "predict", "rnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Rd file 'mosaicPermDialog.Rd':
  \usage lines wider than 90 characters:
                                                             displayPermCommand=TRUE, extendedOptions=TRUE)
     setMosaicPalette(palettename,reverse=FALSE)                                                     

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(epikit)
  > 
  > test_check("epikit")
  ── 1. Failure: case_fatality_rate_df will add a total row to stratified analysis
  `iris_res` not equal to `iris_n`.
  Incompatible type for column `Species`: x character, y factor
  
  ── 2. Failure: case_fatality_rate_df will add a total row to stratified analysis
  `iris_res` not equal to `iris_n`.
  Incompatible type for column `Species`: x character, y factor
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 107 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: case_fatality_rate_df will add a total row to stratified analysis (@test-proportion.R#152) 
  2. Failure: case_fatality_rate_df will add a total row to stratified analysis and merge CI (@test-proportion.R#173) 
  
  Error: testthat unit tests failed
  Execution halted
plot.episplineDensity: no visible global function definition for ‘plot’
plot.episplineDensity: no visible global function definition for
  ‘points’
postproc: no visible global function definition for ‘plot’
postproc: no visible global function definition for ‘points’
preprocess.data: no visible global function definition for ‘sd’
Undefined global functions or variables:
  plot points sd
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "sd")
to your NAMESPACE file.
FCIplot: no visible global function definition for ‘na.omit’
FCIplot: no visible global function definition for ‘plot’
FCIplot: no visible global function definition for ‘tail’
FCIplot: no visible global function definition for ‘grid’
FCIplot: no visible global function definition for ‘polygon’
FCIplot: no visible global function definition for ‘rgb’
linpred: no visible global function definition for ‘lm’
mplott: no visible global function definition for ‘par’
mplott: no visible global function definition for ‘plot’
mplott: no visible global function definition for ‘na.omit’
mplott: no visible global function definition for ‘lines’
mplott: no visible global function definition for ‘legend’
mplott: no visible global function definition for ‘grid’
plott: no visible global function definition for ‘lines’
plott: no visible global function definition for ‘par’
plott: no visible global function definition for ‘plot’
plott: no visible global function definition for ‘grid’
tsideplot: no visible global function definition for ‘par’
tsideplot: no visible global function definition for ‘plot’
tsideplot: no visible global function definition for ‘axis’
tsideplot: no visible global function definition for ‘grid’
Undefined global functions or variables:
  axis grid legend lines lm na.omit par plot polygon rgb tail
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "polygon")
  importFrom("stats", "lm", "na.omit")
  importFrom("utils", "tail")
to your NAMESPACE file.
ESA: no visible binding for global variable ‘var’
plot.esabcv: no visible global function definition for ‘plot’
plot.esabcv: no visible global function definition for ‘points’
plot.esabcv: no visible global function definition for ‘axis’
plot.esabcv: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis plot points title var
Consider adding
  importFrom("graphics", "axis", "plot", "points", "title")
  importFrom("stats", "var")
to your NAMESPACE file.
ESEA.Main: no visible global function definition for ‘rnorm’
ESEA.Main: no visible global function definition for ‘sd’
ESEA.Main: no visible global function definition for ‘p.adjust’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘plot’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘lines’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘colors’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘points’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘legend’
PlotGlobEdgeCorProfile: no visible global function definition for
  ‘text’
PlotPathwayGraph: no visible global function definition for ‘par’
PlotPathwayGraph: no visible global function definition for ‘plot’
PlotRunEnrichment: no visible global function definition for ‘plot’
PlotRunEnrichment: no visible global function definition for ‘lines’
PlotRunEnrichment: no visible global function definition for ‘colors’
PlotRunEnrichment: no visible global function definition for ‘text’
SavePathway2File: no visible global function definition for ‘is’
calEdgeCorScore: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colors is legend lines na.omit p.adjust par plot points rnorm sd text
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "text")
  importFrom("methods", "is")
  importFrom("stats", "na.omit", "p.adjust", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
rAllRisksFactors: no visible global function definition for ‘new’
rAssetDistribution: no visible global function definition for ‘new’
rDefaultSpread: no visible global function definition for ‘new’
rLiquiditySpread: no visible global function definition for ‘new’
rRealEstate: no visible global function definition for ‘new’
rShortRate: no visible global function definition for ‘new’
rStock: no visible global function definition for ‘new’
EuroCall_Stock_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroCall_ZC_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroPut_Stock_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
EuroPut_ZC_PriceDistribution,Scenarios: no visible global function
  definition for ‘pnorm’
MartingaleTest,Scenarios: no visible global function definition for
  ‘plot’
MartingaleTest,Scenarios: no visible global function definition for
  ‘lines’
MartingaleTest,Scenarios: no visible global function definition for
  ‘title’
customPathsGeneration,Scenarios: no visible global function definition
  for ‘rnorm’
Undefined global functions or variables:
  lines new plot pnorm rnorm title
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("methods", "new")
  importFrom("stats", "pnorm", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running ‘testthat.R’ [12s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(estatapi)
  このサービスは、政府統計総合窓口(e-Stat)のAPI機能を使用していますが、サービスの内容は国によって保証されたものではありません。
  > 
  > test_check("estatapi")
  ── 1. Failure: estat_getStatsData processes the API response as expected  ──────
  estat_getStatsData(...) not identical to readRDS("result_getStatsData.rds").
  Objects equal but not identical
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 22 | SKIPPED: 12 | WARNINGS: 7 | FAILED: 1 ]
  1. Failure: estat_getStatsData processes the API response as expected 
  
  Error: testthat unit tests failed
  Execution halted
.Transition: no visible global function definition for ‘rnorm’
.Transition.DC: no visible global function definition for ‘runif’
CondPdf.CC.interval: no visible global function definition for ‘plot’
CondPdf.DC.interval: no visible global function definition for ‘plot’
Simu.Cond.HR: no visible global function definition for ‘rpois’
Simu.Cond.HR: no visible global function definition for ‘runif’
Simu.Cond.HR: no visible global function definition for ‘hist’
Simu.Cond.HR: no visible global function definition for ‘var’
Simu.HR: no visible global function definition for ‘rpois’
Simu.HR: no visible global function definition for ‘runif’
Simu.HR: no visible global function definition for ‘hist’
Simu.HR: no visible global function definition for ‘var’
Simu.PDMP: no visible global function definition for ‘plot’
Simu.PDMP.DC: no visible global function definition for ‘plot’
plotCHR: no visible global function definition for ‘plot’
plotHR: no visible global function definition for ‘plot’
Undefined global functions or variables:
  hist plot rnorm rpois runif var
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "rnorm", "rpois", "runif", "var")
to your NAMESPACE file.
EW : PhiP : Phi: no visible global function definition for ‘pnorm’
EWplot: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot pnorm
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
extfunnel: no visible global function definition for ‘qnorm’
extfunnel: no visible global function definition for ‘meta.summaries’
extfunnel: no visible global function definition for ‘flush.console’
extfunnel: no visible global function definition for ‘qt’
extfunnel: no visible global function definition for ‘dev.new’
extfunnel: no visible global function definition for ‘par’
extfunnel: no visible global function definition for ‘plot’
extfunnel: no visible global function definition for ‘polygon’
extfunnel: no visible global function definition for ‘segments’
extfunnel: no visible global function definition for ‘abline’
extfunnel: no visible global function definition for ‘axis’
extfunnel: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box dev.new flush.console meta.summaries par plot polygon
  qnorm qt segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "par", "plot",
             "polygon", "segments")
  importFrom("stats", "qnorm", "qt")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
createFormula: no visible global function definition for ‘tail’
createFormula: no visible global function definition for ‘head’
createFormula: no visible global function definition for ‘as.formula’
ezsim: no visible global function definition for ‘runif’
plot.ezsim: no visible global function definition for ‘quantile’
plot.ezsim: no visible global function definition for ‘head’
plot.ezsim: no visible global function definition for ‘tail’
plot.ezsim: no visible global function definition for ‘plot’
plot.ezsim: no visible binding for global variable ‘dnorm’
plot.ezsim: no visible binding for global variable ‘pdf’
plot.ezsim: no visible global function definition for ‘dev.off’
plot.ezsim : <anonymous>: no visible global function definition for
  ‘dev.new’
plot.summary.ezsim: no visible global function definition for ‘head’
plot.summary.ezsim: no visible global function definition for ‘tail’
plot.summary.ezsim: no visible binding for global variable ‘pdf’
plot.summary.ezsim: no visible global function definition for ‘dev.off’
plot.summary.ezsim : <anonymous>: no visible global function definition
  for ‘dev.new’
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf plot quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Running ‘testthat.R’ [24s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fable)
  Loading required package: fabletools
  > 
  > test_check("fable")
  ── 1. Failure: Automatic ETS selection (@test-ets.R#14)  ───────────────────────
  tidy(model(UKLungDeaths[1:24, ], ETS(mdeaths)))$estimate not equal to c(1, 2134).
  names for target but not for current
  
  ── 2. Failure: Manual ETS selection (@test-ets.R#51)  ──────────────────────────
  tidy(refit(fable_fit, USAccDeaths_tbl))$estimate == tidy(fable_fit)$estimate not identical to c(rep(TRUE, 2), rep(FALSE, 12)).
  names for target but not for current
  
  ── 3. Failure: Manual ETS selection (@test-ets.R#62)  ──────────────────────────
  tidy(fable_fit)$estimate[3:14] not identical to c(cmp$level[12], cmp$season[12:2]).
  names for target but not for current
  
  ── 4. Failure: Manual ETS selection (@test-ets.R#87)  ──────────────────────────
  coef$estimate[1:4] not identical to c(0.5, 0.006, 1e-04, 0.975).
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 100 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: Automatic ETS selection (@test-ets.R#14) 
  2. Failure: Manual ETS selection (@test-ets.R#51) 
  3. Failure: Manual ETS selection (@test-ets.R#62) 
  4. Failure: Manual ETS selection (@test-ets.R#87) 
  
  Error: testthat unit tests failed
  Execution halted
PTSingleAssetBarrierOption2: no visible global function definition for
  ‘new’
newton: no visible global function definition for ‘plot’
newton: no visible global function definition for ‘abline’
probInRange: no visible global function definition for ‘pnorm’
shortfall_risk: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline new plot pnorm
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "new")
  importFrom("stats", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
FDRreg: no visible global function definition for ‘dnorm’
colnormalize: no visible global function definition for ‘sd’
efron: no visible global function definition for ‘median’
efron: no visible global function definition for ‘hist’
efron: no visible global function definition for ‘glm’
efron: no visible binding for global variable ‘poisson’
efron: no visible global function definition for ‘qchisq’
efron: no visible global function definition for ‘predict’
efron: no visible global function definition for ‘quantile’
efron: no visible global function definition for ‘lm’
efron: no visible global function definition for ‘coef’
make.bspline.matrix: no visible global function definition for
  ‘quantile’
plotFDR: no visible global function definition for ‘hist’
plotFDR: no visible global function definition for ‘par’
plotFDR: no visible global function definition for ‘plot’
plotFDR: no visible global function definition for ‘axis’
plotFDR: no visible global function definition for ‘lines’
plotFDR: no visible global function definition for ‘legend’
plotFDR: no visible global function definition for ‘rug’
plotFDR: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis coef dnorm glm hist legend lines lm median par plot poisson
  predict qchisq quantile rug sd title
Consider adding
  importFrom("graphics", "axis", "hist", "legend", "lines", "par",
             "plot", "rug", "title")
  importFrom("stats", "coef", "dnorm", "glm", "lm", "median", "poisson",
             "predict", "qchisq", "quantile", "sd")
to your NAMESPACE file.
fgeasy: no visible global function definition for ‘dist’
fgeasy : cor.est: no visible global function definition for ‘cor.test’
fgeasy: no visible binding for global variable ‘var’
fgperm : runrand: no visible global function definition for ‘runif’
fgperm : runrand: no visible global function definition for ‘ave’
fgploc : runrand: no visible global function definition for ‘runif’
fgploc : runrand: no visible global function definition for ‘ave’
fyshuffle: no visible global function definition for ‘runif’
plot.fg: no visible global function definition for ‘par’
plot.fg: no visible global function definition for ‘plot’
plot.fg: no visible global function definition for ‘segments’
plot.fg: no visible binding for global variable ‘quantile’
plot.fg: no visible global function definition for ‘abline’
plot.fg: no visible global function definition for ‘axis’
summary.fg: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  abline ave axis cor.test dist par plot quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "plot", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
Rd file 'POICalc.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

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

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

These lines will be truncated in the PDF manual.
lsmacof: no visible global function definition for ‘cmdscale’
plotInc: no visible global function definition for ‘rainbow’
plotInc: no visible global function definition for ‘plot’
prepareCalib: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmdscale lm plot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "plot")
  importFrom("stats", "cmdscale", "lm")
to your NAMESPACE file.
GCV: no visible global function definition for ‘lm’
GCV: no visible global function definition for ‘resid’
ffplot: no visible global function definition for ‘par’
ffplot: no visible global function definition for ‘plot’
ffplot: no visible global function definition for ‘points’
ffplot: no visible global function definition for ‘legend’
flowfield: no visible global function definition for ‘write.table’
gpr: no visible global function definition for ‘quantile’
gpr: no visible global function definition for ‘var’
smoothp: no visible global function definition for ‘lm’
smoothp: no visible global function definition for ‘predict’
smoothp: no visible global function definition for ‘resid’
smoothp: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  legend lm optimize par plot points predict quantile resid var
  write.table
Consider adding
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "lm", "optimize", "predict", "quantile", "resid",
             "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
accuracy:
  function(object, ...)
accuracy.cvts:
  function(f, ...)

accuracy:
  function(object, ...)
accuracy.hybridModel:
  function(f, individual, ...)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
ComputeDCT2FFT: no visible global function definition for ‘fft’
ComputeSemipgramFFT: no visible global function definition for ‘fft’
WaveVarFD: no visible global function definition for ‘modwt’
do.fd.estimate: no visible global function definition for
  ‘performParallel’
do.fd.estimate2d.simple: no visible global function definition for
  ‘median’
fd.Genton: no visible global function definition for ‘qn’
fd.estimate.matrix: no visible global function definition for
  ‘performParallel’
fd.plot.legend: no visible global function definition for ‘legend’
fd.plot.loglog: no visible global function definition for ‘plot’
fd.plot.loglog: no visible global function definition for ‘points’
fd.plot.loglog: no visible global function definition for ‘abline’
summary.FractalDim: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  abline fft legend median modwt performParallel plot points qn sd
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points")
  importFrom("stats", "fft", "median", "sd")
to your NAMESPACE file.
custom.draw.circle: no visible global function definition for ‘lines’
frcc: no visible binding for global variable ‘sd’
frcc: no visible global function definition for ‘cor.shrink’
frcc: no visible global function definition for ‘cor’
frcc: no visible global function definition for ‘p.asym’
generate_multivariate_normal_sample: no visible global function
  definition for ‘mvrnorm’
plot_units: no visible binding for global variable ‘sd’
plot_units: no visible global function definition for ‘plot’
plot_units: no visible global function definition for ‘points’
plot_units: no visible global function definition for ‘textxy’
plot_variables: no visible global function definition for ‘plot’
plot_variables: no visible global function definition for ‘points’
plot_variables: no visible global function definition for ‘textxy’
plot_variables: no visible global function definition for ‘segments’
Undefined global functions or variables:
  cor cor.shrink lines mvrnorm p.asym plot points sd segments textxy
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
.FunFEM.main: no visible global function definition for ‘kmeans’
.FunFEM.main: no visible global function definition for ‘rmultinom’
.FunFEM.main: no visible global function definition for ‘cutree’
.FunFEM.main: no visible global function definition for ‘hclust’
.FunFEM.main: no visible global function definition for ‘dist’
.FunFEM.main: no visible global function definition for ‘par’
.FunFEM.main: no visible global function definition for ‘plot’
.mstep: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov cutree dist hclust kmeans par plot rmultinom
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "cov", "cutree", "dist", "hclust", "kmeans",
             "rmultinom")
to your NAMESPACE file.
FPTsimul: no visible global function definition for ‘runif’
histplot: no visible global function definition for ‘dev.new’
histplot: no visible global function definition for ‘hist’
histplot: no visible global function definition for ‘par’
histplot: no visible global function definition for ‘plot’
histplot: no visible global function definition for ‘legend’
mdt: no visible binding for global variable ‘deltat’
plot.FPTdensity: no visible global function definition for ‘dev.new’
plot.FPTdensity: no visible global function definition for ‘plot’
res_summary: no visible global function definition for ‘write.table’
res_summary: no visible global function definition for ‘sd’
res_summary: no visible global function definition for ‘median’
vdt: no visible binding for global variable ‘deltat’
Undefined global functions or variables:
  deltat dev.new hist legend median par plot runif sd write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "legend", "par", "plot")
  importFrom("stats", "deltat", "median", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CI.RMSEA: no visible global function definition for ‘qchisq’
CI.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘par’
GAIPE.RMSEA: no visible global function definition for ‘plot’
GAIPE.RMSEA: no visible global function definition for ‘abline’
GAIPE.RMSEA: no visible global function definition for ‘colors’
GAIPE.RMSEA: no visible global function definition for ‘text’
GAIPE.RMSEA: no visible global function definition for ‘arrows’
GAIPE.RMSEA: no visible global function definition for ‘points’
GAIPE.RMSEA: no visible global function definition for ‘axis’
GAIPE.RMSEA: no visible global function definition for ‘lines’
GAIPE.RMSEA: no visible global function definition for ‘legend’
GAIPE.RMSEA: no visible global function definition for ‘pchisq’
GAIPE.RMSEA: no visible global function definition for ‘qchisq’
GAIPE.RMSEA: no visible global function definition for ‘mtext’
GAIPE.RMSEA: no visible global function definition for ‘title’
PA.RMSEA: no visible global function definition for ‘pchisq’
PA.RMSEA: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  abline arrows axis colors legend lines mtext par pchisq plot points
  qchisq text title
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "arrows", "axis", "legend", "lines",
             "mtext", "par", "plot", "points", "text", "title")
  importFrom("stats", "pchisq", "qchisq")
to your NAMESPACE file.
‘gs+qpdf’ made some significant size reductions:
     compacted ‘gamboostLSS_Tutorial.pdf’ from 1.4Mb to 1.0Mb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
cvriskMSM: no visible global function definition for ‘predict’
plotcvriskMSM: no visible global function definition for ‘plot’
plotcvriskMSM: no visible binding for global variable ‘lines’
plotcvriskMSM: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot predict
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
GAMBoost: no visible global function definition for ‘binomial’
GAMBoost: no visible global function definition for ‘gaussian’
GAMBoost: no visible global function definition for ‘poisson’
GAMBoost: no visible binding for global variable ‘sd’
GAMBoost: no visible global function definition for ‘Matrix’
calc.confidence.bands: no visible global function definition for
  ‘predict’
cv.GAMBoost: no visible global function definition for ‘binomial’
cv.GAMBoost : eval.fold: no visible global function definition for
  ‘predict’
cv.GAMBoost: no visible global function definition for ‘mclapply’
cv.GAMBoost: no visible binding for global variable ‘var’
estimPVal: no visible global function definition for ‘mclapply’
plot.GAMBoost: no visible global function definition for ‘plot’
plot.GAMBoost: no visible global function definition for ‘lines’
Undefined global functions or variables:
  Matrix binomial gaussian lines mclapply plot poisson predict sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "binomial", "gaussian", "poisson", "predict", "sd",
             "var")
to your NAMESPACE file.
contindic.gb2: no visible global function definition for ‘contour’
contindic.gb2: no visible global function definition for ‘box’
contindic.gb2: no visible global function definition for ‘mtext’
contprof.gb2: no visible global function definition for ‘image’
contprof.gb2: no visible global function definition for ‘heat.colors’
contprof.gb2: no visible global function definition for ‘contour’
contprof.gb2: no visible global function definition for ‘text’
contprof.gb2: no visible global function definition for ‘box’
dplot.cavgb2: no visible global function definition for ‘par’
dplot.cavgb2: no visible global function definition for ‘curve’
dplot.cavgb2: no visible global function definition for ‘legend’
dplot.cavgb2: no visible global function definition for ‘plot’
dplot.cavgb2: no visible global function definition for ‘lines’
dplot.cgb2: no visible global function definition for ‘curve’
dplot.cgb2: no visible global function definition for ‘lines’
dplot.cgb2: no visible global function definition for ‘legend’
plotsML.gb2: no visible global function definition for ‘par’
plotsML.gb2: no visible global function definition for ‘plot’
plotsML.gb2: no visible global function definition for ‘abline’
plotsML.gb2: no visible global function definition for ‘curve’
plotsML.gb2: no visible global function definition for ‘legend’
saveplot : <local>: no visible global function definition for ‘dev.set’
saveplot : <local>: no visible global function definition for
  ‘dev.print’
saveplot : <local>: no visible binding for global variable ‘pdf’
Undefined global functions or variables:
  abline box contour curve dev.print dev.set heat.colors image legend
  lines mtext par pdf plot text
Consider adding
  importFrom("grDevices", "dev.print", "dev.set", "heat.colors", "pdf")
  importFrom("graphics", "abline", "box", "contour", "curve", "image",
             "legend", "lines", "mtext", "par", "plot", "text")
to your NAMESPACE file.
coeplot: no visible global function definition for ‘plot’
coeplot: no visible global function definition for ‘axis’
coeplot: no visible global function definition for ‘lines’
coeplot: no visible global function definition for ‘title’
coeplot: no visible global function definition for ‘legend’
corplot: no visible global function definition for ‘par’
corplot: no visible global function definition for ‘pairs’
corplot: no visible global function definition for ‘strwidth’
lm.estimate: no visible global function definition for ‘as.formula’
lm.estimate: no visible global function definition for ‘glm’
panel.cor: no visible global function definition for ‘par’
panel.cor: no visible global function definition for ‘cor’
panel.cor: no visible global function definition for ‘strwidth’
panel.cor: no visible global function definition for ‘text’
panel.smooth.r: no visible global function definition for ‘par’
panel.smooth.r: no visible global function definition for ‘points’
panel.smooth.r: no visible global function definition for ‘lines’
posplot: no visible global function definition for ‘par’
posplot: no visible global function definition for ‘barplot’
posplot: no visible global function definition for ‘plot’
posplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  as.formula axis barplot cor glm legend lines pairs par plot points
  strwidth text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "pairs",
             "par", "plot", "points", "strwidth", "text", "title")
  importFrom("stats", "as.formula", "cor", "glm")
to your NAMESPACE file.
plot.rbga: no visible global function definition for ‘par’
plot.rbga: no visible global function definition for ‘hist’
plot.rbga: no visible global function definition for ‘plot’
plot.rbga: no visible global function definition for ‘lines’
rbga: no visible global function definition for ‘runif’
rbga: no visible global function definition for ‘dnorm’
rbga.bin: no visible global function definition for ‘dnorm’
rbga.bin: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm hist lines par plot runif
Consider adding
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "dnorm", "runif")
to your NAMESPACE file.
splineAnalyze: no visible global function definition for ‘var’
splineAnalyze: no visible global function definition for ‘par’
splineAnalyze: no visible global function definition for ‘plot’
splineAnalyze: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par plot var
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "var")
to your NAMESPACE file.
PAEA : <anonymous>: no visible global function definition for
  ‘integrate’
PAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
PAEAAnalysis : <anonymous>: no visible global function definition for
  ‘setTxtProgressBar’
PAEAAnalysis: no visible global function definition for ‘par’
PAEAAnalysis: no visible global function definition for ‘barplot’
chdirSig: no visible global function definition for ‘prcomp’
chdirSig: no visible global function definition for ‘rchisq’
chdirSig: no visible global function definition for ‘txtProgressBar’
chdirSig : <anonymous> : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
chdirplots : <anonymous>: no visible global function definition for
  ‘par’
chdirplots : <anonymous>: no visible global function definition for
  ‘plot’
chdirplots : <anonymous>: no visible global function definition for
  ‘arrows’
chdirplots : <anonymous>: no visible global function definition for
  ‘barplot’
multigmtPAEAAnalysis: no visible global function definition for
  ‘txtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘setTxtProgressBar’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘data’
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for ‘write.table’
Undefined global functions or variables:
  arrows barplot data integrate par plot prcomp rchisq
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("graphics", "arrows", "barplot", "par", "plot")
  importFrom("stats", "integrate", "prcomp", "rchisq")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
geoscaleBox: no visible global function definition for ‘boxplot’
geoscaleBox: no visible global function definition for ‘par’
geoscaleBox: no visible global function definition for ‘plot’
geoscaleBox: no visible global function definition for ‘text’
geoscaleBox: no visible global function definition for ‘segments’
geoscaleBox: no visible global function definition for ‘rect’
geoscaleBox: no visible global function definition for ‘rgb’
geoscaleBox: no visible global function definition for ‘polygon’
geoscaleBox: no visible global function definition for ‘points’
geoscaleBox: no visible global function definition for ‘axis’
geoscalePlot: no visible global function definition for ‘par’
geoscalePlot: no visible global function definition for ‘plot’
geoscalePlot: no visible global function definition for ‘text’
geoscalePlot: no visible global function definition for ‘segments’
geoscalePlot: no visible global function definition for ‘rect’
geoscalePlot: no visible global function definition for ‘rgb’
geoscalePlot: no visible global function definition for ‘points’
geoscalePlot: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis boxplot par plot points polygon rect rgb segments text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "boxplot", "par", "plot", "points",
             "polygon", "rect", "segments", "text")
to your NAMESPACE file.
‘gs+qpdf’ made some significant size reductions:
     compacted ‘v70i09.pdf’ from 921Kb to 636Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ggtern.Rcheck/00install.out’ for details.
acovamcmc: no visible global function definition for ‘rnorm’
acovamcmc: no visible global function definition for ‘rgamma’
acovamcmc: no visible binding for global variable ‘quantile’
acovamcmc: no visible global function definition for ‘quantile’
acovamcmc: no visible global function definition for ‘var’
plot.acovamcmc: no visible global function definition for ‘dev.new’
plot.acovamcmc: no visible global function definition for ‘par’
plot.acovamcmc: no visible global function definition for ‘plot’
plot.acovamcmc: no visible global function definition for ‘density’
plot.acovamcmc: no visible global function definition for ‘acf’
plot.acovamcmc: no visible global function definition for ‘contour’
plot.acovamcmc: no visible global function definition for ‘image’
plot.acovamcmc: no visible global function definition for ‘persp’
Undefined global functions or variables:
  acf contour density dev.new image par persp plot quantile rgamma
  rnorm var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "contour", "image", "par", "persp", "plot")
  importFrom("stats", "acf", "density", "quantile", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
CumulativeVarPlot: no visible global function definition for ‘plot’
CumulativeVarPlot: no visible global function definition for ‘axis’
PCplot: no visible global function definition for ‘par’
PCplot: no visible global function definition for ‘plot’
PCplot: no visible global function definition for ‘rainbow’
PCplot: no visible global function definition for ‘density’
gDist: no visible global function definition for ‘plot’
gDist: no visible global function definition for ‘density’
gDist: no visible global function definition for ‘abline’
gPCA.batchdetect: no visible global function definition for ‘var’
Undefined global functions or variables:
  abline axis density par plot rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "par", "plot")
  importFrom("stats", "density", "var")
to your NAMESPACE file.
Resdata : prepdata: no visible global function definition for ‘sqldf’
gpca : Build3d: no visible global function definition for ‘dev.new’
gpca : Build3d: no visible global function definition for
  ‘scatterplot3d’
gpca : Build3d: no visible global function definition for ‘text’
gpca : Build3d: no visible global function definition for ‘plot’
gpca : Build3d: no visible global function definition for ‘abline’
gpca : Build3d: no visible global function definition for ‘rect’
gpca: no visible global function definition for ‘cor’
gpca: no visible global function definition for ‘dev.new’
gpca: no visible global function definition for ‘plot’
gpca: no visible global function definition for ‘text’
gpca: no visible global function definition for ‘abline’
gpca: no visible global function definition for ‘rect’
gpca: no visible global function definition for ‘scatterplot3d’
gpca: no visible global function definition for ‘segments’
gpca: no visible global function definition for ‘points’
gpca: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  abline cor dev.new plot points rect scatterplot3d segments sqldf text
  write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot", "points", "rect", "segments",
             "text")
  importFrom("stats", "cor")
  importFrom("utils", "write.table")
to your NAMESPACE file.
gpfr: no visible global function definition for ‘rnorm’
gpfr: no visible global function definition for ‘runif’
gpfrpred : <anonymous>: no visible global function definition for
  ‘predict’
gpfrtrain: no visible global function definition for ‘nlminb’
gppredict: no visible global function definition for ‘predict’
gpr: no visible global function definition for ‘rnorm’
gpr: no visible global function definition for ‘runif’
gpr: no visible global function definition for ‘lm’
gpr: no visible global function definition for ‘resid’
gpr: no visible global function definition for ‘nlminb’
main1: no visible global function definition for ‘lm’
main1: no visible global function definition for ‘resid’
main2 : <anonymous>: no visible global function definition for
  ‘predict’
main2: no visible global function definition for ‘predict’
main3: no visible global function definition for ‘lm’
main3: no visible global function definition for ‘resid’
plot.gpfr: no visible global function definition for ‘polygon’
plot.gpfr: no visible global function definition for ‘rgb’
plot.gpfr: no visible global function definition for ‘matpoints’
plot.gpfr: no visible global function definition for ‘matlines’
plot.gpfr: no visible global function definition for ‘lines’
plot.gpr: no visible global function definition for ‘plot’
plot.gpr: no visible global function definition for ‘polygon’
plot.gpr: no visible global function definition for ‘rgb’
plot.gpr: no visible global function definition for ‘points’
plot.gpr: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines lm matlines matpoints nlminb plot points polygon predict resid
  rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "matlines", "matpoints", "plot",
             "points", "polygon")
  importFrom("stats", "lm", "nlminb", "predict", "resid", "rnorm",
             "runif")
to your NAMESPACE file.
GriegSmith: no visible global function definition for ‘is.ppp’
envelopes: no visible binding for global variable ‘quantile’
plot.GriegSmith: no visible global function definition for ‘plot’
plot.GriegSmith: no visible global function definition for ‘lines’
plot.GriegSmith: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis is.ppp lines plot quantile
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "quantile")
to your NAMESPACE file.
gte: no visible global function definition for ‘model.extract’
gte: no visible global function definition for ‘model.matrix’
gte: no visible binding for global variable ‘sd’
gte: no visible global function definition for ‘dnorm’
plot.gte: no visible global function definition for ‘plot’
plot.gte: no visible global function definition for ‘par’
plot.gte: no visible global function definition for ‘polygon’
plot.gte: no visible global function definition for ‘gray’
plot.gte: no visible global function definition for ‘lines’
plot.gte: no visible global function definition for ‘legend’
Undefined global functions or variables:
  dnorm gray legend lines model.extract model.matrix par plot polygon
  sd
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "legend", "lines", "par", "plot", "polygon")
  importFrom("stats", "dnorm", "model.extract", "model.matrix", "sd")
to your NAMESPACE file.
PoincarePlot: no visible global function definition for ‘plot’
PoincarePlot: no visible global function definition for ‘lines’
PoincarePlot: no visible global function definition for ‘lowess’
hctest: no visible global function definition for ‘cor.test’
rdplot: no visible global function definition for ‘plot’
rdplot: no visible global function definition for ‘lines’
rdplot: no visible global function definition for ‘lowess’
rdplot: no visible global function definition for ‘rgb’
simer: no visible global function definition for ‘runif’
simer: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  cor.test lines lowess plot rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "cor.test", "lowess", "rnorm", "runif")
to your NAMESPACE file.
heatmap.plus: no visible binding for global variable ‘dist’
heatmap.plus: no visible binding for global variable ‘hclust’
heatmap.plus : <anonymous>: no visible global function definition for
  ‘reorder’
heatmap.plus: no visible global function definition for ‘as.dendrogram’
heatmap.plus: no visible global function definition for
  ‘order.dendrogram’
heatmap.plus: no visible binding for global variable ‘sd’
heatmap.plus: no visible global function definition for ‘par’
heatmap.plus: no visible global function definition for ‘layout’
heatmap.plus: no visible global function definition for ‘image’
heatmap.plus: no visible global function definition for ‘axis’
heatmap.plus: no visible global function definition for ‘mtext’
heatmap.plus: no visible global function definition for ‘plot’
heatmap.plus: no visible global function definition for ‘frame’
heatmap.plus: no visible global function definition for ‘title’
Undefined global functions or variables:
  as.dendrogram axis dist frame hclust image layout mtext
  order.dendrogram par plot reorder sd title
Consider adding
  importFrom("graphics", "axis", "frame", "image", "layout", "mtext",
             "par", "plot", "title")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
Running examples in ‘heemod-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: define_dsa
> ### Title: Define a Sensitivity Analysis
> ### Aliases: define_dsa define_dsa_
> 
> ### ** Examples
> 
> 
> define_dsa(
+   a, 10, 45,
+   b, .5, 1.5
+ )
Error: All columns in a tibble must be vectors.
✖ Column `dots[i]` is a `lazy_dots` object.
Backtrace:
     █
  1. └─heemod::define_dsa(a, 10, 45, b, 0.5, 1.5)
  2.   └─heemod:::define_dsa_(...)
  3.     ├─base::suppressWarnings(...)
  4.     │ └─base::withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  5.     ├─dplyr::bind_rows(...)
  6.     │ ├─dplyr:::flatten_bindable(dots_values(...))
  7.     │ └─rlang::dots_values(...)
  8.     ├─stats::setNames(tibble::tibble(dots[i]), names(dots)[i])
  9.     └─tibble::tibble(dots[i])
 10.       └─tibble:::tibble_quos(xs[!is_null], .rows, .name_repair)
 11.         └─tibble:::check_valid_col(res, col_names[[j]], j)
 12.           └─tibble:::check_valid_cols(set_names(list(x), name))
Execution halted
HubNetwork: no visible global function definition for ‘rbinom’
HubNetwork: no visible global function definition for ‘runif’
HubNetwork: no visible global function definition for ‘cov2cor’
binaryMCMC: no visible global function definition for ‘rbinom’
image.hbn: no visible global function definition for ‘col2rgb’
image.hbn: no visible global function definition for ‘rgb’
image.hbn: no visible global function definition for ‘dev.new’
image.hbn: no visible global function definition for ‘par’
image.hbn: no visible global function definition for ‘image’
image.hcov: no visible global function definition for ‘col2rgb’
image.hcov: no visible global function definition for ‘rgb’
image.hcov: no visible global function definition for ‘dev.new’
image.hcov: no visible global function definition for ‘par’
image.hcov: no visible global function definition for ‘image’
image.hglasso: no visible global function definition for ‘col2rgb’
image.hglasso: no visible global function definition for ‘rgb’
image.hglasso: no visible global function definition for ‘dev.new’
image.hglasso: no visible global function definition for ‘par’
image.hglasso: no visible global function definition for ‘image’
plot.hbn: no visible global function definition for ‘rgb’
plot.hbn: no visible global function definition for ‘plot’
plot.hcov: no visible global function definition for ‘rgb’
plot.hcov: no visible global function definition for ‘plot’
plot.hglasso: no visible global function definition for ‘rgb’
plot.hglasso: no visible global function definition for ‘plot’
Undefined global functions or variables:
  col2rgb cov2cor dev.new image par plot rbinom rgb runif
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rgb")
  importFrom("graphics", "image", "par", "plot")
  importFrom("stats", "cov2cor", "rbinom", "runif")
to your NAMESPACE file.
compute.contrasts: no visible binding for global variable ‘sd’
compute.contrasts: no visible global function definition for ‘cor’
compute.contrasts: no visible global function definition for ‘sd’
plot.estfdr: no visible global function definition for ‘plot’
plot.hiertest: no visible global function definition for ‘plot’
plot.hiertest: no visible global function definition for ‘legend’
Undefined global functions or variables:
  cor legend plot sd
Consider adding
  importFrom("graphics", "legend", "plot")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
overlay.sim: no visible global function definition for ‘points’
plotDistr: no visible global function definition for ‘dev.hold’
plotDistr: no visible global function definition for ‘dev.flush’
plotDistr: no visible global function definition for ‘plot’
plotDistr: no visible global function definition for ‘segments’
Undefined global functions or variables:
  dev.flush dev.hold plot points segments
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold")
  importFrom("graphics", "plot", "points", "segments")
to your NAMESPACE file.
baumwelchcont: no visible global function definition for ‘dnorm’
hmmcontSimul: no visible global function definition for ‘rnorm’
hmmcontSimul: no visible global function definition for ‘rbinom’
plot.ContObservHMM: no visible global function definition for ‘plot’
plot.ContObservHMM: no visible global function definition for ‘lines’
statesDistributionsPlot: no visible global function definition for
  ‘dnorm’
statesDistributionsPlot: no visible global function definition for ‘sd’
statesDistributionsPlot: no visible global function definition for
  ‘plot’
statesDistributionsPlot: no visible global function definition for
  ‘lines’
statesDistributionsPlot: no visible global function definition for
  ‘legend’
summary.ContObservHMM: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dnorm legend lines plot rbinom rnorm sd
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "dnorm", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
dishonestCasino: no visible global function definition for ‘plot’
dishonestCasino: no visible global function definition for ‘axis’
dishonestCasino: no visible global function definition for ‘text’
dishonestCasino: no visible global function definition for ‘rect’
dishonestCasino: no visible global function definition for ‘rgb’
dishonestCasino: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis plot points rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "plot", "points", "rect", "text")
to your NAMESPACE file.
hpbayes.plot: no visible global function definition for ‘par’
hpbayes.plot: no visible global function definition for ‘plot’
hpbayes.plot: no visible global function definition for ‘points’
postpri.plot: no visible global function definition for ‘par’
postpri.plot: no visible global function definition for ‘plot’
postpri.plot: no visible global function definition for ‘points’
postpri.plot: no visible global function definition for ‘segments’
postpri.plot: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot par plot points segments
Consider adding
  importFrom("graphics", "boxplot", "par", "plot", "points", "segments")
to your NAMESPACE file.
Calculate3D: no visible global function definition for ‘persp’
CalculateHUM_Ex: no visible global function definition for ‘combn’
CalculateHUM_Plot: no visible global function definition for ‘plot’
CalculateHUM_Plot: no visible global function definition for ‘polygon’
CalculateHUM_Plot: no visible global function definition for ‘text’
CalculateHUM_Plot: no visible global function definition for ‘points’
CalculateHUM_Plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
ibdhap.barplot: no visible global function definition for ‘plot’
ibdhap.barplot: no visible global function definition for ‘rect’
ibdhap.compare.loci: no visible global function definition for ‘hist’
ibdhap.compare.segs: no visible global function definition for ‘tail’
ibdhap.make.calls: no visible global function definition for
  ‘count.fields’
ibdhap.make.calls: no visible global function definition for
  ‘read.table’
ibdhap.make.true: no visible global function definition for
  ‘read.table’
ibdhap.names: no visible global function definition for ‘count.fields’
ibdhap.names: no visible global function definition for ‘read.table’
ibdhap.reduce.states: no visible global function definition for
  ‘read.table’
ibdhap.reduce.states: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  count.fields hist plot read.table rect tail write.table
Consider adding
  importFrom("graphics", "hist", "plot", "rect")
  importFrom("utils", "count.fields", "read.table", "tail",
             "write.table")
to your NAMESPACE file.
create.ibd.dat: no visible global function definition for ‘read.table’
create.pairs.frame: no visible global function definition for ‘terms’
ibd.moments: no visible global function definition for ‘var’
ibdreg: no visible global function definition for ‘terms’
ibdreg: no visible global function definition for ‘as.formula’
linkage.tests: no visible global function definition for ‘pchisq’
pchibar: no visible global function definition for ‘pchisq’
plot.linkage.all: no visible global function definition for ‘plot’
plot.linkage.all: no visible global function definition for ‘title’
plotpval: no visible global function definition for ‘plot’
plotpval: no visible global function definition for ‘lines’
sim.ibd.var: no visible global function definition for ‘read.table’
sim.mark.prop: no visible global function definition for ‘runif’
Undefined global functions or variables:
  as.formula lines pchisq plot read.table runif terms title var
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("stats", "as.formula", "pchisq", "runif", "terms", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
ICA: no visible global function definition for ‘runif’
plot.ICA: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
ICCbare: no visible global function definition for ‘na.omit’
ICCbare: no visible global function definition for ‘formula’
ICCbare: no visible global function definition for ‘replications’
ICCbare: no visible global function definition for ‘aggregate’
ICCbare: no visible global function definition for ‘anova’
ICCbare: no visible global function definition for ‘aov’
ICCbareF: no visible global function definition for ‘aggregate’
ICCest: no visible global function definition for ‘na.omit’
ICCest: no visible global function definition for ‘anova’
ICCest: no visible global function definition for ‘aov’
ICCest: no visible global function definition for ‘aggregate’
ICCest: no visible global function definition for ‘qf’
ICCest: no visible global function definition for ‘qnorm’
Nest: no visible global function definition for ‘qnorm’
effort : CIW: no visible global function definition for ‘qf’
effort: no visible global function definition for ‘plot’
effort: no visible global function definition for ‘axis’
effort: no visible global function definition for ‘lines’
effort: no visible global function definition for ‘legend’
Undefined global functions or variables:
  aggregate anova aov axis formula legend lines na.omit plot qf qnorm
  replications
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "aggregate", "anova", "aov", "formula", "na.omit",
             "qf", "qnorm", "replications")
to your NAMESPACE file.
INCAncinner : dian: no visible global function definition for ‘cutree’
INCAncinner : bestela: no visible global function definition for
  ‘cutree’
center: no visible global function definition for ‘var’
dbhatta: no visible global function definition for ‘as.dist’
dcor: no visible global function definition for ‘cor’
dcor: no visible global function definition for ‘as.dist’
dgower: no visible global function definition for ‘as.dist’
dmahal: no visible global function definition for ‘as.dist’
dproc2: no visible global function definition for ‘as.dist’
plot.incaix: no visible global function definition for ‘barplot’
plot.incanc: no visible global function definition for ‘plot’
plot.incanc: no visible global function definition for ‘lines’
plot.incanc: no visible global function definition for ‘legend’
selectioncluster : dian: no visible global function definition for
  ‘cutree’
selectioncluster : bestela: no visible global function definition for
  ‘cutree’
Undefined global functions or variables:
  as.dist barplot cor cutree legend lines plot var
Consider adding
  importFrom("graphics", "barplot", "legend", "lines", "plot")
  importFrom("stats", "as.dist", "cor", "cutree", "var")
to your NAMESPACE file.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [17s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ijtiff)
  > 
  > test_check("ijtiff")
  ── 1. Error: text-image-io works (@test-io.R#321)  ─────────────────────────────
  No common type for `col2` <double> and `col2` <character>.
  Backtrace:
    1. dplyr::tribble(~col1, ~col2, 1, 5, 8, "y")
    8. vctrs:::vec_ptype2.double.default(...)
    9. vctrs::vec_default_ptype2(x, y, x_arg = x_arg, y_arg = y_arg)
   10. vctrs::stop_incompatible_type(x, y, x_arg = x_arg, y_arg = y_arg)
   11. vctrs:::stop_incompatible(...)
   12. vctrs:::stop_vctrs(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 96 | SKIPPED: 0 | WARNINGS: 98 | FAILED: 1 ]
  1. Error: text-image-io works (@test-io.R#321) 
  
  Error: testthat unit tests failed
  Execution halted
A.dep.tests: no visible global function definition for ‘combn’
A.dep.tests: no visible global function definition for ‘pchisq’
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’
dependogram: no visible global function definition for ‘combn’
dependogram: no visible global function definition for ‘plot’
dependogram: no visible global function definition for ‘points’
dependogram: no visible global function definition for ‘segments’
Undefined global functions or variables:
  clusterCall clusterSetupSPRNG combn makeCluster pchisq plot points
  segments stopCluster
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "pchisq")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running ‘testthat.R’ [206s/224s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(interactions)
  > 
  > test_check("interactions")
  ── 1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157)  
  `print(p)` produced messages.
  
  ── 2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162)  
  `print(p)` produced messages.
  
  Failed with error:  'there is no package called 'rstanarm''
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 164 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157) 
  2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
ClearBottomMenuPlot: no visible global function definition for ‘rect’
InteractiveIGraph : mousedown: no visible global function definition
  for ‘grconvertX’
InteractiveIGraph : mousedown: no visible global function definition
  for ‘grconvertY’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘grconvertX’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘grconvertY’
InteractiveIGraph : dragmousemove: no visible global function
  definition for ‘polygon’
InteractiveIGraph : mouseup: no visible global function definition for
  ‘grconvertX’
InteractiveIGraph : mouseup: no visible global function definition for
  ‘grconvertY’
InteractiveIGraph : keybd: no visible global function definition for
  ‘par’
PlotRegionGeneral: no visible global function definition for ‘polygon’
plot.InteractiveIGraph: no visible global function definition for
  ‘plot’
plot.InteractiveIGraph: no visible global function definition for ‘par’
plot.Menu: no visible global function definition for ‘par’
plot.Menu: no visible binding for global variable ‘rect’
plot.MenuItem: no visible binding for global variable ‘strwidth’
plot.MenuItem: no visible binding for global variable ‘strheight’
plot.MenuItem: no visible binding for global variable ‘rect’
plot.MenuItem: no visible binding for global variable ‘text’
plot.MenuLine: no visible binding for global variable ‘rect’
Undefined global functions or variables:
  grconvertX grconvertY par plot polygon rect strheight strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "plot",
             "polygon", "rect", "strheight", "strwidth", "text")
to your NAMESPACE file.
interact: no visible global function definition for ‘cor’
plot.interact: no visible global function definition for ‘plot’
standardize.matrix: no visible binding for global variable ‘var’
standardize.matrix: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cor plot sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "sd", "var")
to your NAMESPACE file.
Mo.Th.Ra.: no visible global function definition for ‘aggregate’
daily_mean: no visible global function definition for ‘aggregate’
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’
par_calibration: no visible global function definition for ‘aggregate’
plot_meas_sim: no visible global function definition for ‘as.date’
plot_meas_sim: no visible global function definition for ‘date.mdy’
plot_meas_sim: no visible global function definition for ‘plot’
plot_meas_sim: no visible global function definition for ‘par’
plot_meas_sim: no visible global function definition for ‘legend’
shape_calibration: no visible global function definition for ‘date.mdy’
shape_calibration: no visible global function definition for ‘as.date’
shape_calibration: no visible global function definition for
  ‘aggregate’
Undefined global functions or variables:
  aggregate as.date chron date.mdy days hours legend par plot years
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "aggregate")
to your NAMESPACE file.
icScoreTest: no visible global function definition for ‘pnorm’
icScoreTest: no visible global function definition for ‘pchisq’
icfit.formula: no visible global function definition for ‘terms’
icfit.formula: no visible global function definition for
  ‘model.extract’
icfitBootCI: no visible global function definition for ‘binom.test’
ictest.formula: no visible global function definition for
  ‘model.extract’
plot.icfit: no visible global function definition for ‘gray’
plot.icfit: no visible global function definition for ‘plot’
plot.icfit: no visible global function definition for ‘axis’
plot.icfit : polygon.icfit: no visible global function definition for
  ‘polygon’
scoresFromFit: no visible global function definition for ‘dnorm’
scoresFromFit: no visible global function definition for ‘qnorm’
wsrHLYpclt: no visible global function definition for ‘model.matrix’
wsrHLYpclt: no visible global function definition for ‘pchisq’
wsrHLYpclt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis binom.test dnorm gray model.extract model.matrix pchisq plot
  pnorm polygon qnorm terms
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis", "plot", "polygon")
  importFrom("stats", "binom.test", "dnorm", "model.extract",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
interventionEffects: no visible binding for global variable ‘sd’
interventionEffects: no visible global function definition for ‘pt’
interventionEffects: no visible global function definition for ‘sd’
interventionalInference: no visible global function definition for ‘sd’
interventionalInferenceAdvanced: no visible global function definition
  for ‘sd’
linesROC: no visible global function definition for ‘segments’
plotMaxML: no visible global function definition for ‘plot’
plotMaxML: no visible global function definition for ‘segments’
Undefined global functions or variables:
  plot pt sd segments
Consider adding
  importFrom("graphics", "plot", "segments")
  importFrom("stats", "pt", "sd")
to your NAMESPACE file.
ILik : rbern: no visible global function definition for ‘runif’
ILik : q: no visible global function definition for ‘dnorm’
ILik : SlambdaG: no visible global function definition for ‘rnorm’
ILik : Pi_hat: no visible global function definition for ‘rnorm’
ILik : q: no visible global function definition for ‘dgamma’
ILik : SlambdaG: no visible global function definition for ‘rgamma’
ILik : Pi_hat: no visible global function definition for ‘rgamma’
ILik: no visible global function definition for ‘maxLik’
ILik: no visible global function definition for ‘coef’
ILik: no visible global function definition for ‘hessian’
ILik: no visible global function definition for ‘plot’
Undefined global functions or variables:
  coef dgamma dnorm hessian maxLik plot rgamma rnorm runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dgamma", "dnorm", "rgamma", "rnorm",
             "runif")
to your NAMESPACE file.
f.B: no visible global function definition for ‘pnorm’
f.B.neglog.deriv: no visible global function definition for ‘pnorm’
f.B.neglog.deriv: no visible global function definition for ‘dnorm’
f.grovest3 : f.est: no visible global function definition for ‘survfit’
f.grovest3 : f.est: no visible global function definition for ‘plot’
f.grovest3 : f.est: no visible global function definition for ‘lines’
f.grovest3: no visible global function definition for ‘model.frame’
f.grovest3: no visible global function definition for ‘model.extract’
invGauss: no visible global function definition for ‘model.frame’
invGauss: no visible global function definition for ‘model.extract’
invGauss: no visible global function definition for ‘model.matrix’
predict.invGauss: no visible global function definition for
  ‘model.frame’
predict.invGauss: no visible global function definition for
  ‘model.extract’
predict.invGauss: no visible global function definition for
  ‘model.matrix’
predict.invGauss: no visible binding for global variable ‘formula’
predict.invGauss: no visible binding for global variable ‘data’
summary.invGauss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  data dnorm formula lines model.extract model.frame model.matrix plot
  pnorm survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "dnorm", "formula", "model.extract", "model.frame",
             "model.matrix", "pnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Dependence on R version ‘3.4.3’ not with patchlevel 0
Rd file 'N2.cohen.kappa.Rd':
  \examples lines wider than 100 characters:
       N2.cohen.kappa(c(0.2, 0.25, 0.55), k1=0.6, k0=0.4)                                                            

These lines will be truncated in the PDF manual.
residualplot: no visible global function definition for ‘predict’
residualplot: no visible global function definition for ‘rstandard’
residualplot: no visible global function definition for
  ‘complete.cases’
residualplot: no visible global function definition for ‘plot’
residualplot: no visible global function definition for ‘points’
residualplot: no visible global function definition for ‘lines’
residualplot: no visible global function definition for ‘smooth.spline’
residualplot: no visible global function definition for ‘sd’
residualplot: no visible global function definition for ‘rgb’
residualplot: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  complete.cases lines plot points polygon predict rgb rstandard sd
  smooth.spline
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "complete.cases", "predict", "rstandard", "sd",
             "smooth.spline")
to your NAMESPACE file.
getSysinfo: no visible global function definition for ‘sessionInfo’
getVecInfo: no visible global function definition for ‘sd’
isSeriesConstant: no visible global function definition for ‘median’
labelMargins: no visible global function definition for ‘mtext’
plotBG: no visible global function definition for ‘plot’
plotBG: no visible global function definition for ‘polygon’
plotBG: no visible global function definition for ‘par’
plotColorScale: no visible global function definition for ‘par’
plotColorScale: no visible global function definition for ‘text’
plotImageRotated: no visible global function definition for
  ‘heat.colors’
plotImageRotated: no visible global function definition for ‘par’
plotImageRotated: no visible global function definition for ‘plot’
plotImageRotated: no visible global function definition for ‘image’
plotImageRotated: no visible global function definition for ‘axis’
plotNLines: no visible global function definition for ‘par’
plotNLines: no visible global function definition for ‘plot’
plotNLines: no visible global function definition for ‘mtext’
plotNLines: no visible global function definition for ‘axis’
plotNLines: no visible global function definition for ‘points’
plotNLines: no visible global function definition for ‘sd’
userCoords: no visible global function definition for ‘par’
Undefined global functions or variables:
  axis heat.colors image median mtext par plot points polygon sd
  sessionInfo text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "axis", "image", "mtext", "par", "plot",
             "points", "polygon", "text")
  importFrom("stats", "median", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
Dependence on R version ‘3.4.4’ not with patchlevel 0
binteg: no visible global function definition for ‘contourLines’
binteg: no visible global function definition for ‘approx’
binteg: no visible global function definition for ‘par’
plot1: no visible global function definition for ‘plot’
plot1: no visible global function definition for ‘par’
plot1: no visible global function definition for ‘rect’
plot1: no visible global function definition for ‘axis’
plot1: no visible global function definition for ‘contour’
plot1: no visible global function definition for ‘contourLines’
plot1: no visible binding for global variable ‘approx’
plot1: no visible global function definition for ‘lines’
plot1: no visible global function definition for ‘text’
plot2: no visible global function definition for ‘plot’
plot2: no visible global function definition for ‘abline’
plot2: no visible global function definition for ‘lines’
plot2: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline approx axis contour contourLines legend lines par plot rect
  text
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "abline", "axis", "contour", "legend", "lines",
             "par", "plot", "rect", "text")
  importFrom("stats", "approx")
to your NAMESPACE file.
Running ‘testthat.R’ [9s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(jstor)
  > 
  > test_check("jstor")
  ── 1. Failure: authors are correct (@test-books.R#117)  ────────────────────────
  chap_auth[[5, "authors"]] not identical to `correct_authors`.
  names for current but not for target
  Attributes: < target is NULL, current is list >
  Length mismatch: comparison on first 1 components
  Component 1: Cols in y but not x: `c(NA_character_, NA_character_)`. 
  Component 1: Cols in x but not y: `author_number`, `suffix`, `string_name`, `surname`, `given_name`, `prefix`. 
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 251 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: authors are correct (@test-books.R#117) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [58s/65s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(jtools)
  > 
  > 
  > test_check("jtools")
  Failed with error:  'there is no package called 'rstanarm''
  ── 1. Error: plot_coefs works with brms (@test-export-summs.R#294)  ────────────
  Aesthetics must be either length 1 or the same as the data (8): xmin and xmax
  Backtrace:
    1. testthat::expect_silent(print(plot_coefs(bfit1) + ggtitle("basic brms fit")))
   10. ggplot2:::print.ggplot(plot_coefs(bfit1) + ggtitle("basic brms fit"))
   12. ggplot2:::ggplot_build.ggplot(x)
   13. ggplot2:::by_layer(function(l, d) l$compute_aesthetics(d, plot))
   14. ggplot2:::f(l = layers[[i]], d = data[[i]])
   15. l$compute_aesthetics(d, plot)
   16. ggplot2:::f(..., self = self)
   17. ggplot2:::check_aesthetics(evaled, n)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 356 | SKIPPED: 0 | WARNINGS: 13 | FAILED: 1 ]
  1. Error: plot_coefs works with brms (@test-export-summs.R#294) 
  
  Error: testthat unit tests failed
  Execution halted
expression_up : <anonymous>: no visible global function definition for
  ‘quantile’
expression_up : <anonymous>: no visible global function definition for
  ‘IQR’
expression_up : <anonymous>: no visible global function definition for
  ‘median’
expression_up : <anonymous>: no visible global function definition for
  ‘sd’
plot_up: no visible global function definition for ‘plot’
plot_up: no visible global function definition for ‘text’
Undefined global functions or variables:
  IQR median plot quantile sd text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "IQR", "median", "quantile", "sd")
to your NAMESPACE file.
as.matrix.multiPhylo : tip2tip: no visible global function definition
  for ‘cophenetic’
bw.nn : <anonymous>: no visible global function definition for
  ‘quantile’
dist.diss: no visible binding for global variable ‘median’
dist.diss: no visible global function definition for ‘dist’
hist.kdetrees: no visible binding for global variable ‘density’
kdetrees : cutoff: no visible global function definition for ‘quantile’
kdetrees.complete: no visible global function definition for ‘plot’
kdetrees.complete: no visible global function definition for ‘hist’
kdetrees.complete: no visible global function definition for
  ‘write.csv’
plot.kdetrees: no visible binding for global variable ‘density’
Undefined global functions or variables:
  cophenetic density dist hist median plot quantile write.csv
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "cophenetic", "density", "dist", "median",
             "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for ‘rbeta’
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for ‘runif’
calculate.power : <anonymous>: no visible binding for global variable
  ‘quantile’
generate.benchmark.data: no visible global function definition for
  ‘runif’
generate.benchmark.data: no visible global function definition for
  ‘rnorm’
generate.benchmark.data: no visible global function definition for
  ‘rbinom’
generate.patchwork.copula: no visible global function definition for
  ‘rbeta’
generate.patchwork.copula: no visible global function definition for
  ‘runif’
novelTest.chisq: no visible global function definition for ‘pchisq’
novelTest.chisq4nn: no visible global function definition for ‘pchisq’
optimise.copula.mi : <anonymous>: no visible global function definition
  for ‘optimize’
power.plot: no visible global function definition for ‘plot’
power.plot: no visible global function definition for ‘axis’
power.plot : <anonymous>: no visible global function definition for
  ‘points’
power.plot: no visible global function definition for ‘legend’
roc.plot: no visible global function definition for ‘colorRampPalette’
roc.plot : <anonymous>: no visible global function definition for
  ‘plot’
roc.plot : <anonymous> : <anonymous>: no visible global function
  definition for ‘points’
run.tests : <anonymous> : <anonymous>: no visible global function
  definition for ‘runif’
Undefined global functions or variables:
  axis colorRampPalette legend optimize pchisq plot points quantile
  rbeta rbinom rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "legend", "plot", "points")
  importFrom("stats", "optimize", "pchisq", "quantile", "rbeta",
             "rbinom", "rnorm", "runif")
to your NAMESPACE file.
image.kriging: no visible global function definition for ‘heat.colors’
image.kriging: no visible global function definition for ‘image’
kriging: no visible global function definition for ‘lm’
plot.kriging: no visible global function definition for ‘plot’
plot.kriging: no visible global function definition for ‘curve’
Undefined global functions or variables:
  curve heat.colors image lm plot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "curve", "image", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
kselection: no visible global function definition for ‘txtProgressBar’
kselection: no visible global function definition for
  ‘setTxtProgressBar’
plot.Kselection: no visible global function definition for ‘plot’
plot.Kselection: no visible global function definition for ‘lines’
plot.Kselection: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines plot setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
auc: no visible global function definition for ‘approx’
kulife.colors: no visible global function definition for ‘palette’
rootonorm: no visible global function definition for ‘sd’
rootonorm: no visible global function definition for ‘hist’
rootonorm: no visible global function definition for ‘pnorm’
rootonorm: no visible global function definition for ‘dnorm’
rootonorm: no visible global function definition for ‘plot’
rootonorm: no visible global function definition for ‘rect’
rootonorm: no visible global function definition for ‘lines’
rootonorm: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approx dnorm hist lines palette plot pnorm rect sd
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "hist", "lines", "plot", "rect")
  importFrom("stats", "approx", "dnorm", "pnorm", "sd")
to your NAMESPACE file.
betabreaker: no visible global function definition for ‘predict’
coef.lars: no visible global function definition for ‘predict’
cv.lars: no visible global function definition for ‘predict’
cv.lars: no visible binding for global variable ‘var’
error.bars: no visible global function definition for ‘segments’
plot.lars: no visible global function definition for ‘plot’
plot.lars: no visible global function definition for ‘matplot’
plot.lars: no visible global function definition for ‘title’
plot.lars: no visible global function definition for ‘abline’
plot.lars: no visible global function definition for ‘axis’
plotCVLars: no visible global function definition for ‘plot’
predict.lars: no visible global function definition for ‘approx’
Undefined global functions or variables:
  abline approx axis matplot plot predict segments title var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "plot", "segments",
             "title")
  importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
glassoscore: no visible global function definition for ‘var’
glassoscore: no visible global function definition for ‘pchisq’
lassoscore: no visible global function definition for ‘txtProgressBar’
lassoscore: no visible global function definition for
  ‘setTxtProgressBar’
lassoscore: no visible global function definition for ‘pchisq’
plot.glassoscore: no visible global function definition for ‘legend’
plot.lassoscore: no visible global function definition for ‘legend’
plot.mbscore: no visible global function definition for ‘legend’
qqpval: no visible global function definition for ‘ppoints’
qqpval: no visible global function definition for ‘qbeta’
qqpval: no visible global function definition for ‘points’
qqpval: no visible global function definition for ‘plot’
qqpval: no visible global function definition for ‘abline’
qqpval: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline legend pchisq plot points polygon ppoints qbeta
  setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points", "polygon")
  importFrom("stats", "pchisq", "ppoints", "qbeta", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Package suggested but not available for checking: ‘texmex’
ARConfIntEst: no visible global function definition for ‘sd’
PTLinkFunc: no visible global function definition for ‘pnorm’
PTLinkFunc: no visible global function definition for ‘qnorm’
PTMultiPeriodPD: no visible global function definition for ‘uniroot’
PTOnePeriodPD : f: no visible global function definition for ‘pbinom’
PTOnePeriodPD: no visible global function definition for ‘uniroot’
QMMGetRLogitPD: no visible global function definition for ‘ecdf’
QMMPDlinkFunc: no visible global function definition for ‘qnorm’
QMMPlot: no visible global function definition for ‘plot’
QMMPlot: no visible global function definition for ‘lines’
QMMPlot: no visible global function definition for ‘legend’
VDBCalibratePD: no visible global function definition for ‘ecdf’
VDBGetK: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  ecdf legend lines pbinom plot pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "ecdf", "pbinom", "pnorm", "qnorm", "sd",
             "uniroot")
to your NAMESPACE file.
AlternateSVD: no visible binding for global variable ‘sd’
IPOD: no visible global function definition for ‘mad’
IPOD: no visible global function definition for ‘pnorm’
Pvalue: no visible global function definition for ‘pf’
ROCplot: no visible global function definition for ‘png’
ROCplot: no visible global function definition for ‘matplot’
ROCplot: no visible global function definition for ‘legend’
ROCplot: no visible global function definition for ‘dev.off’
leapp: no visible global function definition for ‘png’
leapp: no visible global function definition for ‘plot’
leapp: no visible global function definition for ‘dev.off’
ridge: no visible global function definition for ‘sd’
ridge: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dev.off legend mad matplot pf plot png pnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "matplot", "plot")
  importFrom("stats", "mad", "pf", "pnorm", "sd")
to your NAMESPACE file.
plotBox: no visible global function definition for ‘sd’
plotBox: no visible global function definition for ‘rect’
plotBox: no visible global function definition for ‘qnorm’
plotBox: no visible global function definition for ‘segments’
plotInit: no visible global function definition for ‘plot’
plotInit: no visible global function definition for ‘runif’
plotInit: no visible global function definition for ‘mtext’
plotInit: no visible global function definition for ‘segments’
plotStack: no visible global function definition for ‘points’
Undefined global functions or variables:
  mtext plot points qnorm rect runif sd segments
Consider adding
  importFrom("graphics", "mtext", "plot", "points", "rect", "segments")
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
gen.lms: no visible global function definition for ‘na.omit’
plot.idf: no visible global function definition for ‘plot’
plot.idf: no visible global function definition for ‘mtext’
plot.idf: no visible global function definition for ‘points’
plot.idf: no visible global function definition for ‘segments’
plot.idf: no visible global function definition for ‘ftable’
plot.idf: no visible global function definition for ‘image’
plot.idf: no visible global function definition for ‘gray’
plot.idf: no visible global function definition for ‘abline’
plot.s.linlir: no visible global function definition for ‘plot’
plot.s.linlir: no visible global function definition for ‘mtext’
plot.s.linlir: no visible global function definition for ‘polygon’
plot.s.linlir: no visible global function definition for ‘points’
plot.s.linlir: no visible global function definition for ‘curve’
s.linlir: no visible global function definition for ‘na.omit’
s.linlir: no visible global function definition for ‘dbinom’
s.linlir: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline curve dbinom ftable gray image mtext na.omit pchisq plot
  points polygon segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "curve", "image", "mtext", "plot",
             "points", "polygon", "segments")
  importFrom("stats", "dbinom", "ftable", "na.omit", "pchisq")
to your NAMESPACE file.
EstimateProbability: no visible global function definition for
  ‘predict’
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’
plot_LOGICOIL: no visible global function definition for ‘png’
plot_LOGICOIL: no visible global function definition for ‘par’
plot_LOGICOIL: no visible global function definition for ‘plot’
plot_LOGICOIL: no visible global function definition for ‘lines’
plot_LOGICOIL: no visible global function definition for ‘axis’
plot_LOGICOIL: no visible global function definition for ‘mtext’
plot_LOGICOIL: no visible global function definition for ‘legend’
plot_LOGICOIL: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  LOGICOILfit Model_Parameters axis dev.off legend lines mtext par plot
  png predict pssm
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:182:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:896:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:196:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
fplot: no visible global function definition for ‘rnorm’
fplot: no visible global function definition for ‘plot’
fplot: no visible global function definition for ‘segments’
fplot: no visible global function definition for ‘points’
fplot: no visible global function definition for ‘text’
fplot.foodweb: no visible global function definition for ‘plot’
fplot.foodweb: no visible global function definition for ‘segments’
fplot.foodweb: no visible global function definition for ‘points’
fplot.foodweb: no visible global function definition for ‘text’
gplot: no visible global function definition for ‘runif’
groupplot: no visible global function definition for ‘rnorm’
groupplot: no visible global function definition for ‘plot’
groupplot: no visible global function definition for ‘segments’
groupplot: no visible global function definition for ‘points’
groupplot: no visible global function definition for ‘text’
groupplot.foodweb: no visible global function definition for ‘rnorm’
groupplot.foodweb: no visible global function definition for ‘plot’
groupplot.foodweb: no visible global function definition for ‘segments’
groupplot.foodweb: no visible global function definition for ‘points’
groupplot.foodweb: no visible global function definition for ‘text’
Undefined global functions or variables:
  plot points rnorm runif segments text
Consider adding
  importFrom("graphics", "plot", "points", "segments", "text")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
learnPattern.default: no visible global function definition for ‘runif’
plot.learnPattern: no visible global function definition for ‘matplot’
plotMDS: no visible global function definition for ‘par’
plotMDS: no visible global function definition for ‘rainbow’
plotMDS: no visible global function definition for ‘plot’
plotMDS: no visible global function definition for ‘pairs’
visualizePattern: no visible global function definition for ‘par’
visualizePattern: no visible global function definition for ‘plot’
visualizePattern: no visible global function definition for ‘points’
visualizePattern: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend matplot pairs par plot points rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "pairs", "par", "plot",
             "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
SelectedInput:
  function(...)
SelectedInput.formula:
  function(..., data, control, metrics, stat, cutoff)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
ageprofile: no visible global function definition for ‘model.frame’
ageprofile: no visible binding for global variable ‘poisson’
ageprofile: no visible global function definition for ‘predict.gam’
ageprofile: no visible global function definition for ‘as.formula’
ageprofile: no visible global function definition for ‘summary.gam’
ageprofile: no visible global function definition for ‘contrasts<-’
ageprofile: no visible global function definition for ‘anova.gam’
plotap: no visible global function definition for ‘dev.new’
plotap: no visible global function definition for ‘plot’
plotap: no visible global function definition for ‘lines’
plotap: no visible global function definition for ‘points’
plotap: no visible global function definition for ‘legend’
splitter: no visible global function definition for ‘reshape’
tabm: no visible global function definition for ‘coef’
tabm: no visible global function definition for ‘AIC’
Undefined global functions or variables:
  AIC anova.gam as.formula coef contrasts<- dev.new legend lines
  model.frame plot points poisson predict.gam reshape summary.gam
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "AIC", "as.formula", "coef", "contrasts<-",
             "model.frame", "poisson", "reshape")
to your NAMESPACE file.
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mapview)
  > 
  > test_check("mapview")
  ── 1. Failure: getProjection() runs without issues (@test-mapviewControls.R#108)
  getProjection(franconia) has type `NULL`, not `character`.
  
  ── 2. Failure: getProjection() runs without issues (@test-mapviewControls.R#109)
  getProjection(franconia) not equal to "+proj=longlat +datum=WGS84 +no_defs".
  target is NULL, current is character
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 63 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Failure: getProjection() runs without issues (@test-mapviewControls.R#108) 
  2. Failure: getProjection() runs without issues (@test-mapviewControls.R#109) 
  
  Error: testthat unit tests failed
  Execution halted
MAT: no visible global function definition for ‘dev.new’
MAT: no visible global function definition for ‘plot’
MAT: no visible global function definition for ‘points’
MAT: no visible global function definition for ‘abline’
MAT: no visible global function definition for ‘text’
MAT: no visible global function definition for ‘legend’
MAT: no visible global function definition for ‘lines’
MAT: no visible global function definition for ‘par’
MAT: no visible global function definition for ‘barplot’
MAT: no visible global function definition for ‘cor’
print.MAT: no visible global function definition for ‘sd’
print.MAT: no visible global function definition for ‘cor’
simM3PL: no visible global function definition for ‘rnorm’
simM3PL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline barplot cor dev.new legend lines par plot points rnorm runif
  sd text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "lines", "par",
             "plot", "points", "text")
  importFrom("stats", "cor", "rnorm", "runif", "sd")
to your NAMESPACE file.
GSTplot : <anonymous>: no visible global function definition for
  ‘t.test’
GSTplot: no visible global function definition for ‘rt’
GSTplot: no visible global function definition for ‘layout’
GSTplot: no visible global function definition for ‘par’
GSTplot: no visible global function definition for ‘plot’
GSTplot: no visible global function definition for ‘text’
GSTplot: no visible global function definition for ‘lines’
GSTplot: no visible global function definition for ‘polygon’
GSTplot: no visible global function definition for ‘abline’
GSTplot: no visible global function definition for ‘ecdf’
GSTplot: no visible global function definition for ‘knots’
GSTplot : <anonymous>: no visible global function definition for ‘aov’
GSTplot: no visible global function definition for ‘qf’
MAVTn : <anonymous>: no visible global function definition for ‘aov’
MAVTn: no visible global function definition for ‘p.adjust’
MAVTn: no visible global function definition for ‘plot’
MAVTn: no visible global function definition for ‘par’
MAVTn: no visible global function definition for ‘abline’
MAVTn: no visible global function definition for ‘legend’
MAVTn: no visible global function definition for ‘locator’
Tols : olsf: no visible global function definition for ‘t.test’
Tols: no visible global function definition for ‘cor’
Undefined global functions or variables:
  abline aov cor ecdf knots layout legend lines locator p.adjust par
  plot polygon qf rt t.test text
Consider adding
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "locator", "par", "plot", "polygon", "text")
  importFrom("stats", "aov", "cor", "ecdf", "knots", "p.adjust", "qf",
             "rt", "t.test")
to your NAMESPACE file.
MI.2: no visible global function definition for ‘xtabs’
RNASeq.Data: no visible binding for global variable ‘quantile’
loc.node: no visible global function definition for ‘head’
loc.node: no visible global function definition for ‘tail’
plotHybrid.Tree: no visible global function definition for ‘par’
plotHybrid.Tree: no visible global function definition for ‘plot’
plotHybrid.Tree: no visible global function definition for ‘text’
plotHybrid.Tree: no visible global function definition for ‘image’
plotHybrid.Tree: no visible global function definition for ‘grey’
plotHybrid.Tree: no visible global function definition for
  ‘heat.colors’
plotHybrid.Tree: no visible global function definition for ‘head’
plotHybrid.Tree: no visible global function definition for ‘segments’
plotbr: no visible global function definition for ‘segments’
Undefined global functions or variables:
  grey head heat.colors image par plot quantile segments tail text
  xtabs
Consider adding
  importFrom("grDevices", "grey", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "segments", "text")
  importFrom("stats", "quantile", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
mcheatmaps : coscolorFun: no visible global function definition for
  ‘rgb’
mcheatmaps : halfcmat: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps : fullcmat: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘hclust’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘as.dist’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘sd’
mcheatmaps : calculateDendrogram: no visible global function definition
  for ‘cophenetic’
mcheatmaps : printDiag: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps: no visible global function definition for ‘strwidth’
mcheatmaps: no visible global function definition for ‘pdf’
mcheatmaps: no visible global function definition for ‘plot.new’
mcheatmaps: no visible global function definition for ‘as.dendrogram’
mcheatmaps: no visible global function definition for ‘reorder’
mcheatmaps: no visible global function definition for ‘par’
mcheatmaps: no visible global function definition for ‘plot’
mcheatmaps: no visible global function definition for
  ‘order.dendrogram’
mcheatmaps: no visible global function definition for ‘heat.colors’
mcheatmaps: no visible global function definition for ‘terrain.colors’
mcheatmaps: no visible global function definition for ‘as.dist’
mcheatmaps: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  as.dendrogram as.dist cophenetic dev.off hclust heat.colors
  order.dendrogram par pdf plot plot.new reorder rgb sd strwidth
  terrain.colors
Consider adding
  importFrom("grDevices", "dev.off", "heat.colors", "pdf", "rgb",
             "terrain.colors")
  importFrom("graphics", "par", "plot", "plot.new", "strwidth")
  importFrom("stats", "as.dendrogram", "as.dist", "cophenetic", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
plot.nsga2: no visible global function definition for ‘plot’
plot.nsga2: no visible global function definition for ‘lines’
plot.nsga2: no visible global function definition for ‘pairs’
plot.nsga2.collection: no visible global function definition for
  ‘devAskNewPage’
plot.nsga2.collection: no visible binding for global variable ‘plot’
Undefined global functions or variables:
  devAskNewPage lines pairs plot
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "lines", "pairs", "plot")
to your NAMESPACE file.
dometa: no visible global function definition for ‘qchisq’
dometa: no visible global function definition for ‘median’
dometa: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘pchisq’
forestplot: no visible global function definition for ‘qnorm’
forestplot: no visible global function definition for ‘plot’
forestplot: no visible global function definition for ‘points’
forestplot: no visible global function definition for ‘text’
metagwa.files: no visible global function definition for ‘read.csv’
metagwa.files: no visible global function definition for ‘write.csv’
metagwa.tables: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  median pchisq plot points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "plot", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Running ‘testthat.R’ [132s/148s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > suppressPackageStartupMessages(library(metacoder))
  > 
  > test_check("metacoder")
  ── 1. Failure: Summing counts per taxon (@test--calculations.R#103)  ───────────
  sum(x$data$tax_data$`700035949`) not equal to result$`700035949`[1].
  names for current but not for target
  
  ── 2. Failure: Summing counts per taxon (@test--calculations.R#126)  ───────────
  `total_counts` not equal to result$total[1].
  names for current but not for target
  
  ── 3. Failure: Parsing the UNITE general release fasta (@test--parsers_and_write
  result$data$tax_data$unite_seq[5] not equal to "CCAAATCATGTCTCCCGGCCGCAAGGCAGGTGCAGGCGTTTAACCCTTTGTGAACCAAAAAACCTTTCGCTTCGGCAGCAGCTCGGTTGGAGACAGCCTCTGTGTCAGCCTGCCGCTAGCACCAATTATCAAAACTTGCGGTTAGCAACATTGTCTGATTACCAAATTTTCGAATGAAAATCAAAACTTTCAACAACGGATCTCTTGGTTCCCGCATCGATGAAGAACGCAGCGAAACGCGATAGTTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCATTGGTATTCCATTGGGCATGTCTGTTTGAGCGTCATTACAACCCTCGGTCACCACCGGTTTTGAGCGAGCAGGGTCTTCGGATCCAGCTGGCTTTAAAGTTGTAAGCTCTGCTGGCTGCTCGGCCCAACCAGAACATAGTAAAATCATGCTTGTTCAAGGTTCGCGGTCGAAGCGGTACGGCCTGAACAATACCTACCACCTCTTAGG".
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 93 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Summing counts per taxon (@test--calculations.R#103) 
  2. Failure: Summing counts per taxon (@test--calculations.R#126) 
  3. Failure: Parsing the UNITE general release fasta (@test--parsers_and_writers.R#119) 
  
  Error: testthat unit tests failed
  Execution halted
calc_z_var: no visible binding for global variable ‘median’
diffScore: no visible global function definition for ‘new’
diffScore: no visible global function definition for ‘model.matrix’
logNORMcdf: no visible global function definition for ‘pnorm’
mGSZ.adj.mean.std: no visible binding for global variable ‘sd’
pick.data.cols: no visible binding for global variable ‘var’
plotProfile: no visible binding for global variable ‘quantile’
plotProfile: no visible global function definition for ‘plot’
plotProfile: no visible global function definition for ‘lines’
plotProfile: no visible global function definition for ‘legend’
Undefined global functions or variables:
  legend lines median model.matrix new plot pnorm quantile sd var
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("methods", "new")
  importFrom("stats", "median", "model.matrix", "pnorm", "quantile",
             "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
BCI: no visible global function definition for ‘quantile’
Metro_Hastings: no visible global function definition for ‘optim’
Metro_Hastings: no visible global function definition for ‘runif’
Metro_Hastings: no visible global function definition for ‘var’
plotMH: no visible global function definition for ‘hist’
plotMH: no visible global function definition for ‘plot’
plotMH: no visible global function definition for ‘frame’
plotMH: no visible global function definition for ‘text’
Undefined global functions or variables:
  frame hist optim plot quantile runif text var
Consider adding
  importFrom("graphics", "frame", "hist", "plot", "text")
  importFrom("stats", "optim", "quantile", "runif", "var")
to your NAMESPACE file.
migration.cv.in : <anonymous>: no visible global function definition
  for ‘sd’
migration.cv.out : <anonymous>: no visible global function definition
  for ‘sd’
migration.field.diagram: no visible global function definition for
  ‘plot’
migration.field.diagram: no visible global function definition for
  ‘lines’
migration.field.diagram: no visible global function definition for
  ‘text’
migration.field.diagram: no visible global function definition for
  ‘polygon’
migration.field.diagram: no visible global function definition for ‘lm’
migration.field.diagram: no visible global function definition for
  ‘predict’
migration.field.diagram: no visible global function definition for
  ‘points’
migration.field.diagram: no visible global function definition for
  ‘resid’
migration.field.diagram: no visible global function definition for
  ‘coef’
migration.field.diagram: no visible global function definition for
  ‘mtext’
migration.field.diagram: no visible global function definition for
  ‘density’
migration.field.diagram: no visible global function definition for
  ‘rug’
migration.gini.col : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.in : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.out : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.row : <anonymous>: no visible global function definition
  for ‘dist’
migration.gini.total: no visible global function definition for ‘dist’
Undefined global functions or variables:
  coef density dist lines lm mtext plot points polygon predict resid
  rug sd text
Consider adding
  importFrom("graphics", "lines", "mtext", "plot", "points", "polygon",
             "rug", "text")
  importFrom("stats", "coef", "density", "dist", "lm", "predict",
             "resid", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘milr-intro.Rmd’ using rmarkdown
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.8390.
trying URL ‘http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz’
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
The penalty term is selected automatically with 100 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 3.2909.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Killed
Running examples in ‘MIMSunit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: import_mhealth_csv
> ### Title: Import raw multi-channel accelerometer data stored in mHealth
> ###   Specification
> ### Aliases: import_mhealth_csv
> 
> ### ** Examples
> 
>   default_ops = options()
>   options(digits.secs=3)
>   # Use the sample mhealth csv file provided by the package
>   filepath = system.file('extdata', 'mhealth.csv', package='MIMSunit')
>   filepath
[1] "/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/MIMSunit/extdata/mhealth.csv"
> 
>   # Load the file
>   df = import_mhealth_csv(filepath)
Error: Assigned data `as.character(df[, factor_cols])` must be compatible with existing data.
✖ Existing data has 5000 rows.
✖ Assigned data has 0 rows.
ℹ Only vectors of size 1 are recycled.
Backtrace:
    █
 1. └─MIMSunit::import_mhealth_csv(filepath)
 2.   ├─base::`[<-`(`*tmp*`, , factor_cols, value = character(0))
 3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, , factor_cols, value = character(0))
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::vectbl_recycle_rhs(...)
 6.         └─base::tryCatch(...)
 7.           └─base:::tryCatchList(expr, classes, parentenv, handlers)
 8.             └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 9.               └─value[[3L]](cond)
Execution halted
miney : plot.initial.matrix: no visible global function definition for
  ‘plot’
miney : plot.initial.matrix: no visible global function definition for
  ‘rect’
miney : plot.known.matrix: no visible global function definition for
  ‘plot’
miney : plot.known.matrix: no visible global function definition for
  ‘rect’
miney : plot.known.matrix: no visible global function definition for
  ‘text’
miney: no visible global function definition for ‘locator’
miney: no visible global function definition for ‘rect’
miney: no visible global function definition for ‘title’
Undefined global functions or variables:
  locator plot rect text title
Consider adding
  importFrom("graphics", "locator", "plot", "rect", "text", "title")
to your NAMESPACE file.
.FCLoess: no visible global function definition for ‘loess’
.FCLoessM: no visible global function definition for ‘loess’
.FCLoessM: no visible global function definition for ‘median’
.Import.Luminex: no visible global function definition for ‘read.csv’
.Intra.Me: no visible global function definition for ‘sd’
.Intra.Me: no visible global function definition for ‘quantile’
.Intra.Me: no visible global function definition for ‘qchisq’
.Intra.Median: no visible global function definition for ‘median’
.boxplot.rtprofile: no visible global function definition for ‘boxplot’
.denplot: no visible global function definition for ‘plot’
.denplot: no visible global function definition for ‘density’
.denplot: no visible global function definition for ‘abline’
.normalize.Luminex: no visible global function definition for ‘sd’
.normalize.qrtpcr: no visible global function definition for ‘density’
.validate.default: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  abline boxplot density loess median plot qchisq quantile read.csv sd
  t.test
Consider adding
  importFrom("graphics", "abline", "boxplot", "plot")
  importFrom("stats", "density", "loess", "median", "qchisq", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
confusionBarplot: no visible global function definition for ‘par’
confusionBarplot: no visible global function definition for ‘barplot’
confusionBarplot: no visible global function definition for ‘lines’
confusionBarplot: no visible global function definition for ‘text’
confusionBarplot: no visible global function definition for ‘legend’
confusionBarplot: no visible global function definition for ‘axis’
confusionDendrogram: no visible global function definition for ‘plot’
confusionImage: no visible global function definition for ‘par’
confusionImage: no visible global function definition for ‘image’
confusionImage: no visible global function definition for ‘text’
confusionImage: no visible global function definition for ‘abline’
confusionImage: no visible global function definition for ‘axis’
confusionImage: no visible global function definition for ‘plot’
confusionImage: no visible global function definition for ‘mtext’
confusionStars: no visible global function definition for ‘par’
confusionStars: no visible global function definition for ‘stars’
confusionStars: no visible global function definition for ‘rect’
plot.mlearning: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline axis barplot image legend lines mtext par plot rect stars text
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
             "lines", "mtext", "par", "plot", "rect", "stars", "text")
to your NAMESPACE file.
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(modelbased)
  > 
  > test_check("modelbased")
  ── 1. Error: estimate_slopes (@test-estimate_slopes.R#3)  ──────────────────────
  there is no package called 'rstanarm'
  Backtrace:
   1. base::library(rstanarm)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 32 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Error: estimate_slopes (@test-estimate_slopes.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("MonoPhy")
  Loading required package: MonoPhy
  Loading required package: ape
  Loading required package: phytools
  Loading required package: maps
  Loading required package: phangorn
  Loading required package: RColorBrewer
  Loading required package: taxize
  ── 1. Error: Multifurcating solution1 is accurate (@test_solutions.R#38)  ──────
  there is no package called 'spacodiR'
  Backtrace:
   1. base::library(spacodiR)
  
  ── 2. Error: Multifurcating solution2 is accurate (@test_solutions.R#75)  ──────
  there is no package called 'spacodiR'
  Backtrace:
   1. base::library(spacodiR)
  
  ── 3. Error: Multifurcating solution3 is accurate (@test_solutions.R#112)  ─────
  there is no package called 'spacodiR'
  Backtrace:
   1. base::library(spacodiR)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 24 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: Multifurcating solution1 is accurate (@test_solutions.R#38) 
  2. Error: Multifurcating solution2 is accurate (@test_solutions.R#75) 
  3. Error: Multifurcating solution3 is accurate (@test_solutions.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Mort1Dsmooth: no visible global function definition for ‘time’
Mort1Dsmooth: no visible global function definition for ‘glm’
Mort1Dsmooth: no visible binding for global variable ‘poisson’
Mort1Dsmooth_optimize: no visible global function definition for
  ‘median’
Mort2Dsmooth: no visible global function definition for ‘glm’
Mort2Dsmooth: no visible binding for global variable ‘poisson’
Mort2Dsmooth: no visible global function definition for ‘median’
Mort2Dsmooth_optimize: no visible global function definition for
  ‘median’
plot.HMDdata: no visible global function definition for ‘plot’
plot.Mort1Dsmooth: no visible global function definition for ‘matplot’
plot.Mort2Dsmooth: no visible global function definition for ‘quantile’
predict.Mort1Dsmooth: no visible global function definition for ‘glm’
predict.Mort1Dsmooth: no visible binding for global variable ‘poisson’
predict.Mort2Dsmooth: no visible global function definition for ‘glm’
predict.Mort2Dsmooth: no visible binding for global variable ‘poisson’
print.summary.Mort1Dsmooth: no visible global function definition for
  ‘quantile’
print.summary.Mort2Dsmooth: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  glm matplot median plot poisson quantile time
Consider adding
  importFrom("graphics", "matplot", "plot")
  importFrom("stats", "glm", "median", "poisson", "quantile", "time")
to your NAMESPACE file.
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'.

diagram.mpa: no visible global function definition for ‘plot’
diagram.mpa: no visible global function definition for ‘abline’
diagram.mpa: no visible global function definition for ‘text’
plotmpa: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline plot text
Consider adding
  importFrom("graphics", "abline", "plot", "text")
to your NAMESPACE file.
mpcv: no visible binding for global variable ‘median’
mpcv: no visible global function definition for ‘cov’
mpcv: no visible global function definition for ‘dist’
plot.mpcv: no visible binding for global variable ‘median’
plot.mpcv: no visible global function definition for ‘par’
plot.mpcv: no visible global function definition for ‘plot’
plot.mpcv: no visible global function definition for ‘rect’
plot.mpcv: no visible global function definition for ‘lines’
plot.mpcv: no visible global function definition for ‘points’
plot.mpcv: no visible global function definition for ‘legend’
Undefined global functions or variables:
  cov dist legend lines median par plot points rect
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "rect")
  importFrom("stats", "cov", "dist", "median")
to your NAMESPACE file.
MRwarp: no visible global function definition for ‘dev.new’
MRwarp: no visible global function definition for ‘plot’
MRwarp: no visible global function definition for ‘lines’
MRwarp: no visible global function definition for ‘points’
MRwarp: no visible global function definition for ‘hist’
Undefined global functions or variables:
  dev.new hist lines plot points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "lines", "plot", "points")
to your NAMESPACE file.
msap: no visible global function definition for ‘packageVersion’
msap: no visible global function definition for ‘read.csv’
msap: no visible global function definition for ‘write.csv’
msap: no visible global function definition for ‘sd’
msap: no visible global function definition for ‘wilcox.test’
msap: no visible global function definition for ‘dist’
msap: no visible global function definition for ‘rainbow’
msap: no visible global function definition for ‘png’
msap: no visible global function definition for ‘legend’
msap: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘cmdscale’
pcoa: no visible global function definition for ‘png’
pcoa: no visible global function definition for ‘par’
pcoa: no visible global function definition for ‘plot’
pcoa: no visible global function definition for ‘rainbow’
pcoa: no visible global function definition for ‘points’
pcoa: no visible global function definition for ‘dev.off’
pcoa: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  cmdscale dev.off dist legend packageVersion par plot png points
  rainbow read.csv sd wilcox.test write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "cmdscale", "dist", "sd", "wilcox.test")
  importFrom("utils", "packageVersion", "read.csv", "write.csv")
to your NAMESPACE file.
CrossValidationMuFicokm: no visible global function definition for
  ‘covMatrix’
CrossValidationMuFicokmAll: no visible global function definition for
  ‘covMatrix’
MuFicokm: no visible global function definition for ‘km’
compute.beta.hat: no visible global function definition for ‘lm’
computeAuxVariables: no visible global function definition for
  ‘covMatrix’
kmCok: no visible global function definition for ‘new’
kmCok: no visible global function definition for ‘drop.response’
kmCok: no visible global function definition for ‘model.matrix’
kmCok: no visible global function definition for ‘covStruct.create’
kmCok: no visible global function definition for ‘validObject’
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’
kmCok: no visible global function definition for ‘plot’
predict.kmCok: no visible global function definition for ‘model.matrix’
predict.kmCok: no visible global function definition for ‘covMat1Mat2’
predict.kmCok: no visible global function definition for ‘qnorm’
predict.kmCok: no visible global function definition for ‘qt’
predict.kmCok: no visible global function definition for ‘covMatrix’
summary.MuFicokm: no visible global function definition for
  ‘covparam2vect’
Undefined global functions or variables:
  covMat1Mat2 covMatrix covParametersBounds covStruct.create
  covparam2vect drop.response km kmEstimate leaveOneOut.km lm
  model.matrix new plot qnorm qt validObject
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "new", "validObject")
  importFrom("stats", "lm", "model.matrix", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plotOptionValues: no visible global function definition for ‘plot’
plotOptionValues: no visible global function definition for ‘persp’
Undefined global functions or variables:
  persp plot
Consider adding
  importFrom("graphics", "persp", "plot")
to your NAMESPACE file.
betas_plot: no visible global function definition for ‘cov2cor’
betas_plot: no visible global function definition for
  ‘colorRampPalette’
betas_plot: no visible global function definition for ‘pdf’
betas_plot: no visible global function definition for ‘dev.off’
mhplot: no visible global function definition for ‘read.table’
mhplot: no visible global function definition for ‘pdf’
mhplot: no visible global function definition for ‘plot’
mhplot: no visible global function definition for ‘points’
mhplot: no visible global function definition for ‘abline’
mhplot: no visible global function definition for ‘axis’
mhplot: no visible global function definition for ‘dev.off’
multi_meta: no visible global function definition for ‘write.table’
multi_meta: no visible global function definition for ‘read.table’
multi_meta: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘read.table’
qqplotter: no visible global function definition for ‘qchisq’
qqplotter: no visible global function definition for ‘ppoints’
qqplotter: no visible global function definition for ‘median’
qqplotter: no visible global function definition for ‘pchisq’
qqplotter: no visible global function definition for ‘pdf’
qqplotter: no visible global function definition for ‘plot’
qqplotter: no visible global function definition for ‘abline’
qqplotter: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline axis colorRampPalette cov2cor dev.off median pchisq pdf plot
  points ppoints qchisq read.table write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "cov2cor", "median", "pchisq", "ppoints", "qchisq")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
.onAttach: no visible global function definition for
  ‘packageDescription’
genoudRob: no visible global function definition for ‘genoud’
get.XYdata: no visible global function definition for ‘terms’
get.xdata: no visible global function definition for ‘terms’
get.xdata: no visible global function definition for ‘model.matrix’
get.xy: no visible global function definition for ‘terms’
get.xynames: no visible global function definition for ‘terms’
get.ydata: no visible global function definition for ‘terms’
get.ydata: no visible global function definition for ‘model.response’
get.ydata: no visible global function definition for ‘model.frame’
mt.dev: no visible global function definition for ‘pt’
mt.dev.grad: no visible global function definition for ‘pt’
mt.dev.grad: no visible global function definition for ‘dt’
mt.mle: no visible global function definition for ‘optim’
multinomRob: no visible global function definition for ‘var’
plot.multinomRob: no visible global function definition for ‘par’
plot.multinomRob: no visible global function definition for ‘plot’
plot.multinomRob: no visible global function definition for ‘title’
rdirich: no visible global function definition for ‘rgamma’
residual.generator: no visible global function definition for ‘median’
rmultinomial: no visible global function definition for ‘runif’
rmultinomial: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  dt genoud median model.frame model.matrix model.response optim
  packageDescription par plot pt rbinom rgamma runif terms title var
Consider adding
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "dt", "median", "model.frame", "model.matrix",
             "model.response", "optim", "pt", "rbinom", "rgamma",
             "runif", "terms", "var")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
plotFID: no visible global function definition for ‘plot’
plotFID: no visible global function definition for ‘points’
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
plot.matchedwake: no visible global function definition for
  ‘filled.contour’
plot.matchedwake: no visible binding for global variable ‘gray.colors’
plot.matchedwake: no visible global function definition for ‘axis’
plot.matchedwake: no visible global function definition for ‘rect’
slideWakeMatch: no visible binding for global variable ‘lm’
slideWakeMatch: no visible global function definition for ‘as.formula’
slideWakeMatch: no visible global function definition for ‘summary.glm’
Undefined global functions or variables:
  as.formula axis filled.contour gray.colors lm rect summary.glm
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "axis", "filled.contour", "rect")
  importFrom("stats", "as.formula", "lm", "summary.glm")
to your NAMESPACE file.
NAPPA: no visible binding for global variable ‘sd’
NAPPA: no visible global function definition for ‘sd’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘coef’
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for ‘lm’
calibrate.sigmoid.curve: no visible global function definition for
  ‘nls’
calibrate.sigmoid.curve: no visible binding for global variable
  ‘weights’
calibrate.sigmoid.curve: no visible global function definition for
  ‘coef’
calibrate.sigmoid.curve: no visible global function definition for
  ‘plot’
calibrate.sigmoid.curve: no visible global function definition for
  ‘rgb’
calibrate.sigmoid.curve: no visible global function definition for
  ‘box’
calibrate.sigmoid.curve: no visible global function definition for
  ‘axis’
calibrate.sigmoid.curve: no visible global function definition for
  ‘abline’
calibrate.sigmoid.curve: no visible global function definition for
  ‘lines’
calibrate.sigmoid.curve: no visible global function definition for
  ‘predict’
calibrate.sigmoid.curve: no visible global function definition for
  ‘smooth.spline’
calibrate.sigmoid.curve : <anonymous>: no visible global function
  definition for ‘nls’
calibrate.sigmoid.curve : <anonymous>: no visible binding for global
  variable ‘weights’
calibrate.sigmoid.curve: no visible binding for global variable ‘coef’
calibrate.sigmoid.curve: no visible global function definition for ‘pf’
calibrate.sigmoid.curve: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  abline axis box coef legend lines lm nls pf plot predict rgb sd
  smooth.spline weights
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "plot")
  importFrom("stats", "coef", "lm", "nls", "pf", "predict", "sd",
             "smooth.spline", "weights")
to your NAMESPACE file.
NB.estimator: no visible global function definition for ‘optimize’
NB.estimator: no visible global function definition for ‘uniroot’
NB.example.dataset: no visible global function definition for
  ‘write.table’
NB.plot.likelihood: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optimize plot uniroot write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
population: no visible global function definition for ‘weighted.mean’
population: no visible global function definition for ‘rpois’
population: no visible global function definition for ‘lm’
population: no visible global function definition for ‘coefficients’
population: no visible global function definition for ‘sd’
population: no visible global function definition for ‘par’
population: no visible global function definition for ‘plot’
population: no visible global function definition for ‘lines’
Undefined global functions or variables:
  coefficients lines lm par plot rpois sd weighted.mean
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "coefficients", "lm", "rpois", "sd",
             "weighted.mean")
to your NAMESPACE file.
clustConfigurations: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
NPHMC: no visible global function definition for ‘integrate’
NPHMC: no visible global function definition for ‘qnorm’
NPHMC: no visible global function definition for ‘pnorm’
NPHMC: no visible global function definition for ‘plot’
NPHMC: no visible global function definition for ‘lines’
NPHMC: no visible global function definition for ‘smcure’
NPHMC: no visible global function definition for ‘coxph’
Undefined global functions or variables:
  coxph integrate lines plot pnorm qnorm smcure
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "integrate", "pnorm", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import ‘sf::st_make_valid’ by ‘lwgeom::st_make_valid’ when loading ‘oceanis’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/oceanis.Rcheck/00install.out’ for details.
Running examples in ‘oceanis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coordonnees_etiquettes
> ### Title: Data table of labels
> ### Aliases: coordonnees_etiquettes
> ### Keywords: documentation
> 
> ### ** Examples
> 
> data("donnees_monoloc")
> data("depm")
> 
> etiquettes <- coordonnees_etiquettes(fondMaille = depm,
+ listeCode = c("06","13","31","33","44","67","69","59","75"))
> etiquettes$LIBELLE <- c("Nice","Marseille","Toulouse","Bordeaux","Nantes",
+ "Lille","Strasbourg","Lyon","Paris")
> etiquettes[etiquettes$CODE=="75","TAILLE"] <- 1.3
> 
> # Ronds proportionnels sur une analyse en classes
> fond_ronds <- plot_classes_ronds(data = donnees_monoloc, fondMaille = depm,
+ idData = "COD_DEP", varVolume = "POP_2015", varRatio = "VAR_AN_MOY", nbClasses = 4,
+ titreLegRonds = "POP_2015", titreLegClasses = "VAR_AN_MOY",
+ xLegClasses = 1150000, yLegClasses = 6600000, etiquettes = etiquettes)
Warning in CPL_crs_from_input(x) :
  GDAL Error 1: PROJ: proj_create: crs not found
Error in CPL_transform(x, crs, aoi, pipeline, reverse) : 
  crs not found: is it missing?
Calls: plot_classes_ronds ... st_transform -> st_transform.sfc -> structure -> CPL_transform
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘integration_shiny.Rmd’ using rmarkdown
--- finished re-building ‘integration_shiny.Rmd’

--- re-building ‘oceanis.Rmd’ using rmarkdown
Quitting from lines 384-506 (oceanis.Rmd) 
Error: processing vignette 'oceanis.Rmd' failed with diagnostics:
crs not found: is it missing?
--- failed re-building ‘oceanis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found an obsolete/platform-specific call in the following function:
  ‘comp.freq’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
comp.freq: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Running examples in ‘openair-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: percentileRose
> ### Title: Function to plot percentiles by wind direction
> ### Aliases: percentileRose
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> # basic percentile plot
> percentileRose(mydata, pollutant = "o3")
Error: Can't use NA as row index in a tibble for assignment.
Backtrace:
    █
 1. └─openair::percentileRose(mydata, pollutant = "o3")
 2.   ├─base::`[<-`(`*tmp*`, pollutant, , value = NA)
 3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, pollutant, , value = NA)
 4.     └─tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
 5.       └─tibble:::tbl_expand_to_nrow(x, i)
Execution halted
Running ‘testthat.R’ [34s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(OpenLand)
  > 
  > test_check("OpenLand")
  ── 1. Error: Behavior of summary_map (@test_generalfunctions.R#53)  ────────────
  Assigned data `c(as.numeric(names(value_map)[i]), value_map[[i]])` must be compatible with row subscript `i`.
  ✖ 1 row must be assigned.
  ✖ Assigned data has 2 rows.
  ℹ Only vectors of size 1 are recycled.
  Backtrace:
    1. testthat::expect_silent(...)
    9. OpenLand::summary_map(...)
   11. tibble:::`[<-.tbl_df`(`*tmp*`, i, c(1:2), value = c(1, 1983))
   12. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   13. tibble:::vectbl_recycle_rhs(...)
   14. base::tryCatch(...)
   15. base:::tryCatchList(expr, classes, parentenv, handlers)
   16. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   17. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 112 | SKIPPED: 0 | WARNINGS: 24 | FAILED: 1 ]
  1. Error: Behavior of summary_map (@test_generalfunctions.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
Rd file 'dmes.Rd':
  \examples lines wider than 100 characters:
     > #cf. Efron, B. & Tibshirani (1993). An Introduction to the Bootstrap. New York/London: Chapman&Hall.
     > #Ruscio, J. & Mullen, T. (2012). Confidence Intervals for the Probability of Superiority Effect Size Measure and the Area Under a Rec ... [TRUNCATED]

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

These lines will be truncated in the PDF manual.
genRidge: no visible global function definition for ‘plogis’
ordGene: no visible global function definition for ‘anova’
ordGene: no visible global function definition for ‘lm’
ordSelect: no visible binding for global variable ‘sd’
ordSmooth: no visible binding for global variable ‘sd’
plot.ordPen: no visible global function definition for ‘grey’
plot.ordPen: no visible global function definition for ‘devAskNewPage’
plot.ordPen: no visible global function definition for ‘plot’
plot.ordPen: no visible global function definition for ‘lines’
predict.ordPen: no visible global function definition for ‘plogis’
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
ORICC1: no visible binding for global variable ‘sd’
ORICC1: no visible global function definition for ‘write.table’
ORICC1: no visible global function definition for ‘postscript’
ORICC1: no visible global function definition for ‘jpeg’
ORICC1: no visible global function definition for ‘plot’
ORICC1: no visible global function definition for ‘points’
ORICC1: no visible global function definition for ‘dev.off’
ORICC1: no visible global function definition for ‘par’
ORICC2: no visible binding for global variable ‘sd’
ORICC2: no visible global function definition for ‘write.table’
ORICC2: no visible global function definition for ‘postscript’
ORICC2: no visible global function definition for ‘jpeg’
ORICC2: no visible global function definition for ‘plot’
ORICC2: no visible global function definition for ‘points’
ORICC2: no visible global function definition for ‘dev.off’
ORICC2: no visible global function definition for ‘par’
Undefined global functions or variables:
  dev.off jpeg par plot points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
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’
plot.osmar: no visible global function definition for ‘gray’
plot_nodes: no visible global function definition for ‘points’
plot_nodes: no visible global function definition for ‘plot’
plot_ways: no visible global function definition for ‘plot’
plot_ways: no visible global function definition for ‘lines’
ways_nodes2Line: no visible global function definition for ‘Line’
ways_nodes2Polygon: no visible global function definition for ‘Polygon’
Undefined global functions or variables:
  CRS E E<- Line Lines Polygon Polygons SpatialLines
  SpatialLinesDataFrame SpatialPointsDataFrame SpatialPolygons
  SpatialPolygonsDataFrame distHaversine graph.edgelist gray lines plot
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
Electre3_AlphaBetaThresholds: no visible global function definition for
  ‘plot’
Electre3_SimpleThresholds: no visible global function definition for
  ‘plot’
Electre_1: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ozmaps.Rmd’ using rmarkdown
Quitting from lines 52-55 (ozmaps.Rmd) 
Error: processing vignette 'ozmaps.Rmd' failed with diagnostics:
All columns in a tibble must be vectors.
✖ Column `geometry` is a `sfc_MULTIPOLYGON/sfc` object.
--- failed re-building ‘ozmaps.Rmd’

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

Error: Vignette re-building failed.
Execution halted
paf: no visible global function definition for ‘as.formula’
paf: no visible global function definition for ‘model.response’
paf: no visible global function definition for ‘model.frame’
paf: no visible global function definition for ‘model.matrix’
plot.paf: no visible global function definition for ‘plot’
plot.paf: no visible global function definition for ‘lines’
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response plot
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
Rd file 'CalGIF.Rd':
  \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 

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

These lines will be truncated in the PDF manual.
GOpredict: no visible global function definition for ‘fisher.test’
KEGGpredict: no visible global function definition for ‘fisher.test’
ProteinCluster: no visible global function definition for ‘ecdf’
ProteinCluster: no visible global function definition for ‘as.hclust’
ProteinCluster: no visible global function definition for
  ‘as.dendrogram’
ProteinCluster : addE: no visible global function definition for
  ‘is.leaf’
ProteinCluster: no visible global function definition for ‘plot’
SignificantSubcluster: no visible global function definition for
  ‘order.dendrogram’
SignificantSubcluster: no visible global function definition for
  ‘fisher.test’
SignificantSubcluster: no visible global function definition for ‘plot’
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
  plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
adalasso: no visible global function definition for ‘predict’
lm.ridge.univariate: no visible global function definition for ‘sd’
mylars: no visible global function definition for ‘predict’
mylars: no visible binding for global variable ‘var’
performance.pcor: no visible global function definition for
  ‘ggm.test.edges’
performance.pcor: no visible global function definition for ‘var’
ridge.cv: no visible global function definition for ‘coef’
ridge.cv: no visible global function definition for ‘plot’
Undefined global functions or variables:
  coef ggm.test.edges plot predict sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "predict", "sd", "var")
to your NAMESPACE file.
draw.pcaBootPlot: no visible global function definition for ‘plot’
draw.pcaBootPlot: no visible global function definition for ‘grid’
draw.pcaBootPlot: no visible global function definition for ‘points’
draw.pcaBootPlot: no visible global function definition for ‘symbols’
draw.pcaBootPlot: no visible global function definition for ‘legend’
pcaBootPlot: no visible global function definition for ‘prcomp’
pcaBootPlot: no visible global function definition for ‘cor’
pcaBootPlot: no visible global function definition for ‘quantile’
pcaBootPlot: no visible global function definition for ‘pdf’
pcaBootPlot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  cor dev.off grid legend pdf plot points prcomp quantile symbols
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "grid", "legend", "plot", "points", "symbols")
  importFrom("stats", "cor", "prcomp", "quantile")
to your NAMESPACE file.
peacf: no visible global function definition for ‘is.ts’
peacf: no visible global function definition for ‘cycle’
peacf: no visible global function definition for ‘ts.intersect’
peacf: no visible global function definition for ‘lag’
peacf: no visible global function definition for ‘ts’
peacf: no visible global function definition for ‘pchisq’
peacf.plot: no visible global function definition for ‘plot’
peacf.plot: no visible global function definition for ‘segments’
peacf.plot: no visible global function definition for ‘title’
pear: no visible global function definition for ‘cycle’
pear: no visible global function definition for ‘pchisq’
peboxplot: no visible global function definition for ‘cycle’
peboxplot: no visible global function definition for ‘boxplot’
peboxplot: no visible global function definition for ‘title’
peplot: no visible global function definition for ‘par’
peplot: no visible global function definition for ‘cycle’
peplot: no visible global function definition for ‘plot’
peplot: no visible global function definition for ‘identify’
peplot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  boxplot cycle identify is.ts lag mtext par pchisq plot segments title
  ts ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par", "plot",
             "segments", "title")
  importFrom("stats", "cycle", "is.ts", "lag", "pchisq", "ts",
             "ts.intersect")
to your NAMESPACE file.
PearsonICA: no visible global function definition for ‘rnorm’
PearsonICAdemo: no visible global function definition for ‘rnorm’
PearsonICAdemo: no visible global function definition for ‘dev.new’
PearsonICAdemo: no visible global function definition for ‘par’
PearsonICAdemo: no visible global function definition for ‘plot’
PearsonICAdemo: no visible global function definition for ‘axis’
PearsonICAdemo: no visible global function definition for ‘title’
PearsonICAdemo: no visible global function definition for ‘lines’
Undefined global functions or variables:
  axis dev.new lines par plot rnorm title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "lines", "par", "plot", "title")
  importFrom("stats", "rnorm")
to your NAMESPACE file.
fox: no visible binding for global variable ‘sd’
fox: no visible global function definition for ‘cor’
fox: no visible global function definition for ‘interaction.plot’
fox: no visible global function definition for ‘reorder’
fox: no visible global function definition for ‘plot’
kang: no visible global function definition for ‘var’
kang: no visible binding for global variable ‘sd’
kang: no visible global function definition for ‘cor’
kang: no visible global function definition for ‘interaction.plot’
kang: no visible global function definition for ‘reorder’
kang: no visible global function definition for ‘plot’
nahu: no visible global function definition for ‘interaction.plot’
nahu: no visible global function definition for ‘reorder’
nahu: no visible global function definition for ‘plot’
thsu: no visible global function definition for ‘median’
thsu: no visible binding for global variable ‘sd’
thsu: no visible global function definition for ‘cor’
thsu: no visible global function definition for ‘interaction.plot’
thsu: no visible global function definition for ‘reorder’
thsu: no visible global function definition for ‘plot’
Undefined global functions or variables:
  cor interaction.plot median plot reorder sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
plotAuto: no visible global function definition for ‘window’
plotAuto: no visible global function definition for ‘title’
plotAuto: no visible global function definition for ‘axis’
plotAuto: no visible global function definition for ‘box’
plotCumu: no visible global function definition for ‘title’
plotCumu: no visible global function definition for ‘axis’
plotCumu: no visible global function definition for ‘box’
plotDens : panel.dens: no visible global function definition for ‘var’
plotDens : panel.dens: no visible global function definition for
  ‘quantile’
plotDens : panel.dens: no visible global function definition for
  ‘median’
plotDens: no visible global function definition for ‘tail’
plotQuant: no visible global function definition for ‘par’
plotQuant: no visible binding for global variable ‘quantile’
plotQuant: no visible global function definition for ‘plot’
plotQuant: no visible global function definition for ‘lines’
plotQuant: no visible global function definition for ‘bxp’
plotQuant: no visible global function definition for ‘matplot’
plotQuant: no visible global function definition for ‘axis’
plotQuant: no visible global function definition for ‘box’
plotQuant: no visible global function definition for ‘title’
plotSplom: no visible global function definition for ‘pairs’
plotTrace : panel.trace: no visible global function definition for
  ‘var’
plotTrace : panel.trace: no visible global function definition for
  ‘median’
plotTrace: no visible global function definition for ‘tail’
Undefined global functions or variables:
  axis box bxp lines matplot median pairs par plot quantile tail title
  var window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "plot", "title")
  importFrom("stats", "median", "quantile", "var", "window")
  importFrom("utils", "tail")
to your NAMESPACE file.
Rd file 'envelopeArea_and_Perimeter.Rd':
  \examples lines wider than 100 characters:
     cat("envelope area = ", envelopeStats["area"], " perimeter = ", envelopeStats["perimeter"],"\n")        
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")

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

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

These lines will be truncated in the PDF manual.
.MCM: no visible global function definition for ‘runif’
.MCM: no visible global function definition for ‘rmultinom’
.MCM: no visible global function definition for ‘mahalanobis’
.MCM: no visible global function definition for ‘optimize’
.MCM : f: no visible global function definition for ‘mahalanobis’
.MCM: no visible global function definition for ‘alarm’
.igpark: no visible global function definition for ‘kmeans’
.loglik: no visible global function definition for ‘mahalanobis’
.plot.gpcm: no visible global function definition for ‘plot’
.plot.gpcm: no visible global function definition for ‘lines’
.plot.gpcm: no visible global function definition for ‘legend’
.rwgpar: no visible global function definition for ‘rexp’
.weights: no visible global function definition for ‘mahalanobis’
Undefined global functions or variables:
  alarm kmeans legend lines mahalanobis optimize plot rexp rmultinom
  runif
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
plot.sigma: no visible global function definition for ‘plot’
smooth: no visible global function definition for ‘genoud’
Undefined global functions or variables:
  genoud plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Running examples in ‘pointblank-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: col_vals_between
> ### Title: Are numerical column data between two specified values?
> ### Aliases: col_vals_between
> 
> ### ** Examples
> 
> library(dplyr)

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> # Create a simple table with
> # a column of numerical values
> tbl <- tibble(a = c(5.6, 8.2, 7.8))
> 
> # Validate that values in
> # column `a` are all between
> # 1 and 9
> agent <-
+   create_agent(tbl = tbl) %>%
+   col_vals_between(vars(a), 1, 9) %>%
+   interrogate()
Error in UseMethod("summarise_") : 
  no applicable method for 'summarise_' applied to an object of class "NULL"
Calls: %>% ... <Anonymous> -> <Anonymous> -> summarise.default -> summarise_
Execution halted
Found the following significant warnings:
  Warning: `data_frame()` is deprecated as of tibble 1.1.0.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/poio.Rcheck/00install.out’ for details.
Rd file 'ppoistweedie.Rd':
  \examples lines wider than 100 characters:
     layout.show(1)                                                                                                                          ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [201s/242s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(portalr)
  > 
  > test_check("portalr")
  ── 1. Failure: data generated by default setting is same (shrub_cover) (@test-99
  Value hashes to 273b981913, not 9e5849fa79
  
  ── 2. Failure: data generated by default setting is same (ant colony_presence_ab
  Value hashes to b16d3f1a01, not 8ce773ce81
  
  ── 3. Failure: data generated by level = 'stake' is same (ant colony_presence_ab
  Value hashes to 2194929e3e, not 4639dbfbf3
  
  ── 4. Failure: data generated by level = 'plot' is same (ant colony_presence_abs
  Value hashes to 255aef31fb, not 60e9306bfc
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 193 | SKIPPED: 10 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: data generated by default setting is same (shrub_cover) (@test-99-regression.R#166) 
  2. Failure: data generated by default setting is same (ant colony_presence_absence) (@test-99-regression.R#177) 
  3. Failure: data generated by level = 'stake' is same (ant colony_presence_absence) (@test-99-regression.R#195) 
  4. Failure: data generated by level = 'plot' is same (ant colony_presence_absence) (@test-99-regression.R#213) 
  
  Error: testthat unit tests failed
  Execution halted
fnfam: no visible global function definition for ‘qnorm’
fx: no visible global function definition for ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘pnorm’
normplot : <local> : replot: no visible global function definition for
  ‘plot’
normplot : <local> : replot: no visible global function definition for
  ‘dnorm’
normplot : <local> : replot: no visible global function definition for
  ‘points’
normplot : <local> : replot: no visible global function definition for
  ‘lines’
normplot : <local> : regen: no visible global function definition for
  ‘rnorm’
normplot : <local> : regen: no visible global function definition for
  ‘rexp’
nsibs: no visible global function definition for ‘qnorm’
ntdt: no visible global function definition for ‘uniroot’
plotDom: no visible global function definition for ‘plot’
plotNsibs: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘lines’
plotNtdt: no visible global function definition for ‘legend’
ptdt: no visible global function definition for ‘optimize’
ptdt: no visible global function definition for ‘uniroot’
ptdt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm legend lines optimize plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
LDA.Tree : Find.proj: no visible binding for global variable ‘var’
LDA.Tree : Find.proj: no visible binding for global variable ‘IQR’
LDA.Tree : Find.proj: no visible binding for global variable ‘median’
PDA.Tree : Find.proj: no visible binding for global variable ‘var’
PDA.Tree : Find.proj: no visible binding for global variable ‘median’
PDA.Tree : Find.proj: no visible binding for global variable ‘IQR’
PP.Tree : Find.proj: no visible binding for global variable ‘var’
PP.Tree : Find.proj: no visible binding for global variable ‘median’
PP.Tree : Find.proj: no visible binding for global variable ‘IQR’
PP.optimize.Huber: no visible binding for global variable ‘sd’
PP.optimize.anneal: no visible binding for global variable ‘sd’
PP.optimize.plot: no visible binding for global variable ‘sd’
PP.optimize.plot: no visible global function definition for ‘hist’
PP.optimize.plot: no visible global function definition for ‘text’
PP.optimize.plot: no visible global function definition for ‘par’
PP.optimize.plot: no visible global function definition for ‘plot’
PP.optimize.plot: no visible global function definition for ‘colors’
PP.optimize.plot: no visible global function definition for ‘pairs’
PP.optimize.random: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  IQR colors hist median pairs par plot sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "plot", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
basisplot: no visible global function definition for ‘plot’
basisplot: no visible global function definition for ‘abline’
basisplot: no visible global function definition for ‘text’
basisplot: no visible global function definition for ‘par’
plot.prinsimp: no visible global function definition for ‘screeplot’
plot.simpart: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘par’
position_text: no visible global function definition for ‘strwidth’
simpart.formula: no visible global function definition for ‘terms’
simpart.formula: no visible global function definition for
  ‘model.matrix’
varperc: no visible global function definition for ‘plot’
varperc: no visible global function definition for ‘lines’
varperc: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘plot’
varsimp: no visible global function definition for ‘points’
varsimp: no visible global function definition for ‘text’
varsimp: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines model.matrix par plot points screeplot strwidth terms
  text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points",
             "strwidth", "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
.pfda.fstep: no visible global function definition for ‘dist’
.pfda.main: no visible global function definition for ‘plot’
.pfda.mstep: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov dist plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
GPois: no visible global function definition for ‘dnorm’
GPois: no visible binding for global variable ‘poisson’
GPois: no visible global function definition for ‘predict’
GPois: no visible global function definition for ‘fitted’
GPois: no visible global function definition for ‘residuals’
GPois: no visible global function definition for ‘smooth.spline’
ProDenICA: no visible global function definition for ‘rnorm’
d.gaussmix: no visible global function definition for ‘dnorm’
djordan: no visible global function definition for ‘dt’
djordan: no visible global function definition for ‘dunif’
mixmat: no visible global function definition for ‘rnorm’
mixmat: no visible global function definition for ‘runif’
plot.ProDenICA: no visible global function definition for ‘plot’
r.gaussmix: no visible global function definition for ‘rmultinom’
r.gaussmix: no visible global function definition for ‘rnorm’
rjordan: no visible global function definition for ‘rt’
rjordan: no visible global function definition for ‘runif’
rmix.dexp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm dt dunif fitted plot poisson predict residuals rmultinom rnorm
  rt runif smooth.spline
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
addpi: no visible global function definition for ‘lines’
genPerms: no visible global function definition for ‘combn’
getVar: no visible global function definition for ‘glm’
getVar: no visible global function definition for ‘binomial’
getVar: no visible global function definition for ‘var’
pba: no visible global function definition for ‘glm’
pba: no visible global function definition for ‘binomial’
pba: no visible global function definition for ‘predict’
pba: no visible global function definition for ‘rbinom’
pcr: no visible global function definition for ‘quantile’
plotpi: no visible global function definition for ‘plot’
plotpi: no visible global function definition for ‘axis’
plotpi: no visible global function definition for ‘abline’
plotpi: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline axis binomial combn glm lines plot predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "plot")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
addcircle: no visible global function definition for ‘lines’
addclassifierboundary: no visible global function definition for ‘par’
addclassifierboundary: no visible global function definition for
  ‘contour’
plot.protoclass: no visible global function definition for ‘plot’
plot.protoclass: no visible global function definition for ‘box’
plot.protoclass: no visible global function definition for ‘rgb2hsv’
plot.protoclass: no visible global function definition for ‘col2rgb’
plot.protoclass: no visible global function definition for ‘points’
plot.protoclass: no visible global function definition for ‘hsv’
predict.protoclass: no visible global function definition for ‘knn1’
Undefined global functions or variables:
  box col2rgb contour hsv knn1 lines par plot points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "plot",
             "points")
to your NAMESPACE file.
Running examples in ‘psychonetrics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: var1
> ### Title: Lag-1 vector autoregression family of psychonetrics models
> ### Aliases: var1 gvar
> 
> ### ** Examples
> 
> library("dplyr")

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library("graphicalVAR")
> 
> beta <- matrix(c(
+   0,0.5,
+   0.5,0
+ ),2,2,byrow=TRUE)
> kappa <- diag(2)
> simData <- graphicalVARsim(50, beta, kappa)
> 
> # Form model:
> model <- gvar(simData)
Error: Column `V1` must be length 51 (the group size) or one, not 102
Execution halted
PurBayes: no visible global function definition for ‘update’
PurBayes: no visible global function definition for ‘sd’
plot.PurBayes: no visible global function definition for ‘plot’
plot.PurBayes: no visible global function definition for ‘quantile’
plot.PurBayes: no visible global function definition for ‘lines’
summary.PurBayes : <anonymous>: no visible global function definition
  for ‘quantile’
Undefined global functions or variables:
  lines plot quantile sd update
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "quantile", "sd", "update")
to your NAMESPACE file.
csQCAbinTest: no visible global function definition for ‘p.adjust’
fsQCApermTest: no visible global function definition for ‘p.adjust’
mvQCAbinTest: no visible global function definition for ‘p.adjust’
p.threshold.adjust: no visible global function definition for
  ‘p.adjust’
plot.fsQCApt: no visible global function definition for ‘dev.cur’
plot.fsQCApt: no visible global function definition for ‘dev.new’
plot.fsQCApt: no visible global function definition for ‘par’
plot.fsQCApt: no visible global function definition for ‘plot’
plot.fsQCApt: no visible global function definition for ‘density’
plot.fsQCApt: no visible global function definition for ‘axis’
plot.fsQCApt: no visible global function definition for ‘polygon’
plot.fsQCApt: no visible global function definition for ‘points’
plot.fsQCApt: no visible global function definition for ‘hist’
summary.csQCAbt: no visible global function definition for
  ‘printCoefmat’
summary.fsQCApt: no visible global function definition for
  ‘printCoefmat’
summary.mvQCAbt: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par plot points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "plot", "points",
             "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/qtbase.Rcheck/00install.out’ for details.
alphaf: no visible global function definition for ‘pchisq’
alphaf: no visible global function definition for ‘dbinom’
conout: no visible global function definition for ‘sd’
ibgaout: no visible global function definition for ‘qnorm’
ibgaout: no visible global function definition for ‘pnorm’
plot.qualint: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘rnorm’
powerval: no visible global function definition for ‘qnorm’
powerval: no visible global function definition for ‘pnorm’
print.expplot: no visible global function definition for ‘gray’
print.expplot: no visible binding for global variable ‘coef’
print.outplot: no visible global function definition for ‘gray’
print.outplot: no visible binding for global variable ‘coef’
qualint: no visible global function definition for ‘qnorm’
qualint: no visible global function definition for ‘plot’
qualval: no visible global function definition for ‘qnorm’
qualval: no visible global function definition for ‘plot’
surout: no visible global function definition for ‘tail’
surout: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef dbinom gray pchisq plot pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
‘gs+qpdf’ made some significant size reductions:
     compacted ‘R2OpenBUGS.pdf’ from 911Kb to 639Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
Error(s) in re-building vignettes:
  ...
--- re-building ‘raceland-intro1.Rmd’ using rmarkdown
Loading required package: sp
Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 7.0.0

Attaching package: 'dplyr'

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

    intersect, select, union

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building ‘raceland-intro1.Rmd’

--- re-building ‘raceland-intro2.Rmd’ using rmarkdown
Loading required package: sp
Linking to GEOS 3.8.1, GDAL 3.0.4, PROJ 7.0.0

Attaching package: 'dplyr'

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

    intersect, select, union

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 256-281 (raceland-intro2.Rmd) 
Error: processing vignette 'raceland-intro2.Rmd' failed with diagnostics:
Assigned data `bivariate_classification(...)` must be compatible with existing data.
✖ Existing data has 36 rows.
✖ Assigned data has 9 rows.
ℹ Only vectors of size 1 are recycled.
--- failed re-building ‘raceland-intro2.Rmd’

--- re-building ‘raceland-intro3.Rmd’ using rmarkdown
--- finished re-building ‘raceland-intro3.Rmd’

SUMMARY: processing the following file failed:
  ‘raceland-intro2.Rmd’

Error: Vignette re-building failed.
Execution halted
getsonde: no visible global function definition for ‘read.table’
plotsonde: no visible global function definition for ‘par’
plotwind: no visible global function definition for ‘plot’
plotwind: no visible global function definition for ‘mtext’
plotwind: no visible global function definition for ‘abline’
skewt.axis: no visible global function definition for ‘par’
skewt.axis: no visible global function definition for ‘plot’
skewt.axis: no visible global function definition for ‘axis’
skewt.axis: no visible global function definition for ‘mtext’
skewt.axis: no visible global function definition for ‘segments’
skewt.axis: no visible global function definition for ‘text’
skewt.axis: no visible global function definition for ‘lines’
skewt.lines: no visible global function definition for ‘lines’
skewt.points: no visible global function definition for ‘points’
station.symbol: no visible global function definition for ‘sd’
station.symbol: no visible global function definition for ‘par’
station.symbol: no visible global function definition for ‘lines’
station.symbol: no visible global function definition for ‘polygon’
station.symbol: no visible global function definition for ‘text’
station.symbol: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline axis lines mtext par plot points polygon read.table sd
  segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "plot", "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Rd file 'predict.randomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

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

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

These lines will be truncated in the PDF manual.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
brewer.pal: no visible global function definition for ‘rgb’
display.brewer.all: no visible global function definition for ‘par’
display.brewer.all: no visible global function definition for ‘plot’
display.brewer.all: no visible global function definition for ‘rect’
display.brewer.all: no visible global function definition for ‘text’
display.brewer.pal: no visible global function definition for ‘image’
Undefined global functions or variables:
  image par plot rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "plot", "rect", "text")
to your NAMESPACE file.
CUR: no visible global function definition for ‘runif’
CUR: no visible global function definition for ‘new’
plotLeverage,CURobj: no visible global function definition for ‘plot’
plotLeverage,CURobj: no visible global function definition for ‘points’
plotLeverage,CURobj: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline new plot points runif
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "new")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
distimage: no visible binding for global variable ‘terrain.colors’
distimage: no visible global function definition for ‘filled.contour’
distimage: no visible global function definition for ‘title’
distimage: no visible global function definition for ‘axis’
distimage: no visible global function definition for ‘lines’
drawkpc: no visible global function definition for ‘plot’
drawkpc: no visible global function definition for ‘segments’
drawkpc: no visible global function definition for ‘lines’
modelimage: no visible binding for global variable ‘topo.colors’
modelimage: no visible global function definition for ‘filled.contour’
modelimage: no visible global function definition for ‘title’
modelimage: no visible global function definition for ‘axis’
modelimage: no visible global function definition for ‘lines’
sincdata: no visible global function definition for ‘runif’
sincdata: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  axis filled.contour lines plot rnorm runif segments terrain.colors
  title topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "plot",
             "segments", "title")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’ using rmarkdown
Loading required package: rJava
Loading required package: Rdroolsjars

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'purrr'

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

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.thoughtworks.xstream.core.util.Fields (file:/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rdroolsjars/java/xstream-1.4.9.jar) to field java.util.TreeMap.comparator
WARNING: Please consider reporting this to the maintainers of com.thoughtworks.xstream.core.util.Fields
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Quitting from lines 183-187 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' failed with diagnostics:
Assigned data `paste(seq(as.numeric(lowerRange), as.numeric(upperRange)), collapse = ",")` must be compatible with existing data.
ℹ Error occurred for column `Indices`.
✖ No common type for `value` <character> and `x` <double>.
--- failed re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(readroper)
  readroper package loaded.
  > 
  > test_check("readroper")
  ── 1. Error: First row of multicard dataset matches (@test-readroper.R#4)  ─────
  Must subset rows with a valid subscript vector.
  ℹ Logical subscripts must match the size of the indexed input.
  ✖ The input has size 1976 but the subscript `card_v` has size 2.
  Backtrace:
    1. readroper::read_rpr(...)
   16. vctrs:::stop_indicator_size(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: First row of multicard dataset matches (@test-readroper.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-all.R’ [4s/8s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > # Modeled after the R6 testing structure: https://github.com/wch/R6/blob/master/tests/testthat.R
  > library(testthat)
  > library(REDCapR)
  > 
  > testthat::test_check("REDCapR")
  ── 1. Failure: validate_no_logical -concern dataset (@test-validate.R#36)  ─────
  ds$field_index not equal to 2.
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 135 | SKIPPED: 79 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: validate_no_logical -concern dataset (@test-validate.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
AutoCorrelationLRtest: no visible global function definition for
  ‘logLik’
AutoCorrelationLRtest: no visible global function definition for
  ‘pchisq’
REEMtree: no visible global function definition for ‘terms’
REEMtree: no visible binding for global variable ‘SubsetVector’
REEMtree: no visible global function definition for ‘predict’
REEMtree: no visible global function definition for ‘logLik’
fitted.REEMtree: no visible global function definition for ‘fitted’
plot.REEMtree: no visible global function definition for ‘plot’
predict.REEMtree: no visible global function definition for ‘predict’
residuals.REEMtree: no visible global function definition for
  ‘residuals’
Undefined global functions or variables:
  SubsetVector fitted logLik pchisq plot predict residuals terms
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "fitted", "logLik", "pchisq", "predict",
             "residuals", "terms")
to your NAMESPACE file.
CapDistSlope: no visible global function definition for ‘coef’
CapDistSlope: no visible global function definition for ‘lm’
EnergyEntropyDecomp: no visible global function definition for ‘legend’
FernholzDecomp: no visible global function definition for ‘legend’
Invest: no visible global function definition for ‘par’
Invest: no visible global function definition for ‘legend’
SimMarketModel: no visible global function definition for ‘rnorm’
plot.capdist: no visible global function definition for ‘plot’
plot.capdist: no visible global function definition for ‘abline’
plot.capdist: no visible global function definition for ‘lm’
plot.toymkt: no visible global function definition for ‘par’
plot.toymkt: no visible global function definition for ‘plot’
plot.toymkt: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline coef legend lm par plot rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
Running examples in ‘rematch2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: re_exec
> ### Title: Extract Data From First Regular Expression Match Into a Data
> ###   Frame
> ### Aliases: re_exec $.rematch_records $.rematch_allrecords
> 
> ### ** Examples
> 
> name_rex <- paste0(
+   "(?<first>[[:upper:]][[:lower:]]+) ",
+   "(?<last>[[:upper:]][[:lower:]]+)"
+ )
> notables <- c(
+   "  Ben Franklin and Jefferson Davis",
+   "\tMillard Fillmore"
+ )
> # Match first occurrence
> pos <- re_exec(notables, name_rex)
> pos
Error: Input must be a vector, not a `rematch_records` object.
Backtrace:
     █
  1. ├─(function (x, ...) ...
  2. ├─tibble:::print.tbl(x)
  3. │ ├─cli::cat_line(format(x, ..., n = n, width = width, n_extra = n_extra))
  4. │ │ └─base::paste0(..., collapse = "\n")
  5. │ ├─base::format(x, ..., n = n, width = width, n_extra = n_extra)
  6. │ └─tibble:::format.tbl(x, ..., n = n, width = width, n_extra = n_extra)
  7. │   └─tibble::trunc_mat(x, n = n, width = width, n_extra = n_extra)
  8. │     ├─base::as.data.frame(head(x, n))
  9. │     ├─utils::head(x, n)
 10. │     └─utils:::head.data.frame(x, n)
 11. │       ├─x[seq_len(n), , drop = FALSE]
 12. │       └─tibble:::`[.tbl_df`(x, seq_len(n), , drop = FALSE)
 13. │         └─tibble:::tbl_subset_row(xo, i = i, i_arg)
 14. │           └─base::lapply(unclass(x), vec_slice, i = i)
 15. │             └─vctrs:::FUN(X[[i]], ...)
 16. └─vctrs:::stop_
Execution halted
RearrangeData: no visible global function definition for ‘rainbow’
RearrangeData: no visible global function definition for ‘hclust’
RearrangeData: no visible global function definition for
  ‘as.dendrogram’
RearrangeData: no visible global function definition for ‘heatmap’
RearrangeData: no visible global function definition for ‘pdf’
RearrangeData: no visible global function definition for
  ‘colorRampPalette’
RearrangeData: no visible global function definition for ‘legend’
RearrangeData: no visible global function definition for ‘dev.off’
RearrangeJoseph: no visible global function definition for
  ‘write.table’
RearrangeJoseph: no visible global function definition for
  ‘as.dendrogram’
RearrangeJoseph: no visible global function definition for
  ‘order.dendrogram’
colorDendClass : colLab: no visible global function definition for
  ‘is.leaf’
colorDendClass: no visible global function definition for ‘dendrapply’
colorDendClass: no visible global function definition for ‘plot’
testData1: no visible global function definition for ‘runif’
testData1: no visible global function definition for ‘image’
testData2: no visible global function definition for ‘runif’
testData2: no visible global function definition for ‘image’
Undefined global functions or variables:
  as.dendrogram colorRampPalette dendrapply dev.off hclust heatmap
  image is.leaf legend order.dendrogram pdf plot rainbow runif
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend", "plot")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
plot.reweight: no visible global function definition for ‘par’
plot.reweight: no visible global function definition for ‘plot’
plot.reweight: no visible global function definition for ‘density’
plot.reweight: no visible global function definition for ‘rug’
reweight: no visible global function definition for ‘aggregate’
search.best.h: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate density par plot quantile rug
Consider adding
  importFrom("graphics", "par", "plot", "rug")
  importFrom("stats", "aggregate", "density", "quantile")
to your NAMESPACE file.
Running examples in ‘rGEDI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clipLevel1BGeo
> ### Title: Clip GEDI Full Waveform Geolocations by Coordinates
> ### Aliases: clipLevel1BGeo
> 
> ### ** Examples
> 
> # Specifying the path to GEDI level1B data (zip file)
> level1B_fp_zip <- system.file("extdata",
+                   "GEDI01_B_2019108080338_O01964_T05337_02_003_01_sub.zip",
+                   package="rGEDI")
> 
> # Unzipping GEDI level1B data
> level1Bpath <- unzip(level1B_fp_zip,exdir = dirname(level1B_fp_zip))
Error in unzip(level1B_fp_zip, exdir = dirname(level1B_fp_zip)) : 
  cannot open file '/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rGEDI/extdata/GEDI01_B_2019108080338_O01964_T05337_02_003_01_sub.h5': Read-only file system
Execution halted
Found the following significant warnings:
  Note: possible error in 'coord_trans(xtrans = "exp", ': unused arguments (xtrans = "exp", ytrans = "exp") 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RGraphics.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
   #warning "The <sys/sysctl.h> header is deprecated and will be removed."
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RhpcBLASctl.Rcheck/00install.out’ for details.
R2ngon: no visible global function definition for ‘approx’
plotR2pre: no visible global function definition for ‘plot’
plotR2pre: no visible global function definition for ‘points’
plotR2pre: no visible global function definition for ‘gray’
plotR2pre: no visible global function definition for ‘legend’
plotR2pre: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  approx gray legend plot points rainbow
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "legend", "plot", "points")
  importFrom("stats", "approx")
to your NAMESPACE file.
plot.ijzip: no visible global function definition for ‘plot’
plot.ijzip : <anonymous>: no visible global function definition for
  ‘plot’
plot.ijzip: no visible global function definition for ‘axis’
read.ijzip: no visible global function definition for ‘unzip’
Undefined global functions or variables:
  axis plot unzip
Consider adding
  importFrom("graphics", "axis", "plot")
  importFrom("utils", "unzip")
to your NAMESPACE file.
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(riskclustr)
  > 
  > test_check("riskclustr")
  ── 1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_message(...)
    6. riskclustr::optimal_kmeans_d(...)
    7. base::lapply(...)
    8. riskclustr:::FUN(X[[i]], ...)
    9. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   12. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   13. tibble:::tbl_subset_row(xo, i = i, i_arg)
   14. tibble:::vectbl_as_row_index(i, x, i_arg)
   15. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   22. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ── 2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_km
  `i` must have one dimension, not 2.
  Backtrace:
    1. testthat::expect_equal(...)
    4. riskclustr::optimal_kmeans_d(...)
    5. base::lapply(...)
    6. riskclustr:::FUN(X[[i]], ...)
    7. riskclustr::d(label = "cls", M = M, factors = factors, data = temp)
   10. tibble:::`[.tbl_df`(data, data[, label] == 0, )
   11. tibble:::tbl_subset_row(xo, i = i, i_arg)
   12. tibble:::vectbl_as_row_index(i, x, i_arg)
   13. tibble:::vectbl_as_row_location(i, nr, i_arg, assign)
   20. vctrs::vec_as_location(i, n, arg = as_label(i_arg))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 26 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Error: optimal_kmeans_d prints message if no seed is set (@test-optimal_kmeans_d.R#49) 
  2. Error: optimal_kmeans_d returns expected optimal_d value (@test-optimal_kmeans_d.R#65) 
  
  Error: testthat unit tests failed
  Execution halted
KM.plot: no visible global function definition for ‘plot’
KM.plot: no visible global function definition for ‘lines’
SchoenSmooth: no visible global function definition for ‘lm’
llCoxReg: no visible binding for global variable ‘time’
risksetAUC: no visible global function definition for ‘abline’
risksetROC: no visible global function definition for ‘abline’
weightedKM: no visible binding for global variable ‘time’
Undefined global functions or variables:
  abline lines lm plot time
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "lm", "time")
to your NAMESPACE file.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cv.coef: no visible global function definition for ‘sd’
normalize.softmax: no visible global function definition for ‘plogis’
plot.rknnBeg: no visible global function definition for ‘plot’
plot.rknnBel: no visible global function definition for ‘plot’
plot.rknnSupport: no visible global function definition for ‘dotchart’
predicted: no visible global function definition for ‘influence’
predicted: no visible global function definition for ‘fitted’
predicted: no visible global function definition for ‘resid’
pressresid: no visible global function definition for ‘influence’
pressresid: no visible global function definition for ‘resid’
Undefined global functions or variables:
  dotchart fitted influence plogis plot resid sd
Consider adding
  importFrom("graphics", "dotchart", "plot")
  importFrom("stats", "fitted", "influence", "plogis", "resid", "sd")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rlgt.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rlo.Rcheck/00install.out’ for details.
GIC: no visible global function definition for ‘integrate’
QM.poisson: no visible global function definition for ‘ppois’
QM.poisson: no visible global function definition for ‘dpois’
cplot.robustgam: no visible global function definition for ‘plot’
expect.poisson: no visible global function definition for ‘dpois’
expect.poisson: no visible global function definition for ‘ppois’
pred.robustgam: no visible global function definition for
  ‘Predict.matrix’
robust.sigma: no visible global function definition for ‘median’
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.GIC.optim: no visible global function definition for ‘optim’
robustgam.crossval : w.fun: no visible global function definition for
  ‘covMcd’
robustgam.crossval: no visible global function definition for
  ‘integrate’
smooth.construct.tr.smooth.spec: no visible global function definition
  for ‘quantile’
w.binomial: no visible global function definition for ‘pbinom’
w.poisson: no visible global function definition for ‘ppois’
Undefined global functions or variables:
  Predict.matrix covMcd dpois integrate median optim pbinom plot ppois
  quantile s smooth.construct.cr.smooth.spec
  smooth.construct.ps.smooth.spec smooth.construct.tp.smooth.spec
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dpois", "integrate", "median", "optim", "pbinom",
             "ppois", "quantile")
to your NAMESPACE file.
ROSE.eval: no visible global function definition for ‘methods’
ROSE.eval: no visible binding for global variable ‘model.frame’
ROSE.eval: no visible binding for global variable ‘predict’
adj.formula: no visible global function definition for ‘terms’
adj.formula: no visible global function definition for ‘as.formula’
omnibus.balancing: no visible binding for global variable ‘model.frame’
ou.sampl: no visible global function definition for ‘rbinom’
over.sampl: no visible global function definition for ‘rbinom’
plot.roc.inner: no visible global function definition for ‘plot’
roc.curve: no visible global function definition for ‘lines’
roc.curve: no visible global function definition for ‘abline’
rose.real: no visible binding for global variable ‘sd’
rose.real: no visible global function definition for ‘sd’
rose.real: no visible global function definition for ‘rnorm’
rose.sampl: no visible global function definition for ‘rbinom’
under.sampl: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  abline as.formula lines methods model.frame plot predict rbinom rnorm
  sd terms
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "predict", "rbinom",
             "rnorm", "sd", "terms")
  importFrom("utils", "methods")
to your NAMESPACE file.
Rd file 'C.FRNN.FRST.Rd':
  \examples lines wider than 100 characters:
                     type.relation = c("tolerance", "eq.1"), t.implicator = "lukasiewicz")                                                   ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rPython.Rcheck/00install.out’ for details.
.computekappa: no visible global function definition for ‘pnorm’
.computekappa: no visible global function definition for ‘dnorm’
.initmethod : <anonymous>: no visible global function definition for
  ‘median’
.initmethod: no visible global function definition for ‘model.matrix’
.mspe: no visible global function definition for ‘rnorm’
.mspe : <anonymous>: no visible global function definition for ‘rnorm’
makedata: no visible global function definition for ‘rnorm’
makedata : addraneff: no visible global function definition for ‘rnorm’
plot.meanssaemodel: no visible global function definition for ‘par’
plot.meanssaemodel: no visible global function definition for ‘plot’
plot.meanssaemodel: no visible global function definition for ‘lines’
plot.meanssaemodel: no visible global function definition for ‘axis’
plot.meanssaemodel: no visible global function definition for ‘grid’
plot.meanssaemodel: no visible global function definition for ‘box’
plot.meanssaemodel: no visible global function definition for ‘legend’
plot.meanssaemodel: no visible global function definition for ‘arrows’
saemodel: no visible global function definition for ‘model.frame’
saemodel: no visible global function definition for ‘model.response’
saemodel: no visible global function definition for ‘model.matrix’
summary.fitsaemodel: no visible global function definition for ‘pt’
summary.fitsaemodel: no visible global function definition for
  ‘printCoefmat’
Undefined global functions or variables:
  arrows axis box dnorm grid legend lines median model.frame
  model.matrix model.response par plot pnorm printCoefmat pt rnorm
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "grid", "legend",
             "lines", "par", "plot")
  importFrom("stats", "dnorm", "median", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "pt", "rnorm")
to your NAMESPACE file.
Running examples in ‘RSDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VeterinaryData
> ### Title: Symbolic interval data example
> ### Aliases: VeterinaryData
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(VeterinaryData)
> VeterinaryData
Error in get(x, envir = ns, inherits = FALSE) : 
  object 'warningc' not found
Calls: <Anonymous> ... head.data.frame -> [ -> [.symbolic_tbl -> getFromNamespace -> get
Execution halted
convexhull: no visible global function definition for ‘chull’
convexhull: no visible global function definition for ‘rnorm’
drawcompletegraph: no visible global function definition for ‘plot’
drawcompletegraph: no visible global function definition for ‘segments’
getbag: no visible global function definition for ‘plot’
getbag: no visible global function definition for ‘chull’
getbag: no visible global function definition for ‘polygon’
getbag: no visible global function definition for ‘points’
inflate: no visible global function definition for ‘rnorm’
rsmed: no visible global function definition for ‘runif’
rsplot: no visible global function definition for ‘plot’
rsplot: no visible global function definition for ‘chull’
rsplot: no visible global function definition for ‘polygon’
rsplot: no visible global function definition for ‘points’
rsrings: no visible global function definition for ‘plot’
rsrings: no visible global function definition for ‘chull’
rsrings: no visible global function definition for ‘polygon’
rsrings: no visible global function definition for ‘points’
rstinterval: no visible global function definition for ‘plot’
rstinterval: no visible global function definition for ‘runif’
rstinterval: no visible global function definition for ‘rnorm’
rstinterval: no visible global function definition for ‘chull’
rstinterval: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  chull plot points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "plot", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
addNoisyCopies: no visible global function definition for ‘rnorm’
eta: no visible global function definition for ‘var’
gaussClassifier: no visible global function definition for ‘runif’
getSigma: no visible global function definition for ‘sd’
getSigma: no visible binding for global variable ‘sd’
sfaClassify: no visible global function definition for ‘rainbow’
sfaClassify: no visible global function definition for ‘par’
sfaClassify: no visible global function definition for ‘plot’
sfaClassify: no visible global function definition for ‘points’
sfaClassify: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines par plot points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rstanarm.Rcheck/00install.out’ for details.
barplot.rtconnect: no visible global function definition for ‘rainbow’
barplot.rtconnect: no visible global function definition for ‘text’
plot.rtconnect: no visible global function definition for ‘par’
plot.rtconnect: no visible global function definition for ‘plot’
plot.rtconnect: no visible global function definition for ‘axis.Date’
rtconnect: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis.Date par plot rainbow read.table text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis.Date", "par", "plot", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
plotGLCM: no visible global function definition for ‘plot’
plotGLCM: no visible global function definition for ‘points’
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
Running examples in ‘rubias-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: write_gsi_sim_mixture
> ### Title: Write a mixture data frame to gsi_sim format baseline and
> ###   repunits file
> ### Aliases: write_gsi_sim_mixture
> 
> ### ** Examples
> 
> # this writes to file prefix "mixfile" in a temporary directory
> dd <- tempdir()
> prefix <- file.path(dd, "mixfile")
> 
> # print that
> prefix
[1] "/tmp/RtmpCq33PX/mixfile"
> 
> # note that in practice you will probably want to specify
> # your own directory...
> 
> # run the function
> write_gsi_sim_mixture(chinook_mix, 5, prefix)
Error: Assigned data `0` must be compatible with existing data.
ℹ Error occurred for column `repunit`.
✖ No common type for `value` <double> and `x` <character>.
Backtrace:
    █
 1. └─rubias::write_gsi_sim_mixture(chinook_mix, 5, prefix)
 2.   ├─base::`[<-`(`*tmp*`, is.na(mix), value = 0)
 3.   └─tibble:::`[<-.tbl_df`(`*tmp*`, is.na(mix), value = 0)
 4.     └─tibble:::tbl_subassign_matrix(x, j, value, j_arg, substitute(value))
 5.       └─base::tryCatch(...)
 6.         └─base:::tryCatchList(expr, classes, parentenv, handlers)
 7.           └─base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8.             └─value[[3L]](cond)
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
RWBP.default: no visible global function definition for ‘na.omit’
RWBP.default: no visible global function definition for ‘kmeans’
RWBP.formula: no visible global function definition for ‘model.extract’
plot.RWBP: no visible global function definition for ‘plot’
predict.RWBP: no visible global function definition for ‘head’
Undefined global functions or variables:
  head kmeans model.extract na.omit plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
.dwt: no visible global function definition for ‘median’
.udwt: no visible global function definition for ‘median’
plotSignalTransformation: no visible global function definition for
  ‘plot’
plotSignalTransformation: no visible global function definition for
  ‘box’
plotSignalTransformation: no visible global function definition for
  ‘axis’
plotSignalTransformation: no visible global function definition for
  ‘lines’
plotSignalTransformation: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  axis box legend lines median plot
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot")
  importFrom("stats", "median")
to your NAMESPACE file.
fit.saery.AR1: no visible global function definition for ‘qnorm’
fit.saery.MA1: no visible global function definition for ‘qnorm’
fit.saery.indep: no visible global function definition for ‘qnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.AR1.typeII: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeI: no visible global function definition for
  ‘write.table’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘rnorm’
mse.saery.boot.MA1.typeII: no visible global function definition for
  ‘write.table’
plot.saery: no visible global function definition for ‘devAskNewPage’
plot.saery: no visible global function definition for ‘par’
plot.saery: no visible global function definition for ‘plot’
plot.saery: no visible global function definition for ‘abline’
plot.saery: no visible global function definition for ‘title’
plot.saery: no visible global function definition for ‘axis’
plot.saery: no visible global function definition for ‘lines’
plot.saery: no visible global function definition for ‘legend’
pvalue: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par plot pnorm qnorm rnorm
  title write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
plot.scair: no visible global function definition for ‘par’
plot.scair: no visible global function definition for ‘plot’
plot.scair: no visible global function definition for ‘points’
plot.scar: no visible global function definition for ‘par’
plot.scar: no visible global function definition for ‘plot’
plot.scar: no visible global function definition for ‘points’
predict.scair: no visible global function definition for ‘approx’
predict.scar: no visible global function definition for ‘approx’
scair: no visible global function definition for ‘gaussian’
scair: no visible global function definition for ‘runif’
scair: no visible global function definition for ‘rnorm’
scar: no visible global function definition for ‘gaussian’
scar: no visible global function definition for ‘glm.fit’
scar: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx gaussian glm.fit par plot points rnorm runif
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
adx: no visible global function definition for ‘abline’
adx: no visible global function definition for ‘legend’
dx: no visible global function definition for ‘abline’
dx: no visible global function definition for ‘legend’
maxd: no visible global function definition for ‘abline’
maxd: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘rainbow’
pc: no visible global function definition for ‘plot’
pc: no visible global function definition for ‘abline’
pc: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘points’
pcu: no visible global function definition for ‘rainbow’
pcu: no visible global function definition for ‘plot’
pcu: no visible global function definition for ‘abline’
pcu: no visible global function definition for ‘legend’
pcu: no visible global function definition for ‘points’
rmsd: no visible global function definition for ‘abline’
rmsd: no visible global function definition for ‘legend’
rsd: no visible global function definition for ‘abline’
rsd: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend plot points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "plot", "points")
to your NAMESPACE file.
SEchart: no visible global function definition for ‘plot’
SEchart: no visible global function definition for ‘rect’
SEchart: no visible global function definition for ‘par’
SEchart: no visible global function definition for ‘grid’
SEchart: no visible global function definition for ‘axis’
SEchart: no visible global function definition for ‘text’
SEchart: no visible global function definition for ‘lines’
SEchart: no visible global function definition for ‘heat.colors’
SEchart: no visible global function definition for ‘topo.colors’
SEchart: no visible global function definition for ‘cm.colors’
SEchart: no visible global function definition for ‘terrain.colors’
SEchart: no visible global function definition for ‘gray.colors’
SEchart: no visible global function definition for ‘rainbow’
SEchart: no visible global function definition for ‘points’
SEchart: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par plot
  points rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "points", "rect", "text")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘segmentr.Rmd’ using rmarkdown
Loading required package: segmentr
Loading required package: tidyr
Loading required package: tibble
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: lubridate

Attaching package: 'lubridate'

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

    date

Loading required package: magrittr

Attaching package: 'magrittr'

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

    extract

Loading required package: purrr

Attaching package: 'purrr'

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

    set_names

Killed
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’
getbinPost: no visible binding for global variable ‘dbeta’
getbinPost: no visible binding for global variable ‘pbeta’
getbinPost : fu: no visible global function definition for ‘dbinom’
getbinPost : fu: no visible global function definition for ‘predict’
getbinPost: no visible global function definition for ‘integrate’
getbinPost: no visible global function definition for ‘splinefun’
int.funct: no visible global function definition for ‘integrate’
int.funct2: no visible global function definition for ‘integrate’
min.abs: no visible global function definition for ‘uniroot’
plot.SEL: no visible global function definition for ‘plot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
plotenz : addmark: no visible global function definition for ‘par’
plotenz : addmark: no visible global function definition for ‘plot’
plotenz : addmark: no visible global function definition for ‘text’
plotenz : addmark: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘layout’
plotenz: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  dev.new layout par plot segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "plot", "segments", "text")
to your NAMESPACE file.
filter.PCA.default: no visible global function definition for
  ‘princomp’
filter.mRMR.default: no visible global function definition for
  ‘discretize’
gaussian.default: no visible global function definition for ‘cov’
gaussian.default: no visible global function definition for
  ‘cov.shrink’
plot.verify.cv: no visible global function definition for ‘plot’
plot.verify.cv: no visible global function definition for ‘points’
plot.verify.ho: no visible global function definition for ‘plot’
plot.verify.ho: no visible global function definition for ‘points’
plot.verify.loo: no visible global function definition for ‘plot’
plot.verify.loo: no visible global function definition for ‘points’
predict.dpa1: no visible global function definition for ‘cor’
predict.filter.PCA: no visible global function definition for ‘predict’
predict.filter.RegressionTreeFilter: no visible global function
  definition for ‘is.struct’
predict.filter.RegressionTreeFilter: no visible global function
  definition for ‘var’
simulator.Simple1: no visible global function definition for ‘rnorm’
verify.ho.default: no visible global function definition for ‘predict’
verify.loo.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct plot points predict princomp
  rnorm var
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
plot.SII: no visible global function definition for ‘plot’
plot.SII: no visible global function definition for ‘lines’
plot.SII: no visible global function definition for ‘abline’
plot.SII: no visible global function definition for ‘legend’
sii : approx.l: no visible global function definition for ‘approx’
sii.excel: no visible global function definition for ‘predict’
sii.excel : approx.l: no visible global function definition for
  ‘approx’
Undefined global functions or variables:
  abline approx legend lines plot predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
cumallcausehr: no visible global function definition for ‘integrate’
plotbe: no visible global function definition for ‘plot’
plotbe: no visible global function definition for ‘lines’
plotbe: no visible global function definition for ‘legend’
plotcph: no visible global function definition for ‘confint’
plotcph: no visible global function definition for ‘plot’
plotcph: no visible global function definition for ‘abline’
plotcph: no visible global function definition for ‘axis’
plotcph: no visible global function definition for ‘polygon’
plotcph: no visible global function definition for ‘lines’
plotnae: no visible global function definition for ‘plot’
simCR: no visible global function definition for ‘rnorm’
simEBMT: no visible global function definition for ‘model.matrix’
simexit: no visible global function definition for ‘runif’
simexitinner: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix plot polygon
  rnorm runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
             "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
Simpsons: no visible global function definition for ‘Mclust’
Simpsons: no visible global function definition for ‘lm’
Simpsons: no visible global function definition for ‘plot’
Simpsons: no visible global function definition for ‘abline’
Simpsons: no visible global function definition for ‘par’
Simpsons: no visible global function definition for ‘legend’
Simpsons: no visible global function definition for ‘txtProgressBar’
Simpsons: no visible global function definition for ‘setTxtProgressBar’
Simpsons: no visible global function definition for ‘quantile’
plot.Simpson: no visible global function definition for ‘plot’
plot.Simpson: no visible global function definition for ‘lm’
plot.Simpson: no visible global function definition for ‘abline’
plot.Simpson: no visible global function definition for ‘par’
plot.Simpson: no visible global function definition for ‘legend’
Undefined global functions or variables:
  Mclust abline legend lm par plot quantile setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
slcestimates: no visible global function definition for ‘par’
slcestimates: no visible global function definition for ‘plot’
slcestimates: no visible global function definition for ‘abline’
slcestimates: no visible global function definition for ‘lines’
slcestimates: no visible global function definition for ‘axis’
slcestimates: no visible global function definition for ‘points’
slcestimates: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline axis lines par plot points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "title")
to your NAMESPACE file.
em: no visible global function definition for ‘coxph’
em: no visible global function definition for ‘optim’
plotpredictsmcure: no visible global function definition for ‘plot’
plotpredictsmcure: no visible global function definition for ‘matplot’
plotpredictsmcure: no visible global function definition for ‘lines’
smcure: no visible binding for global variable ‘na.omit’
smcure: no visible global function definition for ‘model.frame’
smcure: no visible global function definition for ‘model.extract’
smcure: no visible global function definition for ‘model.matrix’
smcure: no visible global function definition for ‘coxph’
smcure: no visible global function definition for ‘survreg’
smcure: no visible binding for global variable ‘var’
smcure: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim plot pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot", "plot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
Grad.sph: no visible global function definition for ‘dist’
IMDS: no visible global function definition for ‘cmdscale’
IMDS: no visible global function definition for ‘as.dist’
IMDS: no visible global function definition for ‘runif’
IMDS: no visible global function definition for ‘optim’
idistSph: no visible global function definition for ‘dist’
obj.sph: no visible global function definition for ‘dist’
plot.imds: no visible binding for global variable ‘lines’
plot.imds: no visible global function definition for ‘plot’
plot.imds: no visible global function definition for ‘text’
plot.imds: no visible global function definition for ‘rect’
Undefined global functions or variables:
  as.dist cmdscale dist lines optim plot rect runif text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
lines.SmithWilsonYieldCurve: no visible global function definition for
  ‘lines’
plot.SmithWilsonYieldCurve: no visible global function definition for
  ‘plot’
points.SmithWilsonYieldCurve: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
plot.soma: no visible global function definition for ‘plot’
soma: no visible global function definition for ‘runif’
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
analyzeSP23Design: no visible global function definition for ‘plot’
exploreSP23Design: no visible global function definition for
  ‘txtProgressBar’
exploreSP23Design: no visible global function definition for
  ‘setTxtProgressBar’
generateClinicalTrialData : <anonymous>: no visible global function
  definition for ‘runif’
generateClinicalTrialData: no visible global function definition for
  ‘rbinom’
generateClinicalTrialData: no visible global function definition for
  ‘rexp’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘pnorm’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.b: no visible global function definition for ‘qnorm’
mHP.b: no visible global function definition for ‘uniroot’
mHP.c : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.c: no visible global function definition for ‘uniroot’
mHP.c: no visible global function definition for ‘qnorm’
performInterimLook: no visible global function definition for ‘optim’
performInterimLook: no visible global function definition for
  ‘constrOptim’
performInterimLook: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  Miwa constrOptim optim plot pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Running ‘testthat.R’ [51s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spbabel)
  > 
  > test_check("spbabel")
  ── 1. Failure: sf conversion works (@test-sf.R#34)  ────────────────────────────
  `map_table(st_as_sf(as(as(nc, "Spatial"), "SpatialLinesDataFrame")))` produced warnings.
  
  ── 2. Failure: sf conversion works (@test-sf.R#35)  ────────────────────────────
  `map_table(...)` produced warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 85 | SKIPPED: 4 | WARNINGS: 5 | FAILED: 2 ]
  1. Failure: sf conversion works (@test-sf.R#34) 
  2. Failure: sf conversion works (@test-sf.R#35) 
  
  Error: testthat unit tests failed
  Execution halted
Ell.Theta: no visible global function definition for ‘ell.theta’
confid.int.theta: no visible global function definition for ‘qchisq’
confid.int.theta : sim.c: no visible global function definition for
  ‘runif’
confid.int.theta: no visible global function definition for ‘quantile’
dd.est: no visible global function definition for ‘ecdf’
ks.sporm : Simul: no visible global function definition for ‘runif’
ks.stat: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘plot’
test.theta: no visible global function definition for ‘ecdf’
test.theta : sim: no visible global function definition for ‘runif’
Undefined global functions or variables:
  ecdf ell.theta plot qchisq quantile runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
plot.SPRT: no visible global function definition for ‘par’
plot.SPRT: no visible global function definition for ‘plot’
plot.SPRT: no visible global function definition for ‘abline’
print.SPRT: no visible global function definition for ‘head’
Undefined global functions or variables:
  abline head par plot
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("utils", "head")
to your NAMESPACE file.
File ‘sqp/libs/sqp.so’:
  Found ‘__assert_fail’, possibly from ‘assert’ (C)
    Object: ‘solver_dense.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [22s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #    Copyright 2015 Province of British Columbia
  > #
  > #    Licensed under the Apache License, Version 2.0 (the "License");
  > #    you may not use this file except in compliance with the License.
  > #    You may obtain a copy of the License at
  > #
  > #       http://www.apache.org/licenses/LICENSE-2.0
  > #
  > #    Unless required by applicable law or agreed to in writing, software
  > #    distributed under the License is distributed on an "AS IS" BASIS,
  > #    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  > #    See the License for the specific language governing permissions and
  > #    limitations under the License.
  > 
  > library(testthat)
  > library(ssdtools)
  
  Attaching package: 'ssdtools'
  
  The following objects are masked from 'package:stats':
  
      dgamma, dweibull, pgamma, pweibull, qgamma, qweibull, rgamma,
      rweibull
  
  > 
  > test_check("ssdtools")
  ── 1. Failure: ssd_gof fitdistscens (@test-gof.R#46)  ──────────────────────────
  as.data.frame(ssd_gof(fluazinam_dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ── 2. Failure: manual (@test-schwarz-tillmans.R#24)  ───────────────────────────
  as.data.frame(ssd_gof(dists)) not equal to structure(...).
  Attributes: < Component "row.names": Modes: numeric, character >
  Attributes: < Component "row.names": target is numeric, current is character >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 269 | SKIPPED: 0 | WARNINGS: 12 | FAILED: 2 ]
  1. Failure: ssd_gof fitdistscens (@test-gof.R#46) 
  2. Failure: manual (@test-schwarz-tillmans.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
genericPlot: no visible global function definition for ‘dev.new’
genericPlot: no visible global function definition for ‘par’
genericPlot: no visible global function definition for ‘rainbow’
genericPlot: no visible global function definition for ‘plot’
genericPlot: no visible global function definition for ‘lines’
genericPlot: no visible global function definition for ‘legend’
genericPlot: no visible global function definition for ‘dev.copy2pdf’
genericPlot: no visible global function definition for ‘dev.copy2eps’
genericPlot: no visible global function definition for ‘dev.print’
genericPlot: no visible binding for global variable ‘png’
genericPlot: no visible binding for global variable ‘tiff’
plotStrains: no visible global function definition for ‘rainbow’
plotStrains: no visible global function definition for ‘dev.new’
plotStrains: no visible global function definition for ‘par’
plotStrains: no visible global function definition for ‘plot’
plotStrains: no visible global function definition for ‘lines’
plotStrains: no visible global function definition for ‘legend’
plotStrains: no visible global function definition for ‘dev.copy2pdf’
plotStrains: no visible global function definition for ‘dev.copy2eps’
plotStrains: no visible global function definition for ‘dev.print’
plotStrains: no visible binding for global variable ‘png’
plotStrains: no visible binding for global variable ‘tiff’
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
actvspred: no visible global function definition for ‘quantile’
actvspred: no visible global function definition for ‘aggregate’
actvspred: no visible global function definition for ‘par’
actvspred: no visible global function definition for ‘plot’
actvspred: no visible global function definition for ‘lines’
auc: no visible global function definition for ‘par’
auc: no visible global function definition for ‘plot’
decile: no visible global function definition for ‘quantile’
dqcontinuous : numoutliers: no visible global function definition for
  ‘quantile’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘sd’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘quantile’
gini: no visible global function definition for ‘par’
gini: no visible global function definition for ‘plot’
gini: no visible global function definition for ‘abline’
iv: no visible global function definition for ‘quantile’
iv: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘par’
ks: no visible global function definition for ‘plot’
ks: no visible global function definition for ‘lines’
outliers: no visible global function definition for ‘quantile’
outliers: no visible global function definition for ‘na.omit’
pentile: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline aggregate lines na.omit par plot quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
getStp: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘plot’
plot.steeptest: no visible global function definition for ‘axis’
plot.steeptest: no visible global function definition for ‘box’
plot.steeptest: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘abline’
plot.steeptest: no visible global function definition for ‘legend’
plot.steeptest: no visible global function definition for
  ‘as.graphicsAnnot’
steeptest: no visible global function definition for ‘lm’
summary.steeptest: no visible global function definition for ‘var’
summary.steeptest: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm plot quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend", "plot")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
identifyGraph: no visible global function definition for ‘phyper’
mytriangle: no visible global function definition for ‘symbols’
plotGraph: no visible global function definition for ‘par’
plotGraph: no visible global function definition for ‘plot’
updateOrgEnvir: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  par phyper plot read.table symbols
Consider adding
  importFrom("graphics", "par", "plot", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
playSudoku : replot: no visible global function definition for ‘par’
playSudoku : replot: no visible global function definition for ‘plot’
playSudoku : replot: no visible global function definition for
  ‘segments’
playSudoku : replot: no visible global function definition for ‘text’
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
  ‘getGraphicsEvent’
playSudoku: no visible global function definition for ‘tkbind’
playSudoku: no visible global function definition for ‘tkwait.window’
Undefined global functions or variables:
  getGraphicsEvent par plot segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "plot", "segments", "text")
to your NAMESPACE file.
SUE.fitted.values: no visible global function definition for
  ‘model.frame’
SUE.lm: no visible global function definition for ‘model.frame’
SUE.lm: no visible global function definition for ‘lm’
SUE.lm: no visible global function definition for ‘anova’
SUE.plot: no visible global function definition for ‘plot’
SUE.residuals: no visible global function definition for ‘model.frame’
parameters : para2: no visible global function definition for ‘uniroot’
parameters: no visible global function definition for ‘optimize’
parameters: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  anova lm model.frame optimize plot uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for ‘plot’
plot.survAUC: no visible global function definition for ‘lines’
plot.survErr: no visible global function definition for ‘plot’
plot.survErr: no visible global function definition for ‘lines’
schemper: no visible global function definition for ‘predict’
schemper: no visible global function definition for ‘survfit’
schemper: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx lines plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
pearson: no visible global function definition for ‘cor’
plot.survcorr: no visible global function definition for ‘pnorm’
plot.survcorr: no visible global function definition for ‘par’
plot.survcorr: no visible global function definition for ‘plot’
plot.survcorr: no visible global function definition for ‘points’
survcorr: no visible global function definition for ‘model.frame’
survcorr: no visible global function definition for ‘qnorm’
survcorr: no visible global function definition for ‘runif’
survcorr: no visible global function definition for ‘pnorm’
survcorr: no visible global function definition for ‘var’
survcorr: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
Est.HR.FUN: no visible global function definition for ‘coxph’
Est.HR.FUN: no visible global function definition for ‘basehaz’
Est.HR.FUN: no visible global function definition for ‘approx’
Ghat.FUN: no visible global function definition for ‘survfit’
IDI.INF: no visible global function definition for ‘kmcens’
IDI.INF: no visible global function definition for ‘quantile’
IDI.INF.GRAPH: no visible global function definition for ‘plot’
IDI.INF.GRAPH: no visible global function definition for ‘lines’
IDI.INF.GRAPH: no visible global function definition for ‘abline’
IDI.INF.GRAPH: no visible global function definition for ‘points’
IDI.INF.GRAPH: no visible global function definition for ‘title’
PTB.IDI.FUN: no visible global function definition for ‘rexp’
shade: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines plot points polygon quantile
  rexp survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points", "polygon",
             "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
svycox.calibrate: no visible global function definition for ‘quantile’
svycox.calibrate: no visible binding for global variable ‘median’
svycox.calibrate: no visible global function definition for
  ‘as.formula’
svycox.calibrate: no visible global function definition for ‘plot’
svycox.calibrate: no visible global function definition for ‘arrows’
svycox.calibrate: no visible global function definition for ‘abline’
svycox.nomogram: no visible global function definition for ‘predict’
svycox.nomogram: no visible global function definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘formula’
Undefined global functions or variables:
  abline arrows as.formula formula median plot predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows", "plot")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
Rd file 'SyNet-package.rd':
  \examples lines wider than 100 characters:
       # Run NAM method on the previously inferred sympatry network                                           

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

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

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

These lines will be truncated in the PDF manual.
mainNetFunction: no visible global function definition for ‘png’
mainNetFunction: no visible global function definition for ‘plot’
mainNetFunction: no visible global function definition for ‘lines’
mainNetFunction: no visible global function definition for ‘legend’
mainNetFunction: no visible global function definition for ‘dev.off’
plotPR: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘lines’
simulatedData: no visible global function definition for ‘rpois’
simulatedData : <anonymous>: no visible global function definition for
  ‘rpois’
simulatedData : rlognormpois: no visible global function definition for
  ‘rnorm’
simulatedData : rlognormpois: no visible global function definition for
  ‘rpois’
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
Running ‘testthat.R’ [25s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(taxa)
  
  Attaching package: 'taxa'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  > 
  > test_check("taxa")
  ── 1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ── 3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers
  test_obj$data$my_data$taxon_id not equal to c("j", "i").
  names for target but not for current
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 607 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#52) 
  2. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#56) 
  3. Failure: Taxmap can be intialized from complex data (@test--taxmap_parsers.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
BootTree: no visible global function definition for ‘hclust’
BootTree: no visible global function definition for ‘dist’
BootTree: no visible global function definition for ‘as.dist’
BootTree: no visible global function definition for ‘cor’
BootTree: no visible binding for global variable ‘var’
Pgpd: no visible global function definition for ‘optim’
Pgpd : <anonymous>: no visible global function definition for ‘optim’
Pgpd: no visible global function definition for ‘var’
Pgpd: no visible global function definition for ‘rnorm’
Pgpd: no visible global function definition for ‘quantile’
Pvalue: no visible global function definition for ‘rnorm’
SigTree: no visible global function definition for ‘data’
TreeStat: no visible global function definition for ‘hclust’
TreeStat: no visible global function definition for ‘as.dist’
TreeStat: no visible global function definition for ‘dist’
TreeStat: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘hclust’
plot.best: no visible global function definition for ‘as.dist’
plot.best: no visible global function definition for ‘dist’
plot.best: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘plot’
treetext: no visible global function definition for ‘par’
treetext: no visible global function definition for ‘text’
Undefined global functions or variables:
  as.dist cor data dist hclust optim par plot quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/terra.Rcheck/00install.out’ for details.
phyper_right: no visible global function definition for ‘dhyper’
progression: no visible global function definition for ‘density’
progression: no visible global function definition for ‘plot’
progression: no visible global function definition for ‘points’
progression: no visible global function definition for ‘legend’
progression: no visible global function definition for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘dhyper’
specificities.distribution.plot: no visible global function definition
  for ‘plot’
specificities.distribution.plot: no visible global function definition
  for ‘Axis’
specificities.distribution.plot: no visible global function definition
  for ‘arrows’
specificities.distribution.plot: no visible global function definition
  for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘title’
specificities.probabilities.vector: no visible global function
  definition for ‘phyper’
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
coef_traceplot: no visible global function definition for ‘rainbow’
coef_traceplot: no visible global function definition for ‘plot’
coef_traceplot: no visible global function definition for ‘abline’
coef_traceplot : <anonymous>: no visible global function definition for
  ‘lines’
coef_traceplot: no visible global function definition for ‘text’
ee.GEE.aux : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running ‘testthat.R’ [17s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidytext)
  > 
  > test_check("tidytext")
  ── 1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15)  ────
  paste(as.character(ovid[[1]]), collapse = " ") not equal to td$text[1].
  names for current but not for target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 297 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Can tidy corpus from tm package (@test-corpus-tidiers.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: `data_frame()` is deprecated as of tibble 1.1.0.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/tidytree.Rcheck/00install.out’ for details.
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘plot’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Warning in x :
  closing unused connection 4 (https://www.tiobe.com/tiobe-index/)
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
tipom.car: no visible global function definition for ‘abline’
tipom.car: no visible global function definition for ‘axis’
tipom.heat: no visible global function definition for ‘image’
tipom.heat: no visible global function definition for ‘gray’
tipom.lw: no visible global function definition for ‘plot’
tipom.lw: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import ‘sf::st_make_valid’ by ‘lwgeom::st_make_valid’ when loading ‘tmap’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/tmap.Rcheck/00install.out’ for details.
ConfA: no visible global function definition for ‘qf’
EstM2Sn: no visible global function definition for ‘nlm’
EstM2Sn: no visible global function definition for ‘qnorm’
TV.model: no visible global function definition for ‘dev.new’
TV.model: no visible global function definition for ‘points’
betaBino: no visible global function definition for ‘pbinom’
doseD: no visible global function definition for ‘lm’
doseD: no visible global function definition for ‘dev.new’
doseD: no visible global function definition for ‘par’
doseD: no visible global function definition for ‘plot’
doseD: no visible global function definition for ‘axTicks’
doseD: no visible global function definition for ‘axis’
doseD: no visible global function definition for ‘lines’
doseD: no visible global function definition for ‘abline’
doseD: no visible global function definition for ‘legend’
setD: no visible global function definition for ‘dev.new’
setD: no visible global function definition for ‘par’
setD: no visible global function definition for ‘pbinom’
setD: no visible global function definition for ‘abline’
setD: no visible global function definition for ‘axis’
setD: no visible global function definition for ‘rect’
setD: no visible global function definition for ‘lines’
setD: no visible global function definition for ‘text’
setD: no visible global function definition for ‘axTicks’
setD: no visible global function definition for ‘legend’
spoD : spoD_A: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
LikAge: no visible global function definition for ‘read.table’
bd.ME.optim: no visible global function definition for ‘optim’
bd.ME.optim.rho: no visible global function definition for ‘optim’
bd.ME.optim.rho.all: no visible global function definition for ‘optim’
bd.MEyule.optim: no visible global function definition for ‘optimize’
bd.MEyule.optim: no visible global function definition for ‘optim’
bd.age.optim.matlab: no visible global function definition for
  ‘read.table’
bd.groups.conf: no visible global function definition for ‘uniroot’
bd.shifts.plot: no visible global function definition for ‘plot’
bd.shifts.plot: no visible global function definition for ‘lines’
bdsky.stt.optim: no visible global function definition for ‘optim’
create.mat: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines optim optimize plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
HtoGp: no visible global function definition for ‘odd’
HtoGp: no visible global function definition for ‘even’
plot.pirls.gam: no visible global function definition for ‘par’
plot.pirls.gam: no visible global function definition for ‘plot’
plot.pirls.gam: no visible global function definition for ‘title’
plot.pirls.gam: no visible global function definition for ‘lines’
plot.pirls.gam: no visible global function definition for ‘rug’
plot.pirls.gam: no visible global function definition for ‘mtext’
test.trioGxE: no visible global function definition for ‘write.table’
trioGxE: no visible global function definition for ‘quantile’
trioGxE: no visible global function definition for ‘qtnorm’
trioplot: no visible global function definition for ‘quantile’
trioplot: no visible global function definition for ‘formula’
trioplot: no visible global function definition for ‘gam’
trioplot: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
cdens: no visible global function definition for ‘head’
dplot: no visible global function definition for ‘knots’
dplot: no visible global function definition for ‘median’
dplot: no visible global function definition for ‘par’
dplot: no visible global function definition for ‘plot.stepfun’
dplot: no visible global function definition for ‘abline’
edf: no visible global function definition for ‘approxfun’
mctest : rdist: no visible global function definition for ‘runif’
mctest : S: no visible global function definition for ‘optim’
qplot: no visible global function definition for ‘plot’
qplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approxfun head knots median optim par plot plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
dLag : dlag.f: no visible global function definition for
  ‘complete.cases’
distmat: no visible global function definition for ‘dist’
fitCity: no visible global function definition for ‘glm.control’
fitCity: no visible global function definition for ‘terms’
ldmvnorm: no visible global function definition for ‘mahalanobis’
lspline: no visible global function definition for ‘quantile’
plot.tsdecomp: no visible global function definition for ‘par’
plot.tsdecomp: no visible global function definition for ‘plot’
setupFormula: no visible global function definition for ‘as.formula’
spatialgibbs: no visible global function definition for ‘rnorm’
spatialgibbs: no visible global function definition for ‘rgamma’
spatialgibbs: no visible global function definition for ‘runif’
tsdecomp: no visible global function definition for ‘fft’
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
Crm: no visible global function definition for ‘integrate’
Crm : <anonymous>: no visible global function definition for
  ‘integrate’
Crm: no visible global function definition for ‘optimize’
ail1: no visible global function definition for ‘uniroot’
ail2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ail2: no visible global function definition for ‘uniroot’
aip : fu : <anonymous>: no visible global function definition for
  ‘integrate’
aip: no visible global function definition for ‘uniroot’
ait1: no visible global function definition for ‘uniroot’
ait2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ait2: no visible global function definition for ‘uniroot’
sim3p3: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘palette’
simCrm: no visible global function definition for ‘gray’
simCrm: no visible global function definition for ‘plot’
simCrm: no visible global function definition for ‘abline’
simCrm: no visible global function definition for ‘lines’
ssim3p3: no visible global function definition for ‘txtProgressBar’
ssim3p3: no visible global function definition for ‘setTxtProgressBar’
ssimCrm: no visible global function definition for ‘txtProgressBar’
ssimCrm: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘UniprotR.Rmd’ using rmarkdown
Quitting from lines 47-48 (UniprotR.Rmd) 
Error: processing vignette 'UniprotR.Rmd' failed with diagnostics:
R: improper image header `/tmp/Rtmp1Y1xfx/file4ad277c33c57.png' @ error/png.c/ReadPNGImage/4092
--- failed re-building ‘UniprotR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Mammen: no visible global function definition for ‘runif’
PR2: no visible global function definition for ‘ar.burg’
PR2: no visible global function definition for ‘pt’
PR2: no visible global function definition for ‘pf’
PR3: no visible global function definition for ‘ar.burg’
PR3: no visible global function definition for ‘pt’
PR3: no visible global function definition for ‘pf’
VAR.FOR: no visible global function definition for ‘qnorm’
VAR.ForeB: no visible global function definition for ‘runif’
VAR.LRtest: no visible global function definition for ‘pchisq’
VAR.LRtest: no visible global function definition for ‘pf’
VAR.PI: no visible global function definition for ‘quantile’
VAR.Waldtest: no visible global function definition for ‘pf’
VAR.irf: no visible global function definition for ‘par’
VAR.irf: no visible global function definition for ‘plot’
VAR.irf: no visible global function definition for ‘abline’
VAR1.sim: no visible global function definition for ‘rnorm’
resamp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Compare2FDS: no visible global function definition for ‘runif’
Compare2FDS: no visible global function definition for ‘lm’
Compare2FDS: no visible global function definition for ‘model.matrix’
Compare2FDS: no visible global function definition for ‘plot’
Compare2FDS: no visible global function definition for ‘abline’
Compare2FDS: no visible global function definition for ‘lines’
Compare2FDS: no visible global function definition for ‘text’
Compare2Vdg: no visible global function definition for ‘par’
Compare2Vdg: no visible global function definition for ‘plot’
Compare2Vdg: no visible global function definition for ‘lines’
Compare2Vdg: no visible global function definition for ‘legend’
FDSPlot: no visible global function definition for ‘runif’
FDSPlot: no visible global function definition for ‘lm’
FDSPlot: no visible global function definition for ‘model.matrix’
FDSPlot: no visible global function definition for ‘plot’
FDSPlot: no visible global function definition for ‘abline’
Vdgraph: no visible global function definition for ‘par’
Vdgraph: no visible global function definition for ‘plot’
Vdgraph: no visible global function definition for ‘lines’
Vdgraph: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
Decile.Plot: no visible global function definition for ‘barplot’
Decile.Plot: no visible global function definition for ‘axis’
Sliding.Window: no visible global function definition for ‘plot’
Sliding.Window: no visible global function definition for ‘lines’
Sliding.Window: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
plotTrait: no visible global function definition for ‘plot’
plotTrait: no visible global function definition for ‘points’
plotTrait: no visible global function definition for ‘legend’
test.windex: no visible global function definition for ‘hist’
test.windex: no visible global function definition for ‘abline’
test.windex: no visible global function definition for ‘legend’
windex: no visible global function definition for ‘sd’
windex: no visible global function definition for ‘var’
windex: no visible global function definition for ‘dist’
windex: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for ‘lm’
plotfit,Leader: no visible global function definition for ‘par’
plotfit,Leader: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
simul.wsvm: no visible binding for global variable ‘mixture.example’
wsvm.boost: no visible global function definition for ‘plot’
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘zoomgrid-vignette.Rmd’ using rmarkdown
Could not fetch https://latex.codecogs.com/gif.latex?f%28x_1%2C%20x_2%29%20%3D%202%20A%20+%20%5Csum_%7Bi%3D1%7D%5E2%20%5Cleft%28%20x_i%5E2%20-%20A%20%5Ccos%282%20%5Cpi%20x_i%29%20%5Cright%29
HttpExceptionRequest Request {
  host                 = "latex.codecogs.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/gif.latex"
  queryString          = "?f%28x_1%2C%20x_2%29%20%3D%202%20A%20+%20%5Csum_%7Bi%3D1%7D%5E2%20%5Cleft%28%20x_i%5E2%20-%20A%20%5Ccos%282%20%5Cpi%20x_i%29%20%5Cright%29"
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 ConnectionTimeout
Error: processing vignette 'zoomgrid-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘zoomgrid-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
multiplot: no visible global function definition for 'rainbow'
multiplot: no visible global function definition for 'plot'
multiplot: no visible global function definition for 'text'
multiplot: no visible global function definition for 'lines'
multiplot: no visible global function definition for 'par'
plot.abf2: no visible global function definition for 'plot'
plot.abf2: no visible global function definition for 'abline'
plot.abf2: no visible global function definition for 'text'
plot.abf2split: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline lines par plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "par", "plot", "text")
to your NAMESPACE file.
fillCSVData: no visible global function definition for 'read.table'
fillData: no visible global function definition for 'edit'
plotGraphs: no visible global function definition for 'par'
plotGraphs: no visible global function definition for 'plot'
plotGraphs: no visible global function definition for 'lines'
plotGraphs: no visible global function definition for 'legend'
plotGraphs: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new edit legend lines par plot read.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    R  13.7Mb
Package suggested but not available for checking: 'REBayes'
get.est.ATT: no visible global function definition for 'tail'
get.est.MT: no visible global function definition for 'tail'
get.est.simple: no visible global function definition for 'tail'
newton.r: no visible global function definition for 'tail'
plot.ATE: no visible global function definition for 'par'
plot.ATE: no visible global function definition for 'plot'
plot.ATE: no visible global function definition for 'axis'
plot.ATE: no visible global function definition for 'abline'
plot.ATE: no visible global function definition for 'lines'
plot.ATE: no visible global function definition for 'legend'
plot.ATE: no visible global function definition for 'points'
print.summary.ATE: no visible global function definition for
  'printCoefmat'
summary.ATE: no visible global function definition for 'qnorm'
summary.ATE: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis legend lines par plot pnorm points printCoefmat qnorm
  tail
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "points")
  importFrom("stats", "pnorm", "printCoefmat", "qnorm")
  importFrom("utils", "tail")
to your NAMESPACE file.
atmcmc : rmvtnorm: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'rnorm'
atmcmc: no visible global function definition for 'runif'
atmcmc: no visible global function definition for 'par'
atmcmc: no visible global function definition for 'lm'
atmcmc: no visible global function definition for 'lines'
atmcmc: no visible global function definition for 'var'
atmcmc: no visible global function definition for 'cov'
atmcmc: no visible global function definition for 'quantile'
atmcmc: no visible global function definition for 'sd'
plotmcmc: no visible global function definition for 'pdf'
plotmcmc: no visible global function definition for 'par'
plotmcmc: no visible global function definition for 'dev.new'
plotmcmc: no visible global function definition for 'png'
plotmcmc: no visible global function definition for 'hist'
plotmcmc: no visible global function definition for 'dev.off'
plotmcmc: no visible global function definition for 'plot'
plotmcmc: no visible global function definition for 'lines'
Undefined global functions or variables:
  cov dev.new dev.off hist lines lm par pdf plot png quantile rnorm
  runif sd var
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf", "png")
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "cov", "lm", "quantile", "rnorm", "runif", "sd",
             "var")
to your NAMESPACE file.
plot.AUC: no visible global function definition for 'plot'
plot.AUC: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot
Consider adding
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(autocogs)
  > 
  > test_check("autocogs")
  -- 1. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246)  ---------------------
  EXPR must be a length 1 vector
  Backtrace:
    1. ggplot2::qplot(cty, hwy, data = mpg, geom = "smooth")
    9. autocogs:::expect_auto_cogs(...)
   11. autocogs:::plot_cogs(.)
   19. autocogs:::get_layer_info(p, keep = keep_layers, ...)
   21. autocogs:::layer_info.ggplot(p, keep = keep, ...)
   22. base::lapply(...)
   23. autocogs:::FUN(X[[i]], ...)
  
  == testthat results  ===========================================================
  [ OK: 242 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: ggplot2::geom_smooth (@test-plot_cogs.R#246) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

  Natural language support but running in an English locale

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

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

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.3Mb
    libs   1.8Mb
BACprior.CV: no visible global function definition for 'na.fail'
BACprior.CV: no visible global function definition for 'plot'
BACprior.CV: no visible global function definition for 'abline'
BACprior.boot: no visible global function definition for 'na.fail'
BACprior.boot: no visible global function definition for 'plot'
BACprior.boot: no visible global function definition for 'abline'
BACprior.lm: no visible global function definition for 'na.fail'
BACprior.lm: no visible global function definition for 'coef'
BACprior.lm: no visible global function definition for 'vcov'
Undefined global functions or variables:
  abline coef na.fail plot vcov
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("stats", "coef", "na.fail", "vcov")
to your NAMESPACE file.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
MHratioPopPref: no visible global function definition for 'runif'
MratioPopMult: no visible global function definition for 'dunif'
MratioPopMult: no visible global function definition for 'runif'
bayesPref: no visible global function definition for 'runif'
calcP: no visible global function definition for 'dunif'
calcP: no visible global function definition for 'dmultinom'
calcdic: no visible global function definition for 'median'
calcdic: no visible binding for global variable 'median'
calcdic: no visible global function definition for 'dmultinom'
calcdicExtern: no visible global function definition for 'median'
calcdicExtern: no visible global function definition for 'dmultinom'
calcdicExtern: no visible binding for global variable 'median'
credibleIntervals: no visible global function definition for 'quantile'
prefPlot: no visible global function definition for 'postscript'
prefPlot: no visible global function definition for 'plot'
prefPlot: no visible global function definition for 'lines'
prefPlot: no visible global function definition for 'density'
prefPlot: no visible global function definition for 'median'
prefPlot: no visible global function definition for 'legend'
prefPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  density dev.off dmultinom dunif legend lines median plot postscript
  quantile runif
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "density", "dmultinom", "dunif", "median",
             "quantile", "runif")
to your NAMESPACE file.
validate: no visible binding for global variable 'qnorm'
validate: no visible global function definition for 'pchisq'
validate: no visible global function definition for 'qnorm'
validate: no visible global function definition for 'plot'
validate: no visible global function definition for 'axis'
validate: no visible global function definition for 'points'
validate: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis pchisq plot points qnorm
Consider adding
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "pchisq", "qnorm")
to your NAMESPACE file.
bbo: no visible global function definition for 'runif'
bbo: no visible global function definition for 'tail'
plot.bbo: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot runif tail
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
plot.cvsvd: no visible binding for global variable 'sd'
plot.cvsvd: no visible global function definition for 'plot'
plot.cvsvd: no visible global function definition for 'lines'
plot.cvsvd: no visible global function definition for 'segments'
plot.cvsvd: no visible global function definition for 'points'
print.cvsvd: no visible binding for global variable 'sd'
summary.cvsvd: no visible binding for global variable 'sd'
Undefined global functions or variables:
  lines plot points sd segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
beadtypeFilter: no visible global function definition for 'na.omit'
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'
emCDF: no visible global function definition for 'plot'
emCDF: no visible global function definition for 'ecdf'
emCDF: no visible global function definition for 'legend'
emCDF: no visible global function definition for 'lines'
emCDF: no visible global function definition for 'text'
emCDF: no visible global function definition for 'reshape'
iccFun : <anonymous>: no visible global function definition for
  'quantile'
varianceplot: no visible global function definition for 'reshape'
varianceplot: no visible global function definition for 'plot'
varianceplot: no visible global function definition for 'points'
varianceplot: no visible global function definition for 'legend'
Undefined global functions or variables:
  beadNum brewer.pal ecdf exprs fData legend lines na.omit plot points
  quantile reshape se.exprs text
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text")
  importFrom("stats", "ecdf", "na.omit", "quantile", "reshape")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 134.1Mb
  sub-directories of 1Mb or more:
    include  133.1Mb
Running 'spelling.R' [0s]
  Running 'testthat.R' [291s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(bigsnpr)
  Loading required package: bigstatsr
  > 
  > test_check("bigsnpr", filter = "7-")
  == testthat results  ===========================================================
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
  > test_check("bigsnpr", filter = "1-")
  == testthat results  ===========================================================
  [ OK: 166 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
  > test_check("bigsnpr", filter = "2-")
  == testthat results  ===========================================================
  [ OK: 32 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 0 ]
  > test_check("bigsnpr", filter = "3-")
  -- 1. Failure: (unknown) (@test-3-plink-QC.R#14)  ------------------------------
  grepl("plink2", plink2) isn't true.
  
  -- 2. Error: (unknown) (@test-3-plink-QC.R#15)  --------------------------------
  '--version' not found
  Backtrace:
   1. base::system(paste(plink2, "--version"), intern = TRUE)
  
  == testthat results  ===========================================================
  [ OK: 12 | SKIPPED: 1 | WARNINGS: 2 | FAILED: 2 ]
  1. Failure: (unknown) (@test-3-plink-QC.R#14) 
  2. Error: (unknown) (@test-3-plink-QC.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
BOGest: no visible global function definition for 'read.table'
BOGstat: no visible global function definition for 'phyper'
BOGstat: no visible global function definition for 'wilcox.test'
BOGstat: no visible global function definition for 'p.adjust'
gseaplot: no visible global function definition for 'par'
gseaplot: no visible global function definition for 'plot'
gseaplot: no visible global function definition for 'points'
gseaplot: no visible global function definition for 'axis'
gseaplot: no visible global function definition for 'segments'
hgplot: no visible global function definition for 'par'
hgplot: no visible global function definition for 'barplot'
Undefined global functions or variables:
  axis barplot p.adjust par phyper plot points read.table segments
  wilcox.test
Consider adding
  importFrom("graphics", "axis", "barplot", "par", "plot", "points",
             "segments")
  importFrom("stats", "p.adjust", "phyper", "wilcox.test")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is 59.8Mb
  sub-directories of 1Mb or more:
    include   8.8Mb
    lib      50.6Mb
bPeaksAnalysis: no visible global function definition for 'write.table'
dataReading: no visible global function definition for 'read.table'
dataSmoothing: no visible global function definition for 'filter'
peakDetection: no visible global function definition for 'quantile'
peakDetection: no visible global function definition for 'pdf'
peakDetection: no visible global function definition for 'par'
peakDetection: no visible global function definition for 'plot'
peakDetection: no visible global function definition for 'text'
peakDetection: no visible global function definition for 'abline'
peakDetection: no visible global function definition for 'points'
peakDetection: no visible global function definition for 'dev.off'
peakDetection: no visible global function definition for 'write.table'
peakDrawing: no visible global function definition for 'par'
peakDrawing: no visible global function definition for 'plot'
peakDrawing: no visible global function definition for 'abline'
peakLocation: no visible global function definition for 'read.table'
peakLocation: no visible global function definition for 'pdf'
peakLocation: no visible global function definition for 'barplot'
peakLocation: no visible global function definition for 'dev.off'
peakLocation: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline barplot dev.off filter par pdf plot points quantile read.table
  text write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "abline", "barplot", "par", "plot", "points",
             "text")
  importFrom("stats", "filter", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
apply.breaks: no visible binding for global variable 'median'
break.clust: no visible global function definition for 'plot'
break.clust: no visible global function definition for 'median'
breakage.plot: no visible binding for global variable 'median'
breakage.plot: no visible global function definition for 'plot'
breakage.plot: no visible global function definition for 'abline'
breakage.plot: no visible global function definition for 'lm'
find.bottom: no visible global function definition for 'filter'
fit.breakage: no visible global function definition for 'optim'
fit.breakage: no visible global function definition for 'plot'
fit.breakage: no visible global function definition for 'points'
fit.sensitivity.plot: no visible global function definition for
  'contour'
fit.sensitivity.plot: no visible global function definition for
  'points'
fit.sensitivity.plot: no visible global function definition for 'text'
Undefined global functions or variables:
  abline contour filter lm median optim plot points text
Consider adding
  importFrom("graphics", "abline", "contour", "plot", "points", "text")
  importFrom("stats", "filter", "lm", "median", "optim")
to your NAMESPACE file.
plot.bspec: no visible global function definition for 'par'
plot.bspec: no visible global function definition for 'plot'
plot.bspec: no visible global function definition for 'matlines'
plot.bspec: no visible global function definition for 'points'
plot.bspec: no visible global function definition for 'axis'
plot.bspec: no visible global function definition for 'mtext'
plot.bspec: no visible global function definition for 'axTicks'
plot.bspec: no visible global function definition for 'box'
plot.bspecACF: no visible global function definition for 'plot'
plot.bspecACF: no visible global function definition for 'abline'
plot.bspecACF: no visible global function definition for 'matlines'
Undefined global functions or variables:
  abline axTicks axis box matlines mtext par plot points
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "box", "matlines",
             "mtext", "par", "plot", "points")
to your NAMESPACE file.
plot.bursts: no visible global function definition for 'plot'
plot.bursts: no visible global function definition for 'axis'
plot.bursts: no visible global function definition for 'arrows'
Undefined global functions or variables:
  arrows axis plot
Consider adding
  importFrom("graphics", "arrows", "axis", "plot")
to your NAMESPACE file.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for 'cor'
img.estim.regul: no visible global function definition for 'par'
img.estim.regul: no visible global function definition for 'image'
img.estim.regul: no visible global function definition for
  'heat.colors'
img.estim.regul: no visible global function definition for 'axis'
img.estim.regul: no visible global function definition for 'box'
img.matcor: no visible global function definition for 'par'
img.matcor: no visible global function definition for 'image'
img.matcor: no visible global function definition for 'box'
img.matcor: no visible global function definition for 'abline'
img.matcor: no visible global function definition for 'layout'
loo: no visible global function definition for 'cor'
matcor: no visible global function definition for 'cor'
plt.cc: no visible global function definition for 'par'
plt.cc: no visible global function definition for 'layout'
plt.indiv: no visible global function definition for 'plot'
plt.indiv: no visible global function definition for 'text'
plt.indiv: no visible global function definition for 'abline'
plt.var: no visible global function definition for 'plot'
plt.var: no visible global function definition for 'points'
plt.var: no visible global function definition for 'text'
plt.var: no visible global function definition for 'abline'
plt.var: no visible global function definition for 'lines'
rcc: no visible global function definition for 'var'
rcc: no visible global function definition for 'cov'
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
ccd.sequential: no visible global function definition for 'qchisq'
dominate.random.sample: no visible global function definition for
  'runif'
draw.circle: no visible global function definition for 'polygon'
juggle2: no visible global function definition for 'rbinom'
plot.cccd: no visible global function definition for 'gray'
plot.cccd: no visible global function definition for 'plot'
plot.cccd: no visible global function definition for 'points'
plot.cccdClassifier: no visible global function definition for 'points'
plot.cccdClassifier: no visible global function definition for 'plot'
plot.ccd: no visible global function definition for 'plot'
Undefined global functions or variables:
  gray plot points polygon qchisq rbinom runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot", "points", "polygon")
  importFrom("stats", "qchisq", "rbinom", "runif")
to your NAMESPACE file.
p.Roy: no visible global function definition for 'pf'
p.asym: no visible global function definition for 'pf'
p.perm: no visible global function definition for 'cancor'
plt.asym: no visible global function definition for 'qf'
plt.asym: no visible global function definition for 'plot'
plt.asym: no visible global function definition for 'df'
plt.asym: no visible global function definition for 'abline'
plt.perm: no visible global function definition for 'hist'
plt.perm: no visible global function definition for 'mtext'
plt.perm: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline cancor df hist mtext pf plot qf
Consider adding
  importFrom("graphics", "abline", "hist", "mtext", "plot")
  importFrom("stats", "cancor", "df", "pf", "qf")
to your NAMESPACE file.
CM: no visible global function definition for 'sd'
Erf: no visible global function definition for 'pnorm'
Erfc: no visible global function definition for 'pnorm'
boot.Cenarma: no visible global function definition for 'coef'
boot.Cenarma: no visible global function definition for 'arima.sim'
cenarma: no visible global function definition for 'arima'
cenarma: no visible global function definition for 'coef'
cenarma: no visible global function definition for 'ARMAacf'
cenarma: no visible global function definition for 'var'
plot.cents: no visible global function definition for 'plot'
plot.cents: no visible global function definition for 'segments'
plot.cents: no visible global function definition for 'rgb'
plot.cents: no visible global function definition for 'points'
rcarma: no visible global function definition for 'arima.sim'
rcarma: no visible global function definition for 'quantile'
scenNID: no visible global function definition for 'sd'
se.Cenarma: no visible global function definition for 'coef'
se.Cenarma: no visible global function definition for 'sd'
Undefined global functions or variables:
  ARMAacf arima arima.sim coef plot pnorm points quantile rgb sd
  segments var
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "ARMAacf", "arima", "arima.sim", "coef", "pnorm",
             "quantile", "sd", "var")
to your NAMESPACE file.
sw.plot : <anonymous>: no visible global function definition for
  'median'
sw.plot : <anonymous>: no visible global function definition for 'mad'
sw.plot : my.line: no visible global function definition for 'lines'
sw.plot : island.line: no visible global function definition for
  'lines'
sw.plot: no visible global function definition for 'plot'
sw.plot: no visible global function definition for 'rug'
sw.plot: no visible global function definition for 'axis'
sw.plot: no visible global function definition for 'mtext'
sw.plot: no visible global function definition for 'abline'
sw.plot: no visible global function definition for 'points'
sw.rob : <anonymous>: no visible global function definition for
  'median'
sw.rob : <anonymous>: no visible global function definition for 'mad'
sw.threshold : <anonymous>: no visible global function definition for
  'median'
sw.threshold : <anonymous>: no visible global function definition for
  'mad'
Undefined global functions or variables:
  abline axis lines mad median mtext plot points rug
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "plot",
             "points", "rug")
  importFrom("stats", "mad", "median")
to your NAMESPACE file.
CityPlot: no visible global function definition for 'read.table'
CityPlot: no visible global function definition for 'tail'
CityPlot: no visible global function definition for 'pdf'
CityPlot: no visible global function definition for 'split.screen'
CityPlot: no visible global function definition for 'screen'
CityPlot: no visible global function definition for 'par'
CityPlot: no visible global function definition for 'plot'
CityPlot: no visible global function definition for 'rect'
CityPlot: no visible global function definition for 'text'
CityPlot: no visible global function definition for 'lines'
CityPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off lines par pdf plot read.table rect screen split.screen tail
  text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "rect", "screen",
             "split.screen", "text")
  importFrom("utils", "read.table", "tail")
to your NAMESPACE file.
alpha.cronbach: no visible global function definition for 'cov'
alpha.curve: no visible global function definition for 'plot'
alpha.curve: no visible global function definition for 'text'
Undefined global functions or variables:
  cov plot text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "cov")
to your NAMESPACE file.
copynumberBootstrap: no visible global function definition for
  'txtProgressBar'
copynumberBootstrap: no visible global function definition for
  'quantile'
copynumberBootstrap: no visible global function definition for
  'setTxtProgressBar'
gethits: no visible global function definition for 'read.table'
normalizeGC: no visible global function definition for 'median'
plotCNOGpro: no visible global function definition for 'par'
plotCNOGpro: no visible global function definition for 'plot'
plotCNOGpro: no visible global function definition for 'rainbow'
plotCNOGpro: no visible global function definition for 'density'
plotCNOGpro: no visible global function definition for 'polygon'
plotCNOGpro: no visible global function definition for 'lines'
plotCNOGpro: no visible global function definition for 'legend'
plotCNOGpro: no visible global function definition for 'boxplot'
sampleChromosome: no visible global function definition for 'median'
sampleChromosome: no visible binding for global variable 'var'
setupEmissionMatrix: no visible global function definition for 'dgeom'
store: no visible global function definition for 'write.table'
Undefined global functions or variables:
  boxplot density dgeom legend lines median par plot polygon quantile
  rainbow read.table setTxtProgressBar txtProgressBar var write.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "boxplot", "legend", "lines", "par", "plot",
             "polygon")
  importFrom("stats", "density", "dgeom", "median", "quantile", "var")
  importFrom("utils", "read.table", "setTxtProgressBar",
             "txtProgressBar", "write.table")
to your NAMESPACE file.
coalescentMCMC: no visible global function definition for
  'packageVersion'
coalescentMCMC : getparams: no visible global function definition for
  'nlminb'
sim.coalescent: no visible global function definition for 'plot'
sim.coalescent: no visible global function definition for 'segments'
sim.coalescent: no visible global function definition for 'points'
Undefined global functions or variables:
  nlminb packageVersion plot points segments
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "nlminb")
  importFrom("utils", "packageVersion")
to your NAMESPACE file.
addxaxis: no visible global function definition for 'par'
addxaxis: no visible global function definition for 'axis'
addxaxis: no visible global function definition for 'mtext'
eplot: no visible global function definition for 'plot'
eplot: no visible global function definition for 'par'
eplot: no visible global function definition for 'axis'
eplot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis mtext par plot
Consider adding
  importFrom("graphics", "axis", "mtext", "par", "plot")
to your NAMESPACE file.
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(compstatr)
  > 
  > test_check("compstatr")
  -- 1. Failure: correct output is returned on sample data (@test_projectXY.R#36) 
  sf::st_crs(results)[[1]] not equal to 4269.
  Types not compatible: character is not double
  
  == testthat results  ===========================================================
  [ OK: 225 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: correct output is returned on sample data (@test_projectXY.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
conicPlot: no visible global function definition for 'palette'
conicPlotAsymptotes: no visible global function definition for
  'palette'
conicPlotAsymptotes: no visible global function definition for 'abline'
conicPlotAxes: no visible global function definition for 'palette'
conicPlotAxes: no visible global function definition for 'abline'
plotDegenerateConic: no visible global function definition for 'plot'
plotDegenerateConic: no visible global function definition for 'points'
plotDegenerateConic: no visible global function definition for 'abline'
plotEllipsis: no visible global function definition for 'lines'
plotEllipsis: no visible global function definition for 'plot'
plotEllipsis: no visible global function definition for 'points'
plotHyperbola: no visible global function definition for 'lines'
plotHyperbola: no visible global function definition for 'plot'
plotHyperbola: no visible global function definition for 'points'
plotParabola: no visible global function definition for 'lines'
plotParabola: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline lines palette plot points
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "lines", "plot", "points")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
maCooperative: no visible global function definition for 'points'
maCooperative: no visible global function definition for 'legend'
maPessimistic: no visible global function definition for 'combn'
maRules: no visible global function definition for 'capture.output'
mstCooperative: no visible global function definition for 'points'
mstCooperative: no visible global function definition for 'legend'
mstOptimistic: no visible global function definition for 'combn'
mstPessimistic: no visible global function definition for 'combn'
mstRules: no visible global function definition for 'capture.output'
plotCoreSet: no visible global function definition for 'points'
plotCoreSet: no visible global function definition for 'polygon'
plotImputationSet: no visible global function definition for 'par'
plotImputationSet: no visible global function definition for 'plot'
plotImputationSet: no visible global function definition for 'box'
plotImputationSet: no visible global function definition for 'polygon'
plotImputationSet: no visible global function definition for 'text'
shapleyValue: no visible global function definition for 'combn'
Undefined global functions or variables:
  box capture.output combn legend par plot points polygon text
Consider adding
  importFrom("graphics", "box", "legend", "par", "plot", "points",
             "polygon", "text")
  importFrom("utils", "capture.output", "combn")
to your NAMESPACE file.
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
CoxBoost: no visible global function definition for 'Matrix'
CoxBoost: no visible binding for global variable 'sd'
CoxBoost: no visible global function definition for 'predict'
cv.CoxBoost : eval.fold: no visible global function definition for
  'predict'
cv.CoxBoost: no visible global function definition for 'mclapply'
cv.CoxBoost: no visible binding for global variable 'sd'
estimPVal: no visible global function definition for 'mclapply'
iCoxBoost: no visible global function definition for 'terms'
iCoxBoost: no visible global function definition for 'model.response'
iCoxBoost: no visible global function definition for 'model.frame'
iCoxBoost: no visible global function definition for 'model.matrix'
iCoxBoost: no visible global function definition for 'Matrix'
plot.CoxBoost: no visible global function definition for 'plot'
plot.CoxBoost: no visible global function definition for 'lines'
plot.CoxBoost: no visible global function definition for 'text'
predict.iCoxBoost: no visible global function definition for
  'model.response'
predict.iCoxBoost: no visible global function definition for
  'model.frame'
predict.iCoxBoost: no visible global function definition for
  'model.matrix'
Undefined global functions or variables:
  Matrix lines mclapply model.frame model.matrix model.response plot
  predict sd terms text
Consider adding
  importFrom("graphics", "lines", "plot", "text")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "predict", "sd", "terms")
to your NAMESPACE file.
comp.graph: no visible global function definition for 'qnorm'
comp.graph: no visible global function definition for 'plot'
comp.graph: no visible global function definition for 'polygon'
comp.graph: no visible global function definition for 'lines'
cox.ridge: no visible global function definition for 'terms'
cox.ridge: no visible global function definition for 'model.extract'
cox.ridge: no visible global function definition for 'model.matrix'
cox.ridge: no visible binding for global variable 'hat'
Undefined global functions or variables:
  hat lines model.extract model.matrix plot polygon qnorm terms
Consider adding
  importFrom("graphics", "lines", "plot", "polygon")
  importFrom("stats", "hat", "model.extract", "model.matrix", "qnorm",
             "terms")
to your NAMESPACE file.
coxr: no visible global function definition for 'model.extract'
coxr: no visible global function definition for 'model.matrix'
coxr.draw: no visible global function definition for 'plot'
coxr.draw: no visible global function definition for 'lines'
coxr.draw: no visible global function definition for 'points'
coxr.fit: no visible global function definition for 'quantile'
gen_data: no visible global function definition for 'rnorm'
gen_data: no visible global function definition for 'rexp'
plot.coxr: no visible global function definition for 'quantile'
plot.coxr: no visible global function definition for 'par'
plot.coxr: no visible global function definition for 'mtext'
plot.coxr: no visible global function definition for 'title'
plot.coxr: no visible global function definition for 'split.screen'
plot.coxr: no visible global function definition for 'screen'
plot.coxr: no visible global function definition for 'close.screen'
print.coxr: no visible global function definition for 'pnorm'
print.coxr: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  close.screen lines model.extract model.matrix mtext par pchisq plot
  pnorm points quantile rexp rnorm screen split.screen title
Consider adding
  importFrom("graphics", "close.screen", "lines", "mtext", "par", "plot",
             "points", "screen", "split.screen", "title")
  importFrom("stats", "model.extract", "model.matrix", "pchisq", "pnorm",
             "quantile", "rexp", "rnorm")
to your NAMESPACE file.
csSAM: no visible binding for global variable 'quantile'
csSAM: no visible global function definition for 'median'
csfit: no visible global function definition for 'lsfit'
csfit: no visible global function definition for 'ls.diag'
plotCsSAM: no visible global function definition for 'pdf'
plotCsSAM: no visible global function definition for 'par'
plotCsSAM: no visible global function definition for 'plot'
plotCsSAM: no visible global function definition for 'title'
plotCsSAM: no visible global function definition for 'dev.off'
runSAM: no visible binding for global variable 'median'
runSAM: no visible global function definition for 'quantile'
Undefined global functions or variables:
  dev.off ls.diag lsfit median par pdf plot quantile title
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "ls.diag", "lsfit", "median", "quantile")
to your NAMESPACE file.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.0Mb
cci.nostrat: no visible global function definition for 'quantile'
cci.nostrat: no visible global function definition for 'plot'
cci.nostrat: no visible global function definition for 'axis'
cci.nostrat: no visible global function definition for 'lines'
cci.nostrat: no visible global function definition for 'legend'
cci.strat: no visible global function definition for 'plot'
cci.strat: no visible global function definition for 'axis'
cci.strat: no visible global function definition for 'lines'
cci.strat: no visible global function definition for 'legend'
clfs.nostrat: no visible global function definition for 'quantile'
clfs.nostrat: no visible global function definition for 'plot'
clfs.nostrat: no visible global function definition for 'axis'
clfs.nostrat: no visible global function definition for 'lines'
clfs.nostrat: no visible global function definition for 'legend'
clfs.strat: no visible global function definition for 'plot'
clfs.strat: no visible global function definition for 'axis'
clfs.strat: no visible global function definition for 'lines'
clfs.strat: no visible global function definition for 'legend'
pvals.2cat: no visible global function definition for 'pchisq'
pvals.cat: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  axis legend lines pchisq plot quantile
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "pchisq", "quantile")
to your NAMESPACE file.
allCombs: no visible global function definition for 'combn'
brute.search: no visible global function definition for 'na.omit'
dag.draw: no visible global function definition for 'plot'
dag.draw: no visible global function definition for 'text'
dag.init: no visible global function definition for
  'installed.packages'
dag.legend: no visible global function definition for 'text'
dag.letter: no visible global function definition for 'text'
dag.move: no visible global function definition for 'identify'
dag.move: no visible global function definition for 'locator'
dag.sim: no visible global function definition for 'rnorm'
dag.sim: no visible global function definition for 'rbinom'
dag.sim : <anonymous>: no visible global function definition for
  'rbinom'
garrows: no visible global function definition for 'arrows'
smoothArc: no visible global function definition for 'points'
summary_dagRdag: no visible global function definition for 'na.omit'
viv: no visible global function definition for 'na.omit'
write.paths: no visible global function definition for 'text'
Undefined global functions or variables:
  arrows combn identify installed.packages locator na.omit plot points
  rbinom rnorm text
Consider adding
  importFrom("graphics", "arrows", "identify", "locator", "plot",
             "points", "text")
  importFrom("stats", "na.omit", "rbinom", "rnorm")
  importFrom("utils", "combn", "installed.packages")
to your NAMESPACE file.
drawAimSpot: no visible global function definition for 'points'
drawBoard: no visible global function definition for 'par'
drawBoard: no visible global function definition for 'plot'
drawBoard: no visible global function definition for 'points'
drawBoard: no visible global function definition for 'text'
drawHeatmap: no visible global function definition for 'heat.colors'
drawHeatmap: no visible global function definition for 'par'
drawHeatmap: no visible global function definition for 'image'
drawHeatmap: no visible global function definition for 'rect'
generalExpScores: no visible global function definition for 'fft'
simpleExpScores: no visible global function definition for 'mvfft'
simpleExpScores: no visible global function definition for 'fft'
Undefined global functions or variables:
  fft heat.colors image mvfft par plot points rect text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "points", "rect",
             "text")
  importFrom("stats", "fft", "mvfft")
to your NAMESPACE file.
datadict.profile: no visible global function definition for
  'txtProgressBar'
datadict.profile: no visible global function definition for
  'setTxtProgressBar'
datadict_profile: no visible global function definition for
  'txtProgressBar'
datadict_profile: no visible global function definition for
  'setTxtProgressBar'
heatmap.quality: no visible global function definition for
  'colorRampPalette'
heatmap.quality: no visible global function definition for 'heatmap'
heatmap_quality: no visible global function definition for
  'colorRampPalette'
heatmap_quality: no visible global function definition for 'heatmap'
is.oneOf: no visible global function definition for 'read.csv'
is_one_of: no visible global function definition for 'read.csv'
pkg.version: no visible global function definition for 'citation'
pkg_version: no visible global function definition for 'citation'
ruleCoverage: no visible global function definition for 'dotchart'
ruleCoverage: no visible global function definition for 'abline'
rule_coverage: no visible global function definition for 'dotchart'
rule_coverage: no visible global function definition for 'abline'
scoreSum: no visible global function definition for 'plot'
score_sum: no visible global function definition for 'plot'
shortSummary: no visible global function definition for 'sd'
short_summary: no visible global function definition for 'sd'
Undefined global functions or variables:
  abline citation colorRampPalette dotchart heatmap plot read.csv sd
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "dotchart", "plot")
  importFrom("stats", "heatmap", "sd")
  importFrom("utils", "citation", "read.csv", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.1Mb
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11993 (sockconn)
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
ifft: no visible global function definition for 'fft'
lines.deamer: no visible global function definition for 'lines'
plot.deamer: no visible global function definition for 'plot'
rlaplace: no visible global function definition for 'runif'
Undefined global functions or variables:
  fft lines plot runif
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "fft", "runif")
to your NAMESPACE file.
compare.relimp: no visible global function definition for 'qchisq'
compare.relimp: no visible global function definition for 'pchisq'
plot_transition: no visible global function definition for 'dnorm'
plot_transition: no visible global function definition for 'par'
plot_transition: no visible global function definition for 'plot'
plot_transition: no visible global function definition for 'lines'
plot_transition: no visible global function definition for 'plogis'
plot_transition: no visible global function definition for 'axis'
plot_transition: no visible global function definition for 'mtext'
relative.importance: no visible global function definition for 'glm'
relative.importance: no visible global function definition for 'sd'
relative.importance : tr.pr: no visible global function definition for
  'pnorm'
relative.importance: no visible global function definition for 'vcov'
Undefined global functions or variables:
  axis dnorm glm lines mtext par pchisq plogis plot pnorm qchisq sd
  vcov
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot")
  importFrom("stats", "dnorm", "glm", "pchisq", "plogis", "pnorm",
             "qchisq", "sd", "vcov")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/DeducerSpatial.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
bootbagg: no visible global function definition for 'runif'
bootworpl: no visible global function definition for 'runif'
des12: no visible global function definition for 'rnorm'
des12: no visible global function definition for 'runif'
eval.stage.gauss: no visible global function definition for 'var'
plotparti: no visible global function definition for 'plot'
plotparti: no visible global function definition for 'lines'
plotpartilev: no visible global function definition for 'plot'
plotpartilev: no visible global function definition for 'polygon'
plotpartilev: no visible global function definition for 'points'
simesi: no visible global function definition for 'runif'
simesi3d: no visible global function definition for 'runif'
simfssk: no visible global function definition for 'rnorm'
simfssk: no visible global function definition for 'runif'
simmix.delt: no visible global function definition for 'rnorm'
simmix.delt: no visible global function definition for 'runif'
simpp: no visible global function definition for 'rnorm'
simpp: no visible global function definition for 'runif'
simutree: no visible global function definition for 'runif'
stage.gaussR: no visible global function definition for 'var'
unidis: no visible global function definition for 'runif'
Undefined global functions or variables:
  lines plot points polygon rnorm runif var
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
MBD: no visible global function definition for 'par'
MBD: no visible global function definition for 'gray'
MBD: no visible global function definition for 'matplot'
MBD: no visible global function definition for 'polygon'
MBD: no visible global function definition for 'lines'
MBD: no visible global function definition for 'legend'
MBD: no visible global function definition for 'matlines'
R.test: no visible global function definition for 'runif'
R.test: no visible global function definition for 'wilcox.test'
centralPlot: no visible global function definition for 'par'
centralPlot: no visible global function definition for
  'colorRampPalette'
centralPlot: no visible global function definition for 'matplot'
centralPlot: no visible global function definition for 'matlines'
centralPlot: no visible global function definition for 'legend'
scalecurve: no visible global function definition for 'plot'
scalecurve: no visible global function definition for 'lines'
scalecurve: no visible global function definition for 'legend'
tmean: no visible global function definition for 'matplot'
tmean: no visible global function definition for 'matlines'
tmean: no visible global function definition for 'lines'
tmean: no visible global function definition for 'legend'
tmean: no visible global function definition for 'colorRampPalette'
Undefined global functions or variables:
  colorRampPalette gray legend lines matlines matplot par plot polygon
  runif wilcox.test
Consider adding
  importFrom("grDevices", "colorRampPalette", "gray")
  importFrom("graphics", "legend", "lines", "matlines", "matplot", "par",
             "plot", "polygon")
  importFrom("stats", "runif", "wilcox.test")
to your NAMESPACE file.
arrayUpdate : pairUpdate: no visible global function definition for
  'runif'
conditionUpdate: no visible global function definition for 'runif'
designGG: no visible global function definition for 'runif'
experimentDesignTable: no visible global function definition for
  'write.csv'
plotAllScores: no visible global function definition for 'png'
plotAllScores: no visible global function definition for 'par'
plotAllScores: no visible global function definition for 'plot'
plotAllScores: no visible global function definition for 'text'
plotAllScores: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  dev.off par plot png runif text write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "runif")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
fs.agreement.part: no visible global function definition for 'as.dist'
fs.agreement.part: no visible global function definition for 'cor'
fs.leave.k.out.combn: no visible global function definition for 'sd'
fs.leave.k.out.sample: no visible global function definition for 'sd'
fs.rd: no visible global function definition for 'pchisq'
fs.selection: no visible global function definition for 'p.adjust'
plot.FIT: no visible global function definition for 'qchisq'
plot.FIT: no visible global function definition for 'ppoints'
plot.FIT: no visible global function definition for 'plot'
plot.FIT: no visible global function definition for 'points'
plot.FIT: no visible global function definition for 'abline'
plotJn: no visible global function definition for 'plot'
plotJn: no visible global function definition for 'points'
robust.distance.signed: no visible global function definition for
  'mahalanobis'
snowball: no visible global function definition for 'is'
snowball: no visible global function definition for 'median'
weight.sd: no visible binding for global variable 'sd'
Undefined global functions or variables:
  abline as.dist cor is mahalanobis median p.adjust pchisq plot points
  ppoints qchisq sd
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "is")
  importFrom("stats", "as.dist", "cor", "mahalanobis", "median",
             "p.adjust", "pchisq", "ppoints", "qchisq", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
makeAdjMatrix: no visible global function definition for 'combn'
plotPosteriorN: no visible global function definition for 'plot'
plotPosteriorN: no visible global function definition for 'title'
plotPosteriorN: no visible global function definition for 'lines'
plotPosteriorN: no visible global function definition for 'legend'
venn3: no visible global function definition for 'plot'
venn3: no visible global function definition for 'runif'
venn3: no visible global function definition for 'points'
venn3: no visible global function definition for 'lines'
venn3: no visible global function definition for 'text'
venn4: no visible global function definition for 'plot'
venn4: no visible global function definition for 'lines'
venn4: no visible global function definition for 'runif'
venn4: no visible global function definition for 'points'
Undefined global functions or variables:
  combn legend lines plot points runif text title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points", "text",
             "title")
  importFrom("stats", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

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

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11661 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11661 (sockconn)
Execution halted
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

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

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11802 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11802 (sockconn)
Execution halted
aLine: no visible global function definition for 'lines'
aLine: no visible global function definition for 'ecdf'
dip.test: no visible global function definition for 'complete.cases'
dip.test: no visible global function definition for 'runif'
dip.test: no visible global function definition for 'approx'
plot.dip: no visible global function definition for 'par'
plot.dip: no visible global function definition for 'ecdf'
plot.dip: no visible global function definition for 'plot'
plot.dip: no visible global function definition for 'title'
plot.dip: no visible global function definition for 'abline'
plot.dip: no visible global function definition for 'axis'
plot.dip: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline approx axis complete.cases ecdf legend lines par plot runif
  title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "approx", "complete.cases", "ecdf", "runif")
to your NAMESPACE file.
dist.multiPhylo: no visible global function definition for 'as.dist'
gromov.hyperbolicity: no visible global function definition for
  'as.dist'
mcmc.target.seq: no visible global function definition for 'runif'
phylo.diff: no visible global function definition for 'par'
phylo.diff: no visible global function definition for 'plot'
Undefined global functions or variables:
  as.dist par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.dist", "runif")
to your NAMESPACE file.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/dplyr.Rcheck/00install.out' for details.
DStree: no visible global function definition for 'model.frame'
DStree: no visible global function definition for 'model.matrix'
DStree: no visible global function definition for 'model.response'
DStree: no visible global function definition for 'as.formula'
bag: no visible global function definition for 'model.frame'
bag: no visible global function definition for 'model.response'
plot.DStree: no visible global function definition for 'par'
plot.DStree: no visible global function definition for 'plot'
plot.DStree: no visible global function definition for 'rainbow'
plot.DStree: no visible global function definition for 'lines'
plot.DStree: no visible global function definition for 'legend'
predict.DStree: no visible global function definition for 'predict'
print.DStree: no visible global function definition for 'naprint'
prune.DStree: no visible global function definition for 'median'
prune.DStree: no visible global function definition for 'predict'
prune.DStree: no visible binding for global variable 'var'
summ.MAE: no visible global function definition for 'predict'
summary.DStree: no visible global function definition for 'naprint'
Undefined global functions or variables:
  as.formula legend lines median model.frame model.matrix
  model.response naprint par plot predict rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "lines", "par", "plot")
  importFrom("stats", "as.formula", "median", "model.frame",
             "model.matrix", "model.response", "naprint", "predict",
             "var")
to your NAMESPACE file.
DCEA: no visible global function definition for 'p.adjust'
DS: no visible global function definition for 'p.adjust'
DS: no visible global function definition for 'pdf'
DS: no visible global function definition for 'plot'
DS: no visible global function definition for 'dev.off'
LFC: no visible global function definition for 'glm'
LFC: no visible global function definition for 'predict'
PartialCor: no visible global function definition for 'na.omit'
comDCGLplot: no visible global function definition for 'pdf'
comDCGLplot: no visible global function definition for 'plot'
comDCGLplot: no visible global function definition for 'dev.off'
percentLinkfilter: no visible global function definition for 'cor'
qLinkfilter: no visible global function definition for 'cor'
qLinkfilter: no visible global function definition for 'pt'
qLinkfilter: no visible global function definition for 'p.adjust'
rLinkfilter: no visible global function definition for 'cor'
varianceBasedfilter: no visible binding for global variable 'var'
varianceBasedfilter: no visible global function definition for 'median'
varianceBasedfilter: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  cor dev.off glm median na.omit p.adjust pchisq pdf plot predict pt
  var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "glm", "median", "na.omit", "p.adjust",
             "pchisq", "predict", "pt", "var")
to your NAMESPACE file.
DTK.plot: no visible global function definition for 'plot'
DTK.plot: no visible global function definition for 'axis'
DTK.plot: no visible global function definition for 'title'
DTK.plot: no visible global function definition for 'lines'
DTK.plot: no visible global function definition for 'points'
DTK.test: no visible binding for global variable 'sd'
DTK.test: no visible global function definition for 'qtukey'
TK.test: no visible global function definition for 'TukeyHSD'
TK.test: no visible global function definition for 'aov'
Undefined global functions or variables:
  TukeyHSD aov axis lines plot points qtukey sd title
Consider adding
  importFrom("graphics", "axis", "lines", "plot", "points", "title")
  importFrom("stats", "TukeyHSD", "aov", "qtukey", "sd")
to your NAMESPACE file.
DTMC: no visible global function definition for 'runif'
DTMC: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import 'sf::st_make_valid' by 'lwgeom::st_make_valid' when loading 'edbuildmapr'
See 'd:/Rcompile/CRANpkg/local/3.6/edbuildmapr.Rcheck/00install.out' for details.
comPlot: no visible global function definition for 'plot'
comPlot: no visible global function definition for 'lines'
convertEiData: no visible global function definition for 'model.frame'
plot.eiwild: no visible global function definition for 'plot'
plot.eiwild: no visible global function definition for 'par'
plotResult: no visible global function definition for 'grey'
plotResult: no visible global function definition for
  'colorRampPalette'
plotResult: no visible global function definition for 'plot.new'
plotResult: no visible global function definition for 'plot.window'
prioriPlot: no visible global function definition for 'par'
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for 'rgamma'
prioriPlot : <anonymous>: no visible global function definition for
  'rbeta'
prioriPlot: no visible global function definition for 'hist'
prioriPlot : <anonymous>: no visible global function definition for
  'rgamma'
prioriPlot : <anonymous> : <anonymous>: no visible global function
  definition for 'rexp'
prioriPlot : <anonymous>: no visible global function definition for
  'rexp'
runMBayes: no visible global function definition for 'runif'
runMBayes: no visible global function definition for 'rgamma'
runMBayes: no visible global function definition for 'rexp'
str0: no visible global function definition for 'str'
tuneVars: no visible global function definition for 'sd'
Undefined global functions or variables:
  colorRampPalette grey hist lines model.frame par plot plot.new
  plot.window rbeta rexp rgamma runif sd str
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey")
  importFrom("graphics", "hist", "lines", "par", "plot", "plot.new",
             "plot.window")
  importFrom("stats", "model.frame", "rbeta", "rexp", "rgamma", "runif",
             "sd")
  importFrom("utils", "str")
to your NAMESPACE file.
empiricalFDR: no visible global function definition for 'axis'
empiricalFDR: no visible global function definition for 'loess'
empiricalFDR: no visible global function definition for 'predict'
empiricalFDR: no visible global function definition for 'lines'
empiricalFDR: no visible global function definition for 'abline'
fdrBiCurve: no visible global function definition for 'plot'
fdrBiCurve: no visible global function definition for 'axis'
fdrBiCurve: no visible global function definition for 'lines'
fdrBiCurve: no visible global function definition for 'abline'
fdrBiCurve: no visible global function definition for 'legend'
simulateCounts: no visible global function definition for
  'txtProgressBar'
simulateCounts: no visible global function definition for
  'setTxtProgressBar'
simulateCounts: no visible global function definition for 'rnorm'
simulateCounts: no visible global function definition for 'hist'
simulateCounts: no visible global function definition for 'colData'
Undefined global functions or variables:
  abline axis colData hist legend lines loess plot predict rnorm
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "lines",
             "plot")
  importFrom("stats", "loess", "predict", "rnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
plot.episplineDensity: no visible global function definition for 'plot'
plot.episplineDensity: no visible global function definition for
  'points'
postproc: no visible global function definition for 'plot'
postproc: no visible global function definition for 'points'
preprocess.data: no visible global function definition for 'sd'
Undefined global functions or variables:
  plot points sd
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "sd")
to your NAMESPACE file.
FCIplot: no visible global function definition for 'na.omit'
FCIplot: no visible global function definition for 'plot'
FCIplot: no visible global function definition for 'tail'
FCIplot: no visible global function definition for 'grid'
FCIplot: no visible global function definition for 'polygon'
FCIplot: no visible global function definition for 'rgb'
linpred: no visible global function definition for 'lm'
mplott: no visible global function definition for 'par'
mplott: no visible global function definition for 'plot'
mplott: no visible global function definition for 'na.omit'
mplott: no visible global function definition for 'lines'
mplott: no visible global function definition for 'legend'
mplott: no visible global function definition for 'grid'
plott: no visible global function definition for 'lines'
plott: no visible global function definition for 'par'
plott: no visible global function definition for 'plot'
plott: no visible global function definition for 'grid'
tsideplot: no visible global function definition for 'par'
tsideplot: no visible global function definition for 'plot'
tsideplot: no visible global function definition for 'axis'
tsideplot: no visible global function definition for 'grid'
Undefined global functions or variables:
  axis grid legend lines lm na.omit par plot polygon rgb tail
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "polygon")
  importFrom("stats", "lm", "na.omit")
  importFrom("utils", "tail")
to your NAMESPACE file.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eqn2svg)
  > 
  > test_check("eqn2svg")
  -- 1. Error: SVG conversion works (@test-eqn2svg.R#3)  -------------------------
  cannot open the connection
  Backtrace:
   1. eqn2svg::eqn2svg(eqn = l_time_domain[25], preview = FALSE)
   2. base::readLines(url, warn = FALSE)
   3. base::file(con, "r")
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: SVG conversion works (@test-eqn2svg.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
ESA: no visible binding for global variable 'var'
plot.esabcv: no visible global function definition for 'plot'
plot.esabcv: no visible global function definition for 'points'
plot.esabcv: no visible global function definition for 'axis'
plot.esabcv: no visible global function definition for 'title'
Undefined global functions or variables:
  axis plot points title var
Consider adding
  importFrom("graphics", "axis", "plot", "points", "title")
  importFrom("stats", "var")
to your NAMESPACE file.
ESEA.Main: no visible global function definition for 'rnorm'
ESEA.Main: no visible global function definition for 'sd'
ESEA.Main: no visible global function definition for 'p.adjust'
PlotGlobEdgeCorProfile: no visible global function definition for
  'plot'
PlotGlobEdgeCorProfile: no visible global function definition for
  'lines'
PlotGlobEdgeCorProfile: no visible global function definition for
  'colors'
PlotGlobEdgeCorProfile: no visible global function definition for
  'points'
PlotGlobEdgeCorProfile: no visible global function definition for
  'legend'
PlotGlobEdgeCorProfile: no visible global function definition for
  'text'
PlotPathwayGraph: no visible global function definition for 'par'
PlotPathwayGraph: no visible global function definition for 'plot'
PlotRunEnrichment: no visible global function definition for 'plot'
PlotRunEnrichment: no visible global function definition for 'lines'
PlotRunEnrichment: no visible global function definition for 'colors'
PlotRunEnrichment: no visible global function definition for 'text'
SavePathway2File: no visible global function definition for 'is'
calEdgeCorScore: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  colors is legend lines na.omit p.adjust par plot points rnorm sd text
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "text")
  importFrom("methods", "is")
  importFrom("stats", "na.omit", "p.adjust", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
rAllRisksFactors: no visible global function definition for 'new'
rAssetDistribution: no visible global function definition for 'new'
rDefaultSpread: no visible global function definition for 'new'
rLiquiditySpread: no visible global function definition for 'new'
rRealEstate: no visible global function definition for 'new'
rShortRate: no visible global function definition for 'new'
rStock: no visible global function definition for 'new'
EuroCall_Stock_PriceDistribution,Scenarios: no visible global function
  definition for 'pnorm'
EuroCall_ZC_PriceDistribution,Scenarios: no visible global function
  definition for 'pnorm'
EuroPut_Stock_PriceDistribution,Scenarios: no visible global function
  definition for 'pnorm'
EuroPut_ZC_PriceDistribution,Scenarios: no visible global function
  definition for 'pnorm'
MartingaleTest,Scenarios: no visible global function definition for
  'plot'
MartingaleTest,Scenarios: no visible global function definition for
  'lines'
MartingaleTest,Scenarios: no visible global function definition for
  'title'
customPathsGeneration,Scenarios: no visible global function definition
  for 'rnorm'
Undefined global functions or variables:
  lines new plot pnorm rnorm title
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("methods", "new")
  importFrom("stats", "pnorm", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.Transition: no visible global function definition for 'rnorm'
.Transition.DC: no visible global function definition for 'runif'
CondPdf.CC.interval: no visible global function definition for 'plot'
CondPdf.DC.interval: no visible global function definition for 'plot'
Simu.Cond.HR: no visible global function definition for 'rpois'
Simu.Cond.HR: no visible global function definition for 'runif'
Simu.Cond.HR: no visible global function definition for 'hist'
Simu.Cond.HR: no visible global function definition for 'var'
Simu.HR: no visible global function definition for 'rpois'
Simu.HR: no visible global function definition for 'runif'
Simu.HR: no visible global function definition for 'hist'
Simu.HR: no visible global function definition for 'var'
Simu.PDMP: no visible global function definition for 'plot'
Simu.PDMP.DC: no visible global function definition for 'plot'
plotCHR: no visible global function definition for 'plot'
plotHR: no visible global function definition for 'plot'
Undefined global functions or variables:
  hist plot rnorm rpois runif var
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "rnorm", "rpois", "runif", "var")
to your NAMESPACE file.
EW : PhiP : Phi: no visible global function definition for 'pnorm'
EWplot: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot pnorm
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "pnorm")
to your NAMESPACE file.
extfunnel: no visible global function definition for 'qnorm'
extfunnel: no visible global function definition for 'meta.summaries'
extfunnel: no visible global function definition for 'flush.console'
extfunnel: no visible global function definition for 'qt'
extfunnel: no visible global function definition for 'dev.new'
extfunnel: no visible global function definition for 'par'
extfunnel: no visible global function definition for 'plot'
extfunnel: no visible global function definition for 'polygon'
extfunnel: no visible global function definition for 'segments'
extfunnel: no visible global function definition for 'abline'
extfunnel: no visible global function definition for 'axis'
extfunnel: no visible global function definition for 'box'
Undefined global functions or variables:
  abline axis box dev.new flush.console meta.summaries par plot polygon
  qnorm qt segments
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "box", "par", "plot",
             "polygon", "segments")
  importFrom("stats", "qnorm", "qt")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
createFormula: no visible global function definition for 'tail'
createFormula: no visible global function definition for 'head'
createFormula: no visible global function definition for 'as.formula'
ezsim: no visible global function definition for 'runif'
plot.ezsim: no visible global function definition for 'quantile'
plot.ezsim: no visible global function definition for 'head'
plot.ezsim: no visible global function definition for 'tail'
plot.ezsim: no visible global function definition for 'plot'
plot.ezsim: no visible binding for global variable 'dnorm'
plot.ezsim: no visible binding for global variable 'pdf'
plot.ezsim: no visible global function definition for 'dev.off'
plot.ezsim : <anonymous>: no visible global function definition for
  'dev.new'
plot.summary.ezsim: no visible global function definition for 'head'
plot.summary.ezsim: no visible global function definition for 'tail'
plot.summary.ezsim: no visible binding for global variable 'pdf'
plot.summary.ezsim: no visible global function definition for 'dev.off'
plot.summary.ezsim : <anonymous>: no visible global function definition
  for 'dev.new'
Undefined global functions or variables:
  as.formula dev.new dev.off dnorm head pdf plot quantile runif tail
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "pdf")
  importFrom("graphics", "plot")
  importFrom("stats", "as.formula", "dnorm", "quantile", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
PTSingleAssetBarrierOption2: no visible global function definition for
  'new'
newton: no visible global function definition for 'plot'
newton: no visible global function definition for 'abline'
probInRange: no visible global function definition for 'pnorm'
shortfall_risk: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline new plot pnorm
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "new")
  importFrom("stats", "pnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
FDRreg: no visible global function definition for 'dnorm'
colnormalize: no visible global function definition for 'sd'
efron: no visible global function definition for 'median'
efron: no visible global function definition for 'hist'
efron: no visible global function definition for 'glm'
efron: no visible binding for global variable 'poisson'
efron: no visible global function definition for 'qchisq'
efron: no visible global function definition for 'predict'
efron: no visible global function definition for 'quantile'
efron: no visible global function definition for 'lm'
efron: no visible global function definition for 'coef'
make.bspline.matrix: no visible global function definition for
  'quantile'
plotFDR: no visible global function definition for 'hist'
plotFDR: no visible global function definition for 'par'
plotFDR: no visible global function definition for 'plot'
plotFDR: no visible global function definition for 'axis'
plotFDR: no visible global function definition for 'lines'
plotFDR: no visible global function definition for 'legend'
plotFDR: no visible global function definition for 'rug'
plotFDR: no visible global function definition for 'title'
Undefined global functions or variables:
  axis coef dnorm glm hist legend lines lm median par plot poisson
  predict qchisq quantile rug sd title
Consider adding
  importFrom("graphics", "axis", "hist", "legend", "lines", "par",
             "plot", "rug", "title")
  importFrom("stats", "coef", "dnorm", "glm", "lm", "median", "poisson",
             "predict", "qchisq", "quantile", "sd")
to your NAMESPACE file.
fgeasy: no visible global function definition for 'dist'
fgeasy : cor.est: no visible global function definition for 'cor.test'
fgeasy: no visible binding for global variable 'var'
fgperm : runrand: no visible global function definition for 'runif'
fgperm : runrand: no visible global function definition for 'ave'
fgploc : runrand: no visible global function definition for 'runif'
fgploc : runrand: no visible global function definition for 'ave'
fyshuffle: no visible global function definition for 'runif'
plot.fg: no visible global function definition for 'par'
plot.fg: no visible global function definition for 'plot'
plot.fg: no visible global function definition for 'segments'
plot.fg: no visible binding for global variable 'quantile'
plot.fg: no visible global function definition for 'abline'
plot.fg: no visible global function definition for 'axis'
summary.fg: no visible binding for global variable 'quantile'
Undefined global functions or variables:
  abline ave axis cor.test dist par plot quantile runif segments var
Consider adding
  importFrom("graphics", "abline", "axis", "par", "plot", "segments")
  importFrom("stats", "ave", "cor.test", "dist", "quantile", "runif",
             "var")
to your NAMESPACE file.
lsmacof: no visible global function definition for 'cmdscale'
plotInc: no visible global function definition for 'rainbow'
plotInc: no visible global function definition for 'plot'
prepareCalib: no visible global function definition for 'lm'
Undefined global functions or variables:
  cmdscale lm plot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "plot")
  importFrom("stats", "cmdscale", "lm")
to your NAMESPACE file.
GCV: no visible global function definition for 'lm'
GCV: no visible global function definition for 'resid'
ffplot: no visible global function definition for 'par'
ffplot: no visible global function definition for 'plot'
ffplot: no visible global function definition for 'points'
ffplot: no visible global function definition for 'legend'
flowfield: no visible global function definition for 'write.table'
gpr: no visible global function definition for 'quantile'
gpr: no visible global function definition for 'var'
smoothp: no visible global function definition for 'lm'
smoothp: no visible global function definition for 'predict'
smoothp: no visible global function definition for 'resid'
smoothp: no visible global function definition for 'optimize'
Undefined global functions or variables:
  legend lm optimize par plot points predict quantile resid var
  write.table
Consider adding
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "lm", "optimize", "predict", "quantile", "resid",
             "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Package required and available but unsuitable version: 'forecast'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/forecast.Rcheck/00install.out' for details.
ComputeDCT2FFT: no visible global function definition for 'fft'
ComputeSemipgramFFT: no visible global function definition for 'fft'
WaveVarFD: no visible global function definition for 'modwt'
do.fd.estimate: no visible global function definition for
  'performParallel'
do.fd.estimate2d.simple: no visible global function definition for
  'median'
fd.Genton: no visible global function definition for 'qn'
fd.estimate.matrix: no visible global function definition for
  'performParallel'
fd.plot.legend: no visible global function definition for 'legend'
fd.plot.loglog: no visible global function definition for 'plot'
fd.plot.loglog: no visible global function definition for 'points'
fd.plot.loglog: no visible global function definition for 'abline'
summary.FractalDim: no visible binding for global variable 'sd'
Undefined global functions or variables:
  abline fft legend median modwt performParallel plot points qn sd
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points")
  importFrom("stats", "fft", "median", "sd")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.6Mb
custom.draw.circle: no visible global function definition for 'lines'
frcc: no visible binding for global variable 'sd'
frcc: no visible global function definition for 'cor.shrink'
frcc: no visible global function definition for 'cor'
frcc: no visible global function definition for 'p.asym'
generate_multivariate_normal_sample: no visible global function
  definition for 'mvrnorm'
plot_units: no visible binding for global variable 'sd'
plot_units: no visible global function definition for 'plot'
plot_units: no visible global function definition for 'points'
plot_units: no visible global function definition for 'textxy'
plot_variables: no visible global function definition for 'plot'
plot_variables: no visible global function definition for 'points'
plot_variables: no visible global function definition for 'textxy'
plot_variables: no visible global function definition for 'segments'
Undefined global functions or variables:
  cor cor.shrink lines mvrnorm p.asym plot points sd segments textxy
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.4Mb
    libs   1.4Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
.FunFEM.main: no visible global function definition for 'kmeans'
.FunFEM.main: no visible global function definition for 'rmultinom'
.FunFEM.main: no visible global function definition for 'cutree'
.FunFEM.main: no visible global function definition for 'hclust'
.FunFEM.main: no visible global function definition for 'dist'
.FunFEM.main: no visible global function definition for 'par'
.FunFEM.main: no visible global function definition for 'plot'
.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov cutree dist hclust kmeans par plot rmultinom
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "cov", "cutree", "dist", "hclust", "kmeans",
             "rmultinom")
to your NAMESPACE file.
FPTsimul: no visible global function definition for 'runif'
histplot: no visible global function definition for 'dev.new'
histplot: no visible global function definition for 'hist'
histplot: no visible global function definition for 'par'
histplot: no visible global function definition for 'plot'
histplot: no visible global function definition for 'legend'
mdt: no visible binding for global variable 'deltat'
plot.FPTdensity: no visible global function definition for 'dev.new'
plot.FPTdensity: no visible global function definition for 'plot'
res_summary: no visible global function definition for 'write.table'
res_summary: no visible global function definition for 'sd'
res_summary: no visible global function definition for 'median'
vdt: no visible binding for global variable 'deltat'
Undefined global functions or variables:
  deltat dev.new hist legend median par plot runif sd write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "legend", "par", "plot")
  importFrom("stats", "deltat", "median", "runif", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CI.RMSEA: no visible global function definition for 'qchisq'
CI.RMSEA: no visible global function definition for 'pchisq'
GAIPE.RMSEA: no visible global function definition for 'par'
GAIPE.RMSEA: no visible global function definition for 'plot'
GAIPE.RMSEA: no visible global function definition for 'abline'
GAIPE.RMSEA: no visible global function definition for 'colors'
GAIPE.RMSEA: no visible global function definition for 'text'
GAIPE.RMSEA: no visible global function definition for 'arrows'
GAIPE.RMSEA: no visible global function definition for 'points'
GAIPE.RMSEA: no visible global function definition for 'axis'
GAIPE.RMSEA: no visible global function definition for 'lines'
GAIPE.RMSEA: no visible global function definition for 'legend'
GAIPE.RMSEA: no visible global function definition for 'pchisq'
GAIPE.RMSEA: no visible global function definition for 'qchisq'
GAIPE.RMSEA: no visible global function definition for 'mtext'
GAIPE.RMSEA: no visible global function definition for 'title'
PA.RMSEA: no visible global function definition for 'pchisq'
PA.RMSEA: no visible global function definition for 'qchisq'
Undefined global functions or variables:
  abline arrows axis colors legend lines mtext par pchisq plot points
  qchisq text title
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "abline", "arrows", "axis", "legend", "lines",
             "mtext", "par", "plot", "points", "text", "title")
  importFrom("stats", "pchisq", "qchisq")
to your NAMESPACE file.
cvriskMSM: no visible global function definition for 'predict'
plotcvriskMSM: no visible global function definition for 'plot'
plotcvriskMSM: no visible binding for global variable 'lines'
plotcvriskMSM: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot predict
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
GAMBoost: no visible global function definition for 'binomial'
GAMBoost: no visible global function definition for 'gaussian'
GAMBoost: no visible global function definition for 'poisson'
GAMBoost: no visible binding for global variable 'sd'
GAMBoost: no visible global function definition for 'Matrix'
calc.confidence.bands: no visible global function definition for
  'predict'
cv.GAMBoost: no visible global function definition for 'binomial'
cv.GAMBoost : eval.fold: no visible global function definition for
  'predict'
cv.GAMBoost: no visible global function definition for 'mclapply'
cv.GAMBoost: no visible binding for global variable 'var'
estimPVal: no visible global function definition for 'mclapply'
plot.GAMBoost: no visible global function definition for 'plot'
plot.GAMBoost: no visible global function definition for 'lines'
Undefined global functions or variables:
  Matrix binomial gaussian lines mclapply plot poisson predict sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "binomial", "gaussian", "poisson", "predict", "sd",
             "var")
to your NAMESPACE file.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.3Mb
contindic.gb2: no visible global function definition for 'contour'
contindic.gb2: no visible global function definition for 'box'
contindic.gb2: no visible global function definition for 'mtext'
contprof.gb2: no visible global function definition for 'image'
contprof.gb2: no visible global function definition for 'heat.colors'
contprof.gb2: no visible global function definition for 'contour'
contprof.gb2: no visible global function definition for 'text'
contprof.gb2: no visible global function definition for 'box'
dplot.cavgb2: no visible global function definition for 'par'
dplot.cavgb2: no visible global function definition for 'curve'
dplot.cavgb2: no visible global function definition for 'legend'
dplot.cavgb2: no visible global function definition for 'plot'
dplot.cavgb2: no visible global function definition for 'lines'
dplot.cgb2: no visible global function definition for 'curve'
dplot.cgb2: no visible global function definition for 'lines'
dplot.cgb2: no visible global function definition for 'legend'
plotsML.gb2: no visible global function definition for 'par'
plotsML.gb2: no visible global function definition for 'plot'
plotsML.gb2: no visible global function definition for 'abline'
plotsML.gb2: no visible global function definition for 'curve'
plotsML.gb2: no visible global function definition for 'legend'
saveplot : <local>: no visible global function definition for 'dev.set'
saveplot : <local>: no visible global function definition for
  'dev.print'
saveplot : <local>: no visible binding for global variable 'pdf'
Undefined global functions or variables:
  abline box contour curve dev.print dev.set heat.colors image legend
  lines mtext par pdf plot text
Consider adding
  importFrom("grDevices", "dev.print", "dev.set", "heat.colors", "pdf")
  importFrom("graphics", "abline", "box", "contour", "curve", "image",
             "legend", "lines", "mtext", "par", "plot", "text")
to your NAMESPACE file.
coeplot: no visible global function definition for 'plot'
coeplot: no visible global function definition for 'axis'
coeplot: no visible global function definition for 'lines'
coeplot: no visible global function definition for 'title'
coeplot: no visible global function definition for 'legend'
corplot: no visible global function definition for 'par'
corplot: no visible global function definition for 'pairs'
corplot: no visible global function definition for 'strwidth'
lm.estimate: no visible global function definition for 'as.formula'
lm.estimate: no visible global function definition for 'glm'
panel.cor: no visible global function definition for 'par'
panel.cor: no visible global function definition for 'cor'
panel.cor: no visible global function definition for 'strwidth'
panel.cor: no visible global function definition for 'text'
panel.smooth.r: no visible global function definition for 'par'
panel.smooth.r: no visible global function definition for 'points'
panel.smooth.r: no visible global function definition for 'lines'
posplot: no visible global function definition for 'par'
posplot: no visible global function definition for 'barplot'
posplot: no visible global function definition for 'plot'
posplot: no visible global function definition for 'points'
Undefined global functions or variables:
  as.formula axis barplot cor glm legend lines pairs par plot points
  strwidth text title
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "pairs",
             "par", "plot", "points", "strwidth", "text", "title")
  importFrom("stats", "as.formula", "cor", "glm")
to your NAMESPACE file.
installed size is 84.5Mb
  sub-directories of 1Mb or more:
    L8NY18   2.2Mb
    gdal     3.8Mb
    libs    72.2Mb
    proj     5.0Mb
plot.rbga: no visible global function definition for 'par'
plot.rbga: no visible global function definition for 'hist'
plot.rbga: no visible global function definition for 'plot'
plot.rbga: no visible global function definition for 'lines'
rbga: no visible global function definition for 'runif'
rbga: no visible global function definition for 'dnorm'
rbga.bin: no visible global function definition for 'dnorm'
rbga.bin: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm hist lines par plot runif
Consider adding
  importFrom("graphics", "hist", "lines", "par", "plot")
  importFrom("stats", "dnorm", "runif")
to your NAMESPACE file.
splineAnalyze: no visible global function definition for 'var'
splineAnalyze: no visible global function definition for 'par'
splineAnalyze: no visible global function definition for 'plot'
splineAnalyze: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines par plot var
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "var")
to your NAMESPACE file.
PAEA : <anonymous>: no visible global function definition for
  'integrate'
PAEAAnalysis: no visible global function definition for
  'txtProgressBar'
PAEAAnalysis : <anonymous>: no visible global function definition for
  'setTxtProgressBar'
PAEAAnalysis: no visible global function definition for 'par'
PAEAAnalysis: no visible global function definition for 'barplot'
chdirSig: no visible global function definition for 'prcomp'
chdirSig: no visible global function definition for 'rchisq'
chdirSig: no visible global function definition for 'txtProgressBar'
chdirSig : <anonymous> : <anonymous>: no visible global function
  definition for 'setTxtProgressBar'
chdirplots : <anonymous>: no visible global function definition for
  'par'
chdirplots : <anonymous>: no visible global function definition for
  'plot'
chdirplots : <anonymous>: no visible global function definition for
  'arrows'
chdirplots : <anonymous>: no visible global function definition for
  'barplot'
multigmtPAEAAnalysis: no visible global function definition for
  'txtProgressBar'
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for 'setTxtProgressBar'
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for 'data'
multigmtPAEAAnalysis : <anonymous>: no visible global function
  definition for 'write.table'
Undefined global functions or variables:
  arrows barplot data integrate par plot prcomp rchisq
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("graphics", "arrows", "barplot", "par", "plot")
  importFrom("stats", "integrate", "prcomp", "rchisq")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
geoscaleBox: no visible global function definition for 'boxplot'
geoscaleBox: no visible global function definition for 'par'
geoscaleBox: no visible global function definition for 'plot'
geoscaleBox: no visible global function definition for 'text'
geoscaleBox: no visible global function definition for 'segments'
geoscaleBox: no visible global function definition for 'rect'
geoscaleBox: no visible global function definition for 'rgb'
geoscaleBox: no visible global function definition for 'polygon'
geoscaleBox: no visible global function definition for 'points'
geoscaleBox: no visible global function definition for 'axis'
geoscalePlot: no visible global function definition for 'par'
geoscalePlot: no visible global function definition for 'plot'
geoscalePlot: no visible global function definition for 'text'
geoscalePlot: no visible global function definition for 'segments'
geoscalePlot: no visible global function definition for 'rect'
geoscalePlot: no visible global function definition for 'rgb'
geoscalePlot: no visible global function definition for 'points'
geoscalePlot: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis boxplot par plot points polygon rect rgb segments text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "boxplot", "par", "plot", "points",
             "polygon", "rect", "segments", "text")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ggtern.Rcheck/00install.out' for details.
acovamcmc: no visible global function definition for 'rnorm'
acovamcmc: no visible global function definition for 'rgamma'
acovamcmc: no visible binding for global variable 'quantile'
acovamcmc: no visible global function definition for 'quantile'
acovamcmc: no visible global function definition for 'var'
plot.acovamcmc: no visible global function definition for 'dev.new'
plot.acovamcmc: no visible global function definition for 'par'
plot.acovamcmc: no visible global function definition for 'plot'
plot.acovamcmc: no visible global function definition for 'density'
plot.acovamcmc: no visible global function definition for 'acf'
plot.acovamcmc: no visible global function definition for 'contour'
plot.acovamcmc: no visible global function definition for 'image'
plot.acovamcmc: no visible global function definition for 'persp'
Undefined global functions or variables:
  acf contour density dev.new image par persp plot quantile rgamma
  rnorm var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "contour", "image", "par", "persp", "plot")
  importFrom("stats", "acf", "density", "quantile", "rgamma", "rnorm",
             "var")
to your NAMESPACE file.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(git2rdata)
  > 
  > test_check("git2rdata")
  -- 1. Failure: (unknown) (@test_d_recent_commit.R#82)  -------------------------
  all(output$commit %in% c(cm_1$sha, cm_2$sha)) isn't true.
  
  == testthat results  ===========================================================
  [ OK: 336 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: (unknown) (@test_d_recent_commit.R#82) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    doc         1.2Mb
    libs       21.2Mb
    test_data   1.2Mb
Found the following significant warnings:
  Warning: namespace 'lme4' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/3.6/GMMAT.Rcheck/00install.out' for details.
CumulativeVarPlot: no visible global function definition for 'plot'
CumulativeVarPlot: no visible global function definition for 'axis'
PCplot: no visible global function definition for 'par'
PCplot: no visible global function definition for 'plot'
PCplot: no visible global function definition for 'rainbow'
PCplot: no visible global function definition for 'density'
gDist: no visible global function definition for 'plot'
gDist: no visible global function definition for 'density'
gDist: no visible global function definition for 'abline'
gPCA.batchdetect: no visible global function definition for 'var'
Undefined global functions or variables:
  abline axis density par plot rainbow var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "axis", "par", "plot")
  importFrom("stats", "density", "var")
to your NAMESPACE file.
Resdata : prepdata: no visible global function definition for 'sqldf'
gpca : Build3d: no visible global function definition for 'dev.new'
gpca : Build3d: no visible global function definition for
  'scatterplot3d'
gpca : Build3d: no visible global function definition for 'text'
gpca : Build3d: no visible global function definition for 'plot'
gpca : Build3d: no visible global function definition for 'abline'
gpca : Build3d: no visible global function definition for 'rect'
gpca: no visible global function definition for 'cor'
gpca: no visible global function definition for 'dev.new'
gpca: no visible global function definition for 'plot'
gpca: no visible global function definition for 'text'
gpca: no visible global function definition for 'abline'
gpca: no visible global function definition for 'rect'
gpca: no visible global function definition for 'scatterplot3d'
gpca: no visible global function definition for 'segments'
gpca: no visible global function definition for 'points'
gpca: no visible global function definition for 'write.table'
Undefined global functions or variables:
  abline cor dev.new plot points rect scatterplot3d segments sqldf text
  write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "plot", "points", "rect", "segments",
             "text")
  importFrom("stats", "cor")
  importFrom("utils", "write.table")
to your NAMESPACE file.
gpfr: no visible global function definition for 'rnorm'
gpfr: no visible global function definition for 'runif'
gpfrpred : <anonymous>: no visible global function definition for
  'predict'
gpfrtrain: no visible global function definition for 'nlminb'
gppredict: no visible global function definition for 'predict'
gpr: no visible global function definition for 'rnorm'
gpr: no visible global function definition for 'runif'
gpr: no visible global function definition for 'lm'
gpr: no visible global function definition for 'resid'
gpr: no visible global function definition for 'nlminb'
main1: no visible global function definition for 'lm'
main1: no visible global function definition for 'resid'
main2 : <anonymous>: no visible global function definition for
  'predict'
main2: no visible global function definition for 'predict'
main3: no visible global function definition for 'lm'
main3: no visible global function definition for 'resid'
plot.gpfr: no visible global function definition for 'polygon'
plot.gpfr: no visible global function definition for 'rgb'
plot.gpfr: no visible global function definition for 'matpoints'
plot.gpfr: no visible global function definition for 'matlines'
plot.gpfr: no visible global function definition for 'lines'
plot.gpr: no visible global function definition for 'plot'
plot.gpr: no visible global function definition for 'polygon'
plot.gpr: no visible global function definition for 'rgb'
plot.gpr: no visible global function definition for 'points'
plot.gpr: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines lm matlines matpoints nlminb plot points polygon predict resid
  rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "matlines", "matpoints", "plot",
             "points", "polygon")
  importFrom("stats", "lm", "nlminb", "predict", "resid", "rnorm",
             "runif")
to your NAMESPACE file.
GriegSmith: no visible global function definition for 'is.ppp'
envelopes: no visible binding for global variable 'quantile'
plot.GriegSmith: no visible global function definition for 'plot'
plot.GriegSmith: no visible global function definition for 'lines'
plot.GriegSmith: no visible global function definition for 'axis'
Undefined global functions or variables:
  axis is.ppp lines plot quantile
Consider adding
  importFrom("graphics", "axis", "lines", "plot")
  importFrom("stats", "quantile")
to your NAMESPACE file.
gte: no visible global function definition for 'model.extract'
gte: no visible global function definition for 'model.matrix'
gte: no visible binding for global variable 'sd'
gte: no visible global function definition for 'dnorm'
plot.gte: no visible global function definition for 'plot'
plot.gte: no visible global function definition for 'par'
plot.gte: no visible global function definition for 'polygon'
plot.gte: no visible global function definition for 'gray'
plot.gte: no visible global function definition for 'lines'
plot.gte: no visible global function definition for 'legend'
Undefined global functions or variables:
  dnorm gray legend lines model.extract model.matrix par plot polygon
  sd
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "legend", "lines", "par", "plot", "polygon")
  importFrom("stats", "dnorm", "model.extract", "model.matrix", "sd")
to your NAMESPACE file.
Package required and available but unsuitable version: 'tibble'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 130.5Mb
  sub-directories of 1Mb or more:
    java  128.5Mb
PoincarePlot: no visible global function definition for 'plot'
PoincarePlot: no visible global function definition for 'lines'
PoincarePlot: no visible global function definition for 'lowess'
hctest: no visible global function definition for 'cor.test'
rdplot: no visible global function definition for 'plot'
rdplot: no visible global function definition for 'lines'
rdplot: no visible global function definition for 'lowess'
rdplot: no visible global function definition for 'rgb'
simer: no visible global function definition for 'runif'
simer: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  cor.test lines lowess plot rgb rnorm runif
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "cor.test", "lowess", "rnorm", "runif")
to your NAMESPACE file.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    CWrappers_1.10.2   2.6Mb
    CWrappers_1.10.3   2.6Mb
    CWrappers_1.12.0   2.9Mb
    libs               6.7Mb
heatmap.plus: no visible binding for global variable 'dist'
heatmap.plus: no visible binding for global variable 'hclust'
heatmap.plus : <anonymous>: no visible global function definition for
  'reorder'
heatmap.plus: no visible global function definition for 'as.dendrogram'
heatmap.plus: no visible global function definition for
  'order.dendrogram'
heatmap.plus: no visible binding for global variable 'sd'
heatmap.plus: no visible global function definition for 'par'
heatmap.plus: no visible global function definition for 'layout'
heatmap.plus: no visible global function definition for 'image'
heatmap.plus: no visible global function definition for 'axis'
heatmap.plus: no visible global function definition for 'mtext'
heatmap.plus: no visible global function definition for 'plot'
heatmap.plus: no visible global function definition for 'frame'
heatmap.plus: no visible global function definition for 'title'
Undefined global functions or variables:
  as.dendrogram axis dist frame hclust image layout mtext
  order.dendrogram par plot reorder sd title
Consider adding
  importFrom("graphics", "axis", "frame", "image", "layout", "mtext",
             "par", "plot", "title")
  importFrom("stats", "as.dendrogram", "dist", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
HubNetwork: no visible global function definition for 'rbinom'
HubNetwork: no visible global function definition for 'runif'
HubNetwork: no visible global function definition for 'cov2cor'
binaryMCMC: no visible global function definition for 'rbinom'
image.hbn: no visible global function definition for 'col2rgb'
image.hbn: no visible global function definition for 'rgb'
image.hbn: no visible global function definition for 'dev.new'
image.hbn: no visible global function definition for 'par'
image.hbn: no visible global function definition for 'image'
image.hcov: no visible global function definition for 'col2rgb'
image.hcov: no visible global function definition for 'rgb'
image.hcov: no visible global function definition for 'dev.new'
image.hcov: no visible global function definition for 'par'
image.hcov: no visible global function definition for 'image'
image.hglasso: no visible global function definition for 'col2rgb'
image.hglasso: no visible global function definition for 'rgb'
image.hglasso: no visible global function definition for 'dev.new'
image.hglasso: no visible global function definition for 'par'
image.hglasso: no visible global function definition for 'image'
plot.hbn: no visible global function definition for 'rgb'
plot.hbn: no visible global function definition for 'plot'
plot.hcov: no visible global function definition for 'rgb'
plot.hcov: no visible global function definition for 'plot'
plot.hglasso: no visible global function definition for 'rgb'
plot.hglasso: no visible global function definition for 'plot'
Undefined global functions or variables:
  col2rgb cov2cor dev.new image par plot rbinom rgb runif
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rgb")
  importFrom("graphics", "image", "par", "plot")
  importFrom("stats", "cov2cor", "rbinom", "runif")
to your NAMESPACE file.
compute.contrasts: no visible binding for global variable 'sd'
compute.contrasts: no visible global function definition for 'cor'
compute.contrasts: no visible global function definition for 'sd'
plot.estfdr: no visible global function definition for 'plot'
plot.hiertest: no visible global function definition for 'plot'
plot.hiertest: no visible global function definition for 'legend'
Undefined global functions or variables:
  cor legend plot sd
Consider adding
  importFrom("graphics", "legend", "plot")
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
overlay.sim: no visible global function definition for 'points'
plotDistr: no visible global function definition for 'dev.hold'
plotDistr: no visible global function definition for 'dev.flush'
plotDistr: no visible global function definition for 'plot'
plotDistr: no visible global function definition for 'segments'
Undefined global functions or variables:
  dev.flush dev.hold plot points segments
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold")
  importFrom("graphics", "plot", "points", "segments")
to your NAMESPACE file.
baumwelchcont: no visible global function definition for 'dnorm'
hmmcontSimul: no visible global function definition for 'rnorm'
hmmcontSimul: no visible global function definition for 'rbinom'
plot.ContObservHMM: no visible global function definition for 'plot'
plot.ContObservHMM: no visible global function definition for 'lines'
statesDistributionsPlot: no visible global function definition for
  'dnorm'
statesDistributionsPlot: no visible global function definition for 'sd'
statesDistributionsPlot: no visible global function definition for
  'plot'
statesDistributionsPlot: no visible global function definition for
  'lines'
statesDistributionsPlot: no visible global function definition for
  'legend'
summary.ContObservHMM: no visible global function definition for 'sd'
Undefined global functions or variables:
  dnorm legend lines plot rbinom rnorm sd
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "dnorm", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
dishonestCasino: no visible global function definition for 'plot'
dishonestCasino: no visible global function definition for 'axis'
dishonestCasino: no visible global function definition for 'text'
dishonestCasino: no visible global function definition for 'rect'
dishonestCasino: no visible global function definition for 'rgb'
dishonestCasino: no visible global function definition for 'points'
Undefined global functions or variables:
  axis plot points rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "axis", "plot", "points", "rect", "text")
to your NAMESPACE file.
hpbayes.plot: no visible global function definition for 'par'
hpbayes.plot: no visible global function definition for 'plot'
hpbayes.plot: no visible global function definition for 'points'
postpri.plot: no visible global function definition for 'par'
postpri.plot: no visible global function definition for 'plot'
postpri.plot: no visible global function definition for 'points'
postpri.plot: no visible global function definition for 'segments'
postpri.plot: no visible global function definition for 'boxplot'
Undefined global functions or variables:
  boxplot par plot points segments
Consider adding
  importFrom("graphics", "boxplot", "par", "plot", "points", "segments")
to your NAMESPACE file.
Calculate3D: no visible global function definition for 'persp'
CalculateHUM_Ex: no visible global function definition for 'combn'
CalculateHUM_Plot: no visible global function definition for 'plot'
CalculateHUM_Plot: no visible global function definition for 'polygon'
CalculateHUM_Plot: no visible global function definition for 'text'
CalculateHUM_Plot: no visible global function definition for 'points'
CalculateHUM_Plot: no visible global function definition for 'lines'
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
ibdhap.barplot: no visible global function definition for 'plot'
ibdhap.barplot: no visible global function definition for 'rect'
ibdhap.compare.loci: no visible global function definition for 'hist'
ibdhap.compare.segs: no visible global function definition for 'tail'
ibdhap.make.calls: no visible global function definition for
  'count.fields'
ibdhap.make.calls: no visible global function definition for
  'read.table'
ibdhap.make.true: no visible global function definition for
  'read.table'
ibdhap.names: no visible global function definition for 'count.fields'
ibdhap.names: no visible global function definition for 'read.table'
ibdhap.reduce.states: no visible global function definition for
  'read.table'
ibdhap.reduce.states: no visible global function definition for
  'write.table'
Undefined global functions or variables:
  count.fields hist plot read.table rect tail write.table
Consider adding
  importFrom("graphics", "hist", "plot", "rect")
  importFrom("utils", "count.fields", "read.table", "tail",
             "write.table")
to your NAMESPACE file.
create.ibd.dat: no visible global function definition for 'read.table'
create.pairs.frame: no visible global function definition for 'terms'
ibd.moments: no visible global function definition for 'var'
ibdreg: no visible global function definition for 'terms'
ibdreg: no visible global function definition for 'as.formula'
linkage.tests: no visible global function definition for 'pchisq'
pchibar: no visible global function definition for 'pchisq'
plot.linkage.all: no visible global function definition for 'plot'
plot.linkage.all: no visible global function definition for 'title'
plotpval: no visible global function definition for 'plot'
plotpval: no visible global function definition for 'lines'
sim.ibd.var: no visible global function definition for 'read.table'
sim.mark.prop: no visible global function definition for 'runif'
Undefined global functions or variables:
  as.formula lines pchisq plot read.table runif terms title var
Consider adding
  importFrom("graphics", "lines", "plot", "title")
  importFrom("stats", "as.formula", "pchisq", "runif", "terms", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
ICA: no visible global function definition for 'runif'
plot.ICA: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
ICCbare: no visible global function definition for 'na.omit'
ICCbare: no visible global function definition for 'formula'
ICCbare: no visible global function definition for 'replications'
ICCbare: no visible global function definition for 'aggregate'
ICCbare: no visible global function definition for 'anova'
ICCbare: no visible global function definition for 'aov'
ICCbareF: no visible global function definition for 'aggregate'
ICCest: no visible global function definition for 'na.omit'
ICCest: no visible global function definition for 'anova'
ICCest: no visible global function definition for 'aov'
ICCest: no visible global function definition for 'aggregate'
ICCest: no visible global function definition for 'qf'
ICCest: no visible global function definition for 'qnorm'
Nest: no visible global function definition for 'qnorm'
effort : CIW: no visible global function definition for 'qf'
effort: no visible global function definition for 'plot'
effort: no visible global function definition for 'axis'
effort: no visible global function definition for 'lines'
effort: no visible global function definition for 'legend'
Undefined global functions or variables:
  aggregate anova aov axis formula legend lines na.omit plot qf qnorm
  replications
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "plot")
  importFrom("stats", "aggregate", "anova", "aov", "formula", "na.omit",
             "qf", "qnorm", "replications")
to your NAMESPACE file.
INCAncinner : dian: no visible global function definition for 'cutree'
INCAncinner : bestela: no visible global function definition for
  'cutree'
center: no visible global function definition for 'var'
dbhatta: no visible global function definition for 'as.dist'
dcor: no visible global function definition for 'cor'
dcor: no visible global function definition for 'as.dist'
dgower: no visible global function definition for 'as.dist'
dmahal: no visible global function definition for 'as.dist'
dproc2: no visible global function definition for 'as.dist'
plot.incaix: no visible global function definition for 'barplot'
plot.incanc: no visible global function definition for 'plot'
plot.incanc: no visible global function definition for 'lines'
plot.incanc: no visible global function definition for 'legend'
selectioncluster : dian: no visible global function definition for
  'cutree'
selectioncluster : bestela: no visible global function definition for
  'cutree'
Undefined global functions or variables:
  as.dist barplot cor cutree legend lines plot var
Consider adding
  importFrom("graphics", "barplot", "legend", "lines", "plot")
  importFrom("stats", "as.dist", "cor", "cutree", "var")
to your NAMESPACE file.
Running examples in 'icrf-Ex.R' failed
The error most likely occurred in:

> ### Name: getTree.icrf
> ### Title: Extract a single tree from an icrf object
> ### Aliases: getTree.icrf getTree
> 
> ### ** Examples
> 
> library(survival) # for Surv()
> data(rat2)
> L = ifelse(rat2$tumor, 0, rat2$survtime)
> R = ifelse(rat2$tumor, rat2$survtime, Inf)
> # Note that this is a toy example. Use a larger ntree and nfold in practice.
> ## Don't show: 
> set.seed(2)
> rats.icrf <-
+   icrf(Surv(L, R, type = "interval2") ~ dose.lvl + weight + male + cage.no,
+        data = rat2, ntree = 2, nfold = 2)
Error in icrf.default(m, L, R, ...) : 
  NA/NaN/Inf in foreign function call (arg 50)
Calls: icrf -> icrf.formula -> icrf.default
Execution halted
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.7Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     15.3Mb
A.dep.tests: no visible global function definition for 'combn'
A.dep.tests: no visible global function definition for 'pchisq'
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'
dependogram: no visible global function definition for 'combn'
dependogram: no visible global function definition for 'plot'
dependogram: no visible global function definition for 'points'
dependogram: no visible global function definition for 'segments'
Undefined global functions or variables:
  clusterCall clusterSetupSPRNG combn makeCluster pchisq plot points
  segments stopCluster
Consider adding
  importFrom("graphics", "plot", "points", "segments")
  importFrom("stats", "pchisq")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running 'testthat.R' [132s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(interactions)
  > 
  > test_check("interactions")
  Failed with error:  'there is no package called 'brms''
  -- 1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157)  
  `print(p)` produced messages.
  
  -- 2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162)  
  `print(p)` produced messages.
  
  Failed with error:  'there is no package called 'brms''
  Failed with error:  'there is no package called 'rstanarm''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  Failed with error:  'there is no package called 'broom.mixed''
  == testthat results  ===========================================================
  [ OK: 161 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: interact_plot linearity.check works (@test_interact_plot.R#157) 
  2. Failure: interact_plot linearity.check works (@test_interact_plot.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
ClearBottomMenuPlot: no visible global function definition for 'rect'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertX'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertX'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'polygon'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertX'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertY'
InteractiveIGraph : keybd: no visible global function definition for
  'readClipboard'
InteractiveIGraph : keybd: no visible global function definition for
  'par'
PlotRegionGeneral: no visible global function definition for 'polygon'
plot.InteractiveIGraph: no visible global function definition for
  'plot'
plot.InteractiveIGraph: no visible global function definition for 'par'
plot.Menu: no visible global function definition for 'par'
plot.Menu: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'strwidth'
plot.MenuItem: no visible binding for global variable 'strheight'
plot.MenuItem: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'text'
plot.MenuLine: no visible binding for global variable 'rect'
Undefined global functions or variables:
  grconvertX grconvertY par plot polygon readClipboard rect strheight
  strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "plot",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("utils", "readClipboard")
to your NAMESPACE file.
interact: no visible global function definition for 'cor'
plot.interact: no visible global function definition for 'plot'
standardize.matrix: no visible binding for global variable 'var'
standardize.matrix: no visible binding for global variable 'sd'
Undefined global functions or variables:
  cor plot sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "sd", "var")
to your NAMESPACE file.
Mo.Th.Ra.: no visible global function definition for 'aggregate'
daily_mean: no visible global function definition for 'aggregate'
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'
par_calibration: no visible global function definition for 'aggregate'
plot_meas_sim: no visible global function definition for 'as.date'
plot_meas_sim: no visible global function definition for 'date.mdy'
plot_meas_sim: no visible global function definition for 'plot'
plot_meas_sim: no visible global function definition for 'par'
plot_meas_sim: no visible global function definition for 'legend'
shape_calibration: no visible global function definition for 'date.mdy'
shape_calibration: no visible global function definition for 'as.date'
shape_calibration: no visible global function definition for
  'aggregate'
Undefined global functions or variables:
  aggregate as.date chron date.mdy days hours legend par plot years
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "aggregate")
to your NAMESPACE file.
icScoreTest: no visible global function definition for 'pnorm'
icScoreTest: no visible global function definition for 'pchisq'
icfit.formula: no visible global function definition for 'terms'
icfit.formula: no visible global function definition for
  'model.extract'
icfitBootCI: no visible global function definition for 'binom.test'
ictest.formula: no visible global function definition for
  'model.extract'
plot.icfit: no visible global function definition for 'gray'
plot.icfit: no visible global function definition for 'plot'
plot.icfit: no visible global function definition for 'axis'
plot.icfit : polygon.icfit: no visible global function definition for
  'polygon'
scoresFromFit: no visible global function definition for 'dnorm'
scoresFromFit: no visible global function definition for 'qnorm'
wsrHLYpclt: no visible global function definition for 'model.matrix'
wsrHLYpclt: no visible global function definition for 'pchisq'
wsrHLYpclt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  axis binom.test dnorm gray model.extract model.matrix pchisq plot
  pnorm polygon qnorm terms
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "axis", "plot", "polygon")
  importFrom("stats", "binom.test", "dnorm", "model.extract",
             "model.matrix", "pchisq", "pnorm", "qnorm", "terms")
to your NAMESPACE file.
interventionEffects: no visible binding for global variable 'sd'
interventionEffects: no visible global function definition for 'pt'
interventionEffects: no visible global function definition for 'sd'
interventionalInference: no visible global function definition for 'sd'
interventionalInferenceAdvanced: no visible global function definition
  for 'sd'
linesROC: no visible global function definition for 'segments'
plotMaxML: no visible global function definition for 'plot'
plotMaxML: no visible global function definition for 'segments'
Undefined global functions or variables:
  plot pt sd segments
Consider adding
  importFrom("graphics", "plot", "segments")
  importFrom("stats", "pt", "sd")
to your NAMESPACE file.
ILik : rbern: no visible global function definition for 'runif'
ILik : q: no visible global function definition for 'dnorm'
ILik : SlambdaG: no visible global function definition for 'rnorm'
ILik : Pi_hat: no visible global function definition for 'rnorm'
ILik : q: no visible global function definition for 'dgamma'
ILik : SlambdaG: no visible global function definition for 'rgamma'
ILik : Pi_hat: no visible global function definition for 'rgamma'
ILik: no visible global function definition for 'maxLik'
ILik: no visible global function definition for 'coef'
ILik: no visible global function definition for 'hessian'
ILik: no visible global function definition for 'plot'
Undefined global functions or variables:
  coef dgamma dnorm hessian maxLik plot rgamma rnorm runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dgamma", "dnorm", "rgamma", "rnorm",
             "runif")
to your NAMESPACE file.
f.B: no visible global function definition for 'pnorm'
f.B.neglog.deriv: no visible global function definition for 'pnorm'
f.B.neglog.deriv: no visible global function definition for 'dnorm'
f.grovest3 : f.est: no visible global function definition for 'survfit'
f.grovest3 : f.est: no visible global function definition for 'plot'
f.grovest3 : f.est: no visible global function definition for 'lines'
f.grovest3: no visible global function definition for 'model.frame'
f.grovest3: no visible global function definition for 'model.extract'
invGauss: no visible global function definition for 'model.frame'
invGauss: no visible global function definition for 'model.extract'
invGauss: no visible global function definition for 'model.matrix'
predict.invGauss: no visible global function definition for
  'model.frame'
predict.invGauss: no visible global function definition for
  'model.extract'
predict.invGauss: no visible global function definition for
  'model.matrix'
predict.invGauss: no visible binding for global variable 'formula'
predict.invGauss: no visible binding for global variable 'data'
summary.invGauss: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  data dnorm formula lines model.extract model.frame model.matrix plot
  pnorm survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "dnorm", "formula", "model.extract", "model.frame",
             "model.matrix", "pnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 293
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11570 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11570 (sockconn)
Execution halted
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11158 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11158 (sockconn)
Execution halted
residualplot: no visible global function definition for 'predict'
residualplot: no visible global function definition for 'rstandard'
residualplot: no visible global function definition for
  'complete.cases'
residualplot: no visible global function definition for 'plot'
residualplot: no visible global function definition for 'points'
residualplot: no visible global function definition for 'lines'
residualplot: no visible global function definition for 'smooth.spline'
residualplot: no visible global function definition for 'sd'
residualplot: no visible global function definition for 'rgb'
residualplot: no visible global function definition for 'polygon'
Undefined global functions or variables:
  complete.cases lines plot points polygon predict rgb rstandard sd
  smooth.spline
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot", "points", "polygon")
  importFrom("stats", "complete.cases", "predict", "rstandard", "sd",
             "smooth.spline")
to your NAMESPACE file.
getSysinfo: no visible global function definition for 'sessionInfo'
getVecInfo: no visible global function definition for 'sd'
isSeriesConstant: no visible global function definition for 'median'
labelMargins: no visible global function definition for 'mtext'
plotBG: no visible global function definition for 'plot'
plotBG: no visible global function definition for 'polygon'
plotBG: no visible global function definition for 'par'
plotColorScale: no visible global function definition for 'par'
plotColorScale: no visible global function definition for 'text'
plotImageRotated: no visible global function definition for
  'heat.colors'
plotImageRotated: no visible global function definition for 'par'
plotImageRotated: no visible global function definition for 'plot'
plotImageRotated: no visible global function definition for 'image'
plotImageRotated: no visible global function definition for 'axis'
plotNLines: no visible global function definition for 'par'
plotNLines: no visible global function definition for 'plot'
plotNLines: no visible global function definition for 'mtext'
plotNLines: no visible global function definition for 'axis'
plotNLines: no visible global function definition for 'points'
plotNLines: no visible global function definition for 'sd'
userCoords: no visible global function definition for 'par'
Undefined global functions or variables:
  axis heat.colors image median mtext par plot points polygon sd
  sessionInfo text
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "axis", "image", "mtext", "par", "plot",
             "points", "polygon", "text")
  importFrom("stats", "median", "sd")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
binteg: no visible global function definition for 'contourLines'
binteg: no visible global function definition for 'approx'
binteg: no visible global function definition for 'par'
plot1: no visible global function definition for 'plot'
plot1: no visible global function definition for 'par'
plot1: no visible global function definition for 'rect'
plot1: no visible global function definition for 'axis'
plot1: no visible global function definition for 'contour'
plot1: no visible global function definition for 'contourLines'
plot1: no visible binding for global variable 'approx'
plot1: no visible global function definition for 'lines'
plot1: no visible global function definition for 'text'
plot2: no visible global function definition for 'plot'
plot2: no visible global function definition for 'abline'
plot2: no visible global function definition for 'lines'
plot2: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline approx axis contour contourLines legend lines par plot rect
  text
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "abline", "axis", "contour", "legend", "lines",
             "par", "plot", "rect", "text")
  importFrom("stats", "approx")
to your NAMESPACE file.
expression_up : <anonymous>: no visible global function definition for
  'quantile'
expression_up : <anonymous>: no visible global function definition for
  'IQR'
expression_up : <anonymous>: no visible global function definition for
  'median'
expression_up : <anonymous>: no visible global function definition for
  'sd'
plot_up: no visible global function definition for 'plot'
plot_up: no visible global function definition for 'text'
Undefined global functions or variables:
  IQR median plot quantile sd text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "IQR", "median", "quantile", "sd")
to your NAMESPACE file.
as.matrix.multiPhylo : tip2tip: no visible global function definition
  for 'cophenetic'
bw.nn : <anonymous>: no visible global function definition for
  'quantile'
dist.diss: no visible binding for global variable 'median'
dist.diss: no visible global function definition for 'dist'
hist.kdetrees: no visible binding for global variable 'density'
kdetrees : cutoff: no visible global function definition for 'quantile'
kdetrees.complete: no visible global function definition for 'plot'
kdetrees.complete: no visible global function definition for 'hist'
kdetrees.complete: no visible global function definition for
  'write.csv'
plot.kdetrees: no visible binding for global variable 'density'
Undefined global functions or variables:
  cophenetic density dist hist median plot quantile write.csv
Consider adding
  importFrom("graphics", "hist", "plot")
  importFrom("stats", "cophenetic", "density", "dist", "median",
             "quantile")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for 'rbeta'
benchmark.patchwork.copula : <anonymous> : <anonymous>: no visible
  global function definition for 'runif'
calculate.power : <anonymous>: no visible binding for global variable
  'quantile'
generate.benchmark.data: no visible global function definition for
  'runif'
generate.benchmark.data: no visible global function definition for
  'rnorm'
generate.benchmark.data: no visible global function definition for
  'rbinom'
generate.patchwork.copula: no visible global function definition for
  'rbeta'
generate.patchwork.copula: no visible global function definition for
  'runif'
novelTest.chisq: no visible global function definition for 'pchisq'
novelTest.chisq4nn: no visible global function definition for 'pchisq'
optimise.copula.mi : <anonymous>: no visible global function definition
  for 'optimize'
power.plot: no visible global function definition for 'plot'
power.plot: no visible global function definition for 'axis'
power.plot : <anonymous>: no visible global function definition for
  'points'
power.plot: no visible global function definition for 'legend'
roc.plot: no visible global function definition for 'colorRampPalette'
roc.plot : <anonymous>: no visible global function definition for
  'plot'
roc.plot : <anonymous> : <anonymous>: no visible global function
  definition for 'points'
run.tests : <anonymous> : <anonymous>: no visible global function
  definition for 'runif'
Undefined global functions or variables:
  axis colorRampPalette legend optimize pchisq plot points quantile
  rbeta rbinom rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "legend", "plot", "points")
  importFrom("stats", "optimize", "pchisq", "quantile", "rbeta",
             "rbinom", "rnorm", "runif")
to your NAMESPACE file.
image.kriging: no visible global function definition for 'heat.colors'
image.kriging: no visible global function definition for 'image'
kriging: no visible global function definition for 'lm'
plot.kriging: no visible global function definition for 'plot'
plot.kriging: no visible global function definition for 'curve'
Undefined global functions or variables:
  curve heat.colors image lm plot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "curve", "image", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
kselection: no visible global function definition for 'txtProgressBar'
kselection: no visible global function definition for
  'setTxtProgressBar'
plot.Kselection: no visible global function definition for 'plot'
plot.Kselection: no visible global function definition for 'lines'
plot.Kselection: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines plot setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
auc: no visible global function definition for 'approx'
kulife.colors: no visible global function definition for 'palette'
rootonorm: no visible global function definition for 'sd'
rootonorm: no visible global function definition for 'hist'
rootonorm: no visible global function definition for 'pnorm'
rootonorm: no visible global function definition for 'dnorm'
rootonorm: no visible global function definition for 'plot'
rootonorm: no visible global function definition for 'rect'
rootonorm: no visible global function definition for 'lines'
rootonorm: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approx dnorm hist lines palette plot pnorm rect sd
Consider adding
  importFrom("grDevices", "palette")
  importFrom("graphics", "abline", "hist", "lines", "plot", "rect")
  importFrom("stats", "approx", "dnorm", "pnorm", "sd")
to your NAMESPACE file.
betabreaker: no visible global function definition for 'predict'
coef.lars: no visible global function definition for 'predict'
cv.lars: no visible global function definition for 'predict'
cv.lars: no visible binding for global variable 'var'
error.bars: no visible global function definition for 'segments'
plot.lars: no visible global function definition for 'plot'
plot.lars: no visible global function definition for 'matplot'
plot.lars: no visible global function definition for 'title'
plot.lars: no visible global function definition for 'abline'
plot.lars: no visible global function definition for 'axis'
plotCVLars: no visible global function definition for 'plot'
predict.lars: no visible global function definition for 'approx'
Undefined global functions or variables:
  abline approx axis matplot plot predict segments title var
Consider adding
  importFrom("graphics", "abline", "axis", "matplot", "plot", "segments",
             "title")
  importFrom("stats", "approx", "predict", "var")
to your NAMESPACE file.
glassoscore: no visible global function definition for 'var'
glassoscore: no visible global function definition for 'pchisq'
lassoscore: no visible global function definition for 'txtProgressBar'
lassoscore: no visible global function definition for
  'setTxtProgressBar'
lassoscore: no visible global function definition for 'pchisq'
plot.glassoscore: no visible global function definition for 'legend'
plot.lassoscore: no visible global function definition for 'legend'
plot.mbscore: no visible global function definition for 'legend'
qqpval: no visible global function definition for 'ppoints'
qqpval: no visible global function definition for 'qbeta'
qqpval: no visible global function definition for 'points'
qqpval: no visible global function definition for 'plot'
qqpval: no visible global function definition for 'abline'
qqpval: no visible global function definition for 'polygon'
Undefined global functions or variables:
  abline legend pchisq plot points polygon ppoints qbeta
  setTxtProgressBar txtProgressBar var
Consider adding
  importFrom("graphics", "abline", "legend", "plot", "points", "polygon")
  importFrom("stats", "pchisq", "ppoints", "qbeta", "var")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   2.3Mb
ARConfIntEst: no visible global function definition for 'sd'
PTLinkFunc: no visible global function definition for 'pnorm'
PTLinkFunc: no visible global function definition for 'qnorm'
PTMultiPeriodPD: no visible global function definition for 'uniroot'
PTOnePeriodPD : f: no visible global function definition for 'pbinom'
PTOnePeriodPD: no visible global function definition for 'uniroot'
QMMGetRLogitPD: no visible global function definition for 'ecdf'
QMMPDlinkFunc: no visible global function definition for 'qnorm'
QMMPlot: no visible global function definition for 'plot'
QMMPlot: no visible global function definition for 'lines'
QMMPlot: no visible global function definition for 'legend'
VDBCalibratePD: no visible global function definition for 'ecdf'
VDBGetK: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  ecdf legend lines pbinom plot pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "ecdf", "pbinom", "pnorm", "qnorm", "sd",
             "uniroot")
to your NAMESPACE file.
AlternateSVD: no visible binding for global variable 'sd'
IPOD: no visible global function definition for 'mad'
IPOD: no visible global function definition for 'pnorm'
Pvalue: no visible global function definition for 'pf'
ROCplot: no visible global function definition for 'png'
ROCplot: no visible global function definition for 'matplot'
ROCplot: no visible global function definition for 'legend'
ROCplot: no visible global function definition for 'dev.off'
leapp: no visible global function definition for 'png'
leapp: no visible global function definition for 'plot'
leapp: no visible global function definition for 'dev.off'
ridge: no visible global function definition for 'sd'
ridge: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dev.off legend mad matplot pf plot png pnorm sd
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "matplot", "plot")
  importFrom("stats", "mad", "pf", "pnorm", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'liayson.Rnw' using Sweave

Error: processing vignette 'liayson.Rnw' failed with diagnostics:
 chunk 1 
Error in bmRequest(request = request, verbose = verbose) : 
  Service Unavailable (HTTP 503).

--- failed re-building 'liayson.Rnw'

SUMMARY: processing the following file failed:
  'liayson.Rnw'

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [84s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(lidR)
  Loading required package: raster
  Loading required package: sp
  > 
  > options(lidR.progress = FALSE)
  > 
  > test_check("lidR")
  -- 1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalo
  projection(req2) not equal to "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clrk66 +units=m +no_defs".
  1/1 mismatches
  x[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  x[1]: k66 +units=m +no_defs "
  y[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  y[1]: k66 +units=m +no_defs"
  
  == testthat results  ===========================================================
  [ OK: 971 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalog_apply-automerge.R#171) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [86s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(lidR)
  Loading required package: raster
  Loading required package: sp
  > 
  > options(lidR.progress = FALSE)
  > 
  > test_check("lidR")
  -- 1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalo
  projection(req2) not equal to "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clrk66 +units=m +no_defs".
  1/1 mismatches
  x[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  x[1]: k66 +units=m +no_defs "
  y[1]: "+proj=tmerc +lat_0=0 +lon_0=-55.5 +k=0.9999 +x_0=304800 +y_0=0 +ellps=clr
  y[1]: k66 +units=m +no_defs"
  
  == testthat results  ===========================================================
  [ OK: 971 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: catalog_apply automerge works with in memory POINTS (@test-catalog_apply-automerge.R#171) 
  
  Error: testthat unit tests failed
  Execution halted
plotBox: no visible global function definition for 'sd'
plotBox: no visible global function definition for 'rect'
plotBox: no visible global function definition for 'qnorm'
plotBox: no visible global function definition for 'segments'
plotInit: no visible global function definition for 'plot'
plotInit: no visible global function definition for 'runif'
plotInit: no visible global function definition for 'mtext'
plotInit: no visible global function definition for 'segments'
plotStack: no visible global function definition for 'points'
Undefined global functions or variables:
  mtext plot points qnorm rect runif sd segments
Consider adding
  importFrom("graphics", "mtext", "plot", "points", "rect", "segments")
  importFrom("stats", "qnorm", "runif", "sd")
to your NAMESPACE file.
gen.lms: no visible global function definition for 'na.omit'
plot.idf: no visible global function definition for 'plot'
plot.idf: no visible global function definition for 'mtext'
plot.idf: no visible global function definition for 'points'
plot.idf: no visible global function definition for 'segments'
plot.idf: no visible global function definition for 'ftable'
plot.idf: no visible global function definition for 'image'
plot.idf: no visible global function definition for 'gray'
plot.idf: no visible global function definition for 'abline'
plot.s.linlir: no visible global function definition for 'plot'
plot.s.linlir: no visible global function definition for 'mtext'
plot.s.linlir: no visible global function definition for 'polygon'
plot.s.linlir: no visible global function definition for 'points'
plot.s.linlir: no visible global function definition for 'curve'
s.linlir: no visible global function definition for 'na.omit'
s.linlir: no visible global function definition for 'dbinom'
s.linlir: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  abline curve dbinom ftable gray image mtext na.omit pchisq plot
  points polygon segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "curve", "image", "mtext", "plot",
             "points", "polygon", "segments")
  importFrom("stats", "dbinom", "ftable", "na.omit", "pchisq")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
EstimateProbability: no visible global function definition for
  'predict'
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'
plot_LOGICOIL: no visible global function definition for 'png'
plot_LOGICOIL: no visible global function definition for 'par'
plot_LOGICOIL: no visible global function definition for 'plot'
plot_LOGICOIL: no visible global function definition for 'lines'
plot_LOGICOIL: no visible global function definition for 'axis'
plot_LOGICOIL: no visible global function definition for 'mtext'
plot_LOGICOIL: no visible global function definition for 'legend'
plot_LOGICOIL: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  LOGICOILfit Model_Parameters axis dev.off legend lines mtext par plot
  png predict pssm
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "legend", "lines", "mtext", "par",
             "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
fplot: no visible global function definition for 'rnorm'
fplot: no visible global function definition for 'plot'
fplot: no visible global function definition for 'segments'
fplot: no visible global function definition for 'points'
fplot: no visible global function definition for 'text'
fplot.foodweb: no visible global function definition for 'plot'
fplot.foodweb: no visible global function definition for 'segments'
fplot.foodweb: no visible global function definition for 'points'
fplot.foodweb: no visible global function definition for 'text'
gplot: no visible global function definition for 'runif'
groupplot: no visible global function definition for 'rnorm'
groupplot: no visible global function definition for 'plot'
groupplot: no visible global function definition for 'segments'
groupplot: no visible global function definition for 'points'
groupplot: no visible global function definition for 'text'
groupplot.foodweb: no visible global function definition for 'rnorm'
groupplot.foodweb: no visible global function definition for 'plot'
groupplot.foodweb: no visible global function definition for 'segments'
groupplot.foodweb: no visible global function definition for 'points'
groupplot.foodweb: no visible global function definition for 'text'
Undefined global functions or variables:
  plot points rnorm runif segments text
Consider adding
  importFrom("graphics", "plot", "points", "segments", "text")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
learnPattern.default: no visible global function definition for 'runif'
plot.learnPattern: no visible global function definition for 'matplot'
plotMDS: no visible global function definition for 'par'
plotMDS: no visible global function definition for 'rainbow'
plotMDS: no visible global function definition for 'plot'
plotMDS: no visible global function definition for 'pairs'
visualizePattern: no visible global function definition for 'par'
visualizePattern: no visible global function definition for 'plot'
visualizePattern: no visible global function definition for 'points'
visualizePattern: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend matplot pairs par plot points rainbow runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend", "matplot", "pairs", "par", "plot",
             "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.1Mb
    libs   1.6Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
    proj   5.0Mb
SelectedInput:
  function(...)
SelectedInput.formula:
  function(..., data, control, metrics, stat, cutoff)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.2Mb
    htmlwidgets   1.8Mb
    libs          6.5Mb
ageprofile: no visible global function definition for 'model.frame'
ageprofile: no visible binding for global variable 'poisson'
ageprofile: no visible global function definition for 'predict.gam'
ageprofile: no visible global function definition for 'as.formula'
ageprofile: no visible global function definition for 'summary.gam'
ageprofile: no visible global function definition for 'contrasts<-'
ageprofile: no visible global function definition for 'anova.gam'
plotap: no visible global function definition for 'dev.new'
plotap: no visible global function definition for 'plot'
plotap: no visible global function definition for 'lines'
plotap: no visible global function definition for 'points'
plotap: no visible global function definition for 'legend'
splitter: no visible global function definition for 'reshape'
tabm: no visible global function definition for 'coef'
tabm: no visible global function definition for 'AIC'
Undefined global functions or variables:
  AIC anova.gam as.formula coef contrasts<- dev.new legend lines
  model.frame plot points poisson predict.gam reshape summary.gam
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "AIC", "as.formula", "coef", "contrasts<-",
             "model.frame", "poisson", "reshape")
to your NAMESPACE file.
MAT: no visible global function definition for 'dev.new'
MAT: no visible global function definition for 'plot'
MAT: no visible global function definition for 'points'
MAT: no visible global function definition for 'abline'
MAT: no visible global function definition for 'text'
MAT: no visible global function definition for 'legend'
MAT: no visible global function definition for 'lines'
MAT: no visible global function definition for 'par'
MAT: no visible global function definition for 'barplot'
MAT: no visible global function definition for 'cor'
print.MAT: no visible global function definition for 'sd'
print.MAT: no visible global function definition for 'cor'
simM3PL: no visible global function definition for 'rnorm'
simM3PL: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline barplot cor dev.new legend lines par plot points rnorm runif
  sd text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "lines", "par",
             "plot", "points", "text")
  importFrom("stats", "cor", "rnorm", "runif", "sd")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
GSTplot : <anonymous>: no visible global function definition for
  't.test'
GSTplot: no visible global function definition for 'rt'
GSTplot: no visible global function definition for 'layout'
GSTplot: no visible global function definition for 'par'
GSTplot: no visible global function definition for 'plot'
GSTplot: no visible global function definition for 'text'
GSTplot: no visible global function definition for 'lines'
GSTplot: no visible global function definition for 'polygon'
GSTplot: no visible global function definition for 'abline'
GSTplot: no visible global function definition for 'ecdf'
GSTplot: no visible global function definition for 'knots'
GSTplot : <anonymous>: no visible global function definition for 'aov'
GSTplot: no visible global function definition for 'qf'
MAVTn : <anonymous>: no visible global function definition for 'aov'
MAVTn: no visible global function definition for 'p.adjust'
MAVTn: no visible global function definition for 'plot'
MAVTn: no visible global function definition for 'par'
MAVTn: no visible global function definition for 'abline'
MAVTn: no visible global function definition for 'legend'
MAVTn: no visible global function definition for 'locator'
Tols : olsf: no visible global function definition for 't.test'
Tols: no visible global function definition for 'cor'
Undefined global functions or variables:
  abline aov cor ecdf knots layout legend lines locator p.adjust par
  plot polygon qf rt t.test text
Consider adding
  importFrom("graphics", "abline", "layout", "legend", "lines",
             "locator", "par", "plot", "polygon", "text")
  importFrom("stats", "aov", "cor", "ecdf", "knots", "p.adjust", "qf",
             "rt", "t.test")
to your NAMESPACE file.
MI.2: no visible global function definition for 'xtabs'
RNASeq.Data: no visible binding for global variable 'quantile'
loc.node: no visible global function definition for 'head'
loc.node: no visible global function definition for 'tail'
plotHybrid.Tree: no visible global function definition for 'par'
plotHybrid.Tree: no visible global function definition for 'plot'
plotHybrid.Tree: no visible global function definition for 'text'
plotHybrid.Tree: no visible global function definition for 'image'
plotHybrid.Tree: no visible global function definition for 'grey'
plotHybrid.Tree: no visible global function definition for
  'heat.colors'
plotHybrid.Tree: no visible global function definition for 'head'
plotHybrid.Tree: no visible global function definition for 'segments'
plotbr: no visible global function definition for 'segments'
Undefined global functions or variables:
  grey head heat.colors image par plot quantile segments tail text
  xtabs
Consider adding
  importFrom("grDevices", "grey", "heat.colors")
  importFrom("graphics", "image", "par", "plot", "segments", "text")
  importFrom("stats", "quantile", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
mcheatmaps : coscolorFun: no visible global function definition for
  'rgb'
mcheatmaps : halfcmat: no visible global function definition for
  'order.dendrogram'
mcheatmaps : fullcmat: no visible global function definition for
  'order.dendrogram'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'hclust'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'as.dist'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'sd'
mcheatmaps : calculateDendrogram: no visible global function definition
  for 'cophenetic'
mcheatmaps : printDiag: no visible global function definition for
  'order.dendrogram'
mcheatmaps: no visible global function definition for 'strwidth'
mcheatmaps: no visible global function definition for 'pdf'
mcheatmaps: no visible global function definition for 'plot.new'
mcheatmaps: no visible global function definition for 'as.dendrogram'
mcheatmaps: no visible global function definition for 'reorder'
mcheatmaps: no visible global function definition for 'par'
mcheatmaps: no visible global function definition for 'plot'
mcheatmaps: no visible global function definition for
  'order.dendrogram'
mcheatmaps: no visible global function definition for 'heat.colors'
mcheatmaps: no visible global function definition for 'terrain.colors'
mcheatmaps: no visible global function definition for 'as.dist'
mcheatmaps: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  as.dendrogram as.dist cophenetic dev.off hclust heat.colors
  order.dendrogram par pdf plot plot.new reorder rgb sd strwidth
  terrain.colors
Consider adding
  importFrom("grDevices", "dev.off", "heat.colors", "pdf", "rgb",
             "terrain.colors")
  importFrom("graphics", "par", "plot", "plot.new", "strwidth")
  importFrom("stats", "as.dendrogram", "as.dist", "cophenetic", "hclust",
             "order.dendrogram", "reorder", "sd")
to your NAMESPACE file.
plot.nsga2: no visible global function definition for 'plot'
plot.nsga2: no visible global function definition for 'lines'
plot.nsga2: no visible global function definition for 'pairs'
plot.nsga2.collection: no visible global function definition for
  'devAskNewPage'
plot.nsga2.collection: no visible binding for global variable 'plot'
Undefined global functions or variables:
  devAskNewPage lines pairs plot
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "lines", "pairs", "plot")
to your NAMESPACE file.
dometa: no visible global function definition for 'qchisq'
dometa: no visible global function definition for 'median'
dometa: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'pchisq'
forestplot: no visible global function definition for 'qnorm'
forestplot: no visible global function definition for 'plot'
forestplot: no visible global function definition for 'points'
forestplot: no visible global function definition for 'text'
metagwa.files: no visible global function definition for 'read.csv'
metagwa.files: no visible global function definition for 'write.csv'
metagwa.tables: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  median pchisq plot points qchisq qnorm read.csv text write.csv
Consider adding
  importFrom("graphics", "plot", "points", "text")
  importFrom("stats", "median", "pchisq", "qchisq", "qnorm")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.7Mb
calc_z_var: no visible binding for global variable 'median'
diffScore: no visible global function definition for 'new'
diffScore: no visible global function definition for 'model.matrix'
logNORMcdf: no visible global function definition for 'pnorm'
mGSZ.adj.mean.std: no visible binding for global variable 'sd'
pick.data.cols: no visible binding for global variable 'var'
plotProfile: no visible binding for global variable 'quantile'
plotProfile: no visible global function definition for 'plot'
plotProfile: no visible global function definition for 'lines'
plotProfile: no visible global function definition for 'legend'
Undefined global functions or variables:
  legend lines median model.matrix new plot pnorm quantile sd var
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("methods", "new")
  importFrom("stats", "median", "model.matrix", "pnorm", "quantile",
             "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
BCI: no visible global function definition for 'quantile'
Metro_Hastings: no visible global function definition for 'optim'
Metro_Hastings: no visible global function definition for 'runif'
Metro_Hastings: no visible global function definition for 'var'
plotMH: no visible global function definition for 'hist'
plotMH: no visible global function definition for 'plot'
plotMH: no visible global function definition for 'frame'
plotMH: no visible global function definition for 'text'
Undefined global functions or variables:
  frame hist optim plot quantile runif text var
Consider adding
  importFrom("graphics", "frame", "hist", "plot", "text")
  importFrom("stats", "optim", "quantile", "runif", "var")
to your NAMESPACE file.
migration.cv.in : <anonymous>: no visible global function definition
  for 'sd'
migration.cv.out : <anonymous>: no visible global function definition
  for 'sd'
migration.field.diagram: no visible global function definition for
  'plot'
migration.field.diagram: no visible global function definition for
  'lines'
migration.field.diagram: no visible global function definition for
  'text'
migration.field.diagram: no visible global function definition for
  'polygon'
migration.field.diagram: no visible global function definition for 'lm'
migration.field.diagram: no visible global function definition for
  'predict'
migration.field.diagram: no visible global function definition for
  'points'
migration.field.diagram: no visible global function definition for
  'resid'
migration.field.diagram: no visible global function definition for
  'coef'
migration.field.diagram: no visible global function definition for
  'mtext'
migration.field.diagram: no visible global function definition for
  'density'
migration.field.diagram: no visible global function definition for
  'rug'
migration.gini.col : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.in : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.out : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.row : <anonymous>: no visible global function definition
  for 'dist'
migration.gini.total: no visible global function definition for 'dist'
Undefined global functions or variables:
  coef density dist lines lm mtext plot points polygon predict resid
  rug sd text
Consider adding
  importFrom("graphics", "lines", "mtext", "plot", "points", "polygon",
             "rug", "text")
  importFrom("stats", "coef", "density", "dist", "lm", "predict",
             "resid", "sd")
to your NAMESPACE file.
miney : plot.initial.matrix: no visible global function definition for
  'plot'
miney : plot.initial.matrix: no visible global function definition for
  'rect'
miney : plot.known.matrix: no visible global function definition for
  'plot'
miney : plot.known.matrix: no visible global function definition for
  'rect'
miney : plot.known.matrix: no visible global function definition for
  'text'
miney: no visible global function definition for 'locator'
miney: no visible global function definition for 'rect'
miney: no visible global function definition for 'title'
Undefined global functions or variables:
  locator plot rect text title
Consider adding
  importFrom("graphics", "locator", "plot", "rect", "text", "title")
to your NAMESPACE file.
.FCLoess: no visible global function definition for 'loess'
.FCLoessM: no visible global function definition for 'loess'
.FCLoessM: no visible global function definition for 'median'
.Import.Luminex: no visible global function definition for 'read.csv'
.Intra.Me: no visible global function definition for 'sd'
.Intra.Me: no visible global function definition for 'quantile'
.Intra.Me: no visible global function definition for 'qchisq'
.Intra.Median: no visible global function definition for 'median'
.boxplot.rtprofile: no visible global function definition for 'boxplot'
.denplot: no visible global function definition for 'plot'
.denplot: no visible global function definition for 'density'
.denplot: no visible global function definition for 'abline'
.normalize.Luminex: no visible global function definition for 'sd'
.normalize.qrtpcr: no visible global function definition for 'density'
.validate.default: no visible global function definition for 't.test'
Undefined global functions or variables:
  abline boxplot density loess median plot qchisq quantile read.csv sd
  t.test
Consider adding
  importFrom("graphics", "abline", "boxplot", "plot")
  importFrom("stats", "density", "loess", "median", "qchisq", "quantile",
             "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: 'REBayes'
confusionBarplot: no visible global function definition for 'par'
confusionBarplot: no visible global function definition for 'barplot'
confusionBarplot: no visible global function definition for 'lines'
confusionBarplot: no visible global function definition for 'text'
confusionBarplot: no visible global function definition for 'legend'
confusionBarplot: no visible global function definition for 'axis'
confusionDendrogram: no visible global function definition for 'plot'
confusionImage: no visible global function definition for 'par'
confusionImage: no visible global function definition for 'image'
confusionImage: no visible global function definition for 'text'
confusionImage: no visible global function definition for 'abline'
confusionImage: no visible global function definition for 'axis'
confusionImage: no visible global function definition for 'plot'
confusionImage: no visible global function definition for 'mtext'
confusionStars: no visible global function definition for 'par'
confusionStars: no visible global function definition for 'stars'
confusionStars: no visible global function definition for 'rect'
plot.mlearning: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline axis barplot image legend lines mtext par plot rect stars text
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "image", "legend",
             "lines", "mtext", "par", "plot", "rect", "stars", "text")
to your NAMESPACE file.
Mort1Dsmooth: no visible global function definition for 'time'
Mort1Dsmooth: no visible global function definition for 'glm'
Mort1Dsmooth: no visible binding for global variable 'poisson'
Mort1Dsmooth_optimize: no visible global function definition for
  'median'
Mort2Dsmooth: no visible global function definition for 'glm'
Mort2Dsmooth: no visible binding for global variable 'poisson'
Mort2Dsmooth: no visible global function definition for 'median'
Mort2Dsmooth_optimize: no visible global function definition for
  'median'
plot.HMDdata: no visible global function definition for 'plot'
plot.Mort1Dsmooth: no visible global function definition for 'matplot'
plot.Mort2Dsmooth: no visible global function definition for 'quantile'
predict.Mort1Dsmooth: no visible global function definition for 'glm'
predict.Mort1Dsmooth: no visible binding for global variable 'poisson'
predict.Mort2Dsmooth: no visible global function definition for 'glm'
predict.Mort2Dsmooth: no visible binding for global variable 'poisson'
print.summary.Mort1Dsmooth: no visible global function definition for
  'quantile'
print.summary.Mort2Dsmooth: no visible global function definition for
  'quantile'
Undefined global functions or variables:
  glm matplot median plot poisson quantile time
Consider adding
  importFrom("graphics", "matplot", "plot")
  importFrom("stats", "glm", "median", "poisson", "quantile", "time")
to your NAMESPACE file.
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'.

diagram.mpa: no visible global function definition for 'plot'
diagram.mpa: no visible global function definition for 'abline'
diagram.mpa: no visible global function definition for 'text'
plotmpa: no visible global function definition for 'plot'
Undefined global functions or variables:
  abline plot text
Consider adding
  importFrom("graphics", "abline", "plot", "text")
to your NAMESPACE file.
mpcv: no visible binding for global variable 'median'
mpcv: no visible global function definition for 'cov'
mpcv: no visible global function definition for 'dist'
plot.mpcv: no visible binding for global variable 'median'
plot.mpcv: no visible global function definition for 'par'
plot.mpcv: no visible global function definition for 'plot'
plot.mpcv: no visible global function definition for 'rect'
plot.mpcv: no visible global function definition for 'lines'
plot.mpcv: no visible global function definition for 'points'
plot.mpcv: no visible global function definition for 'legend'
Undefined global functions or variables:
  cov dist legend lines median par plot points rect
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot", "points",
             "rect")
  importFrom("stats", "cov", "dist", "median")
to your NAMESPACE file.
MRwarp: no visible global function definition for 'dev.new'
MRwarp: no visible global function definition for 'plot'
MRwarp: no visible global function definition for 'lines'
MRwarp: no visible global function definition for 'points'
MRwarp: no visible global function definition for 'hist'
Undefined global functions or variables:
  dev.new hist lines plot points
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "hist", "lines", "plot", "points")
to your NAMESPACE file.
msap: no visible global function definition for 'packageVersion'
msap: no visible global function definition for 'read.csv'
msap: no visible global function definition for 'write.csv'
msap: no visible global function definition for 'sd'
msap: no visible global function definition for 'wilcox.test'
msap: no visible global function definition for 'dist'
msap: no visible global function definition for 'rainbow'
msap: no visible global function definition for 'png'
msap: no visible global function definition for 'legend'
msap: no visible global function definition for 'dev.off'
pcoa: no visible global function definition for 'cmdscale'
pcoa: no visible global function definition for 'png'
pcoa: no visible global function definition for 'par'
pcoa: no visible global function definition for 'plot'
pcoa: no visible global function definition for 'rainbow'
pcoa: no visible global function definition for 'points'
pcoa: no visible global function definition for 'dev.off'
pcoa: no visible global function definition for 'write.csv'
Undefined global functions or variables:
  cmdscale dev.off dist legend packageVersion par plot png points
  rainbow read.csv sd wilcox.test write.csv
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow")
  importFrom("graphics", "legend", "par", "plot", "points")
  importFrom("stats", "cmdscale", "dist", "sd", "wilcox.test")
  importFrom("utils", "packageVersion", "read.csv", "write.csv")
to your NAMESPACE file.
CrossValidationMuFicokm: no visible global function definition for
  'covMatrix'
CrossValidationMuFicokmAll: no visible global function definition for
  'covMatrix'
MuFicokm: no visible global function definition for 'km'
compute.beta.hat: no visible global function definition for 'lm'
computeAuxVariables: no visible global function definition for
  'covMatrix'
kmCok: no visible global function definition for 'new'
kmCok: no visible global function definition for 'drop.response'
kmCok: no visible global function definition for 'model.matrix'
kmCok: no visible global function definition for 'covStruct.create'
kmCok: no visible global function definition for 'validObject'
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'
kmCok: no visible global function definition for 'plot'
predict.kmCok: no visible global function definition for 'model.matrix'
predict.kmCok: no visible global function definition for 'covMat1Mat2'
predict.kmCok: no visible global function definition for 'qnorm'
predict.kmCok: no visible global function definition for 'qt'
predict.kmCok: no visible global function definition for 'covMatrix'
summary.MuFicokm: no visible global function definition for
  'covparam2vect'
Undefined global functions or variables:
  covMat1Mat2 covMatrix covParametersBounds covStruct.create
  covparam2vect drop.response km kmEstimate leaveOneOut.km lm
  model.matrix new plot qnorm qt validObject
Consider adding
  importFrom("graphics", "plot")
  importFrom("methods", "new", "validObject")
  importFrom("stats", "lm", "model.matrix", "qnorm", "qt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
plotOptionValues: no visible global function definition for 'plot'
plotOptionValues: no visible global function definition for 'persp'
Undefined global functions or variables:
  persp plot
Consider adding
  importFrom("graphics", "persp", "plot")
to your NAMESPACE file.
betas_plot: no visible global function definition for 'cov2cor'
betas_plot: no visible global function definition for
  'colorRampPalette'
betas_plot: no visible global function definition for 'pdf'
betas_plot: no visible global function definition for 'dev.off'
mhplot: no visible global function definition for 'read.table'
mhplot: no visible global function definition for 'pdf'
mhplot: no visible global function definition for 'plot'
mhplot: no visible global function definition for 'points'
mhplot: no visible global function definition for 'abline'
mhplot: no visible global function definition for 'axis'
mhplot: no visible global function definition for 'dev.off'
multi_meta: no visible global function definition for 'write.table'
multi_meta: no visible global function definition for 'read.table'
multi_meta: no visible global function definition for 'pchisq'
qqplotter: no visible global function definition for 'read.table'
qqplotter: no visible global function definition for 'qchisq'
qqplotter: no visible global function definition for 'ppoints'
qqplotter: no visible global function definition for 'median'
qqplotter: no visible global function definition for 'pchisq'
qqplotter: no visible global function definition for 'pdf'
qqplotter: no visible global function definition for 'plot'
qqplotter: no visible global function definition for 'abline'
qqplotter: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  abline axis colorRampPalette cov2cor dev.off median pchisq pdf plot
  points ppoints qchisq read.table write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf")
  importFrom("graphics", "abline", "axis", "plot", "points")
  importFrom("stats", "cov2cor", "median", "pchisq", "ppoints", "qchisq")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
.onAttach: no visible global function definition for
  'packageDescription'
genoudRob: no visible global function definition for 'genoud'
get.XYdata: no visible global function definition for 'terms'
get.xdata: no visible global function definition for 'terms'
get.xdata: no visible global function definition for 'model.matrix'
get.xy: no visible global function definition for 'terms'
get.xynames: no visible global function definition for 'terms'
get.ydata: no visible global function definition for 'terms'
get.ydata: no visible global function definition for 'model.response'
get.ydata: no visible global function definition for 'model.frame'
mt.dev: no visible global function definition for 'pt'
mt.dev.grad: no visible global function definition for 'pt'
mt.dev.grad: no visible global function definition for 'dt'
mt.mle: no visible global function definition for 'optim'
multinomRob: no visible global function definition for 'var'
plot.multinomRob: no visible global function definition for 'par'
plot.multinomRob: no visible global function definition for 'plot'
plot.multinomRob: no visible global function definition for 'title'
rdirich: no visible global function definition for 'rgamma'
residual.generator: no visible global function definition for 'median'
rmultinomial: no visible global function definition for 'runif'
rmultinomial: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  dt genoud median model.frame model.matrix model.response optim
  packageDescription par plot pt rbinom rgamma runif terms title var
Consider adding
  importFrom("graphics", "par", "plot", "title")
  importFrom("stats", "dt", "median", "model.frame", "model.matrix",
             "model.response", "optim", "pt", "rbinom", "rgamma",
             "runif", "terms", "var")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
plotFID: no visible global function definition for 'plot'
plotFID: no visible global function definition for 'points'
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
NAPPA: no visible binding for global variable 'sd'
NAPPA: no visible global function definition for 'sd'
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for 'coef'
calibrate.sigmoid.curve : <anonymous> : <anonymous>: no visible global
  function definition for 'lm'
calibrate.sigmoid.curve: no visible global function definition for
  'nls'
calibrate.sigmoid.curve: no visible binding for global variable
  'weights'
calibrate.sigmoid.curve: no visible global function definition for
  'coef'
calibrate.sigmoid.curve: no visible global function definition for
  'plot'
calibrate.sigmoid.curve: no visible global function definition for
  'rgb'
calibrate.sigmoid.curve: no visible global function definition for
  'box'
calibrate.sigmoid.curve: no visible global function definition for
  'axis'
calibrate.sigmoid.curve: no visible global function definition for
  'abline'
calibrate.sigmoid.curve: no visible global function definition for
  'lines'
calibrate.sigmoid.curve: no visible global function definition for
  'predict'
calibrate.sigmoid.curve: no visible global function definition for
  'smooth.spline'
calibrate.sigmoid.curve : <anonymous>: no visible global function
  definition for 'nls'
calibrate.sigmoid.curve : <anonymous>: no visible binding for global
  variable 'weights'
calibrate.sigmoid.curve: no visible binding for global variable 'coef'
calibrate.sigmoid.curve: no visible global function definition for 'pf'
calibrate.sigmoid.curve: no visible global function definition for
  'legend'
Undefined global functions or variables:
  abline axis box coef legend lines lm nls pf plot predict rgb sd
  smooth.spline weights
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "abline", "axis", "box", "legend", "lines",
             "plot")
  importFrom("stats", "coef", "lm", "nls", "pf", "predict", "sd",
             "smooth.spline", "weights")
to your NAMESPACE file.
NB.estimator: no visible global function definition for 'optimize'
NB.estimator: no visible global function definition for 'uniroot'
NB.example.dataset: no visible global function definition for
  'write.table'
NB.plot.likelihood: no visible global function definition for 'plot'
Undefined global functions or variables:
  optimize plot uniroot write.table
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "optimize", "uniroot")
  importFrom("utils", "write.table")
to your NAMESPACE file.
population: no visible global function definition for 'weighted.mean'
population: no visible global function definition for 'rpois'
population: no visible global function definition for 'lm'
population: no visible global function definition for 'coefficients'
population: no visible global function definition for 'sd'
population: no visible global function definition for 'par'
population: no visible global function definition for 'plot'
population: no visible global function definition for 'lines'
Undefined global functions or variables:
  coefficients lines lm par plot rpois sd weighted.mean
Consider adding
  importFrom("graphics", "lines", "par", "plot")
  importFrom("stats", "coefficients", "lm", "rpois", "sd",
             "weighted.mean")
to your NAMESPACE file.
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/3.6/NestedCategBayesImpute.Rcheck/00install.out' for details.
clustConfigurations: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    CppCode   2.6Mb
    R         6.0Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.6Mb
NPHMC: no visible global function definition for 'integrate'
NPHMC: no visible global function definition for 'qnorm'
NPHMC: no visible global function definition for 'pnorm'
NPHMC: no visible global function definition for 'plot'
NPHMC: no visible global function definition for 'lines'
NPHMC: no visible global function definition for 'smcure'
NPHMC: no visible global function definition for 'coxph'
Undefined global functions or variables:
  coxph integrate lines plot pnorm qnorm smcure
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "integrate", "pnorm", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import 'sf::st_make_valid' by 'lwgeom::st_make_valid' when loading 'oceanis'
See 'd:/Rcompile/CRANpkg/local/3.6/oceanis.Rcheck/00install.out' for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    doc    2.3Mb
    help   2.7Mb
    libs   2.0Mb
MLparameters: no visible global function definition for 'optim'
comp.freq: no visible global function definition for 'x11'
comp.freq: no visible global function definition for 'par'
comp.freq: no visible global function definition for 'plot'
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.6Mb
    models   4.6Mb
genRidge: no visible global function definition for 'plogis'
ordGene: no visible global function definition for 'anova'
ordGene: no visible global function definition for 'lm'
ordSelect: no visible binding for global variable 'sd'
ordSmooth: no visible binding for global variable 'sd'
plot.ordPen: no visible global function definition for 'grey'
plot.ordPen: no visible global function definition for 'devAskNewPage'
plot.ordPen: no visible global function definition for 'plot'
plot.ordPen: no visible global function definition for 'lines'
predict.ordPen: no visible global function definition for 'plogis'
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
ORICC1: no visible binding for global variable 'sd'
ORICC1: no visible global function definition for 'write.table'
ORICC1: no visible global function definition for 'postscript'
ORICC1: no visible global function definition for 'jpeg'
ORICC1: no visible global function definition for 'plot'
ORICC1: no visible global function definition for 'points'
ORICC1: no visible global function definition for 'dev.off'
ORICC1: no visible global function definition for 'par'
ORICC2: no visible binding for global variable 'sd'
ORICC2: no visible global function definition for 'write.table'
ORICC2: no visible global function definition for 'postscript'
ORICC2: no visible global function definition for 'jpeg'
ORICC2: no visible global function definition for 'plot'
ORICC2: no visible global function definition for 'points'
ORICC2: no visible global function definition for 'dev.off'
ORICC2: no visible global function definition for 'par'
Undefined global functions or variables:
  dev.off jpeg par plot points postscript sd write.table
Consider adding
  importFrom("grDevices", "dev.off", "jpeg", "postscript")
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
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'
plot.osmar: no visible global function definition for 'gray'
plot_nodes: no visible global function definition for 'points'
plot_nodes: no visible global function definition for 'plot'
plot_ways: no visible global function definition for 'plot'
plot_ways: no visible global function definition for 'lines'
ways_nodes2Line: no visible global function definition for 'Line'
ways_nodes2Polygon: no visible global function definition for 'Polygon'
Undefined global functions or variables:
  CRS E E<- Line Lines Polygon Polygons SpatialLines
  SpatialLinesDataFrame SpatialPointsDataFrame SpatialPolygons
  SpatialPolygonsDataFrame distHaversine graph.edgelist gray lines plot
  points
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
Electre3_AlphaBetaThresholds: no visible global function definition for
  'plot'
Electre3_SimpleThresholds: no visible global function definition for
  'plot'
Electre_1: no visible global function definition for 'plot'
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
paf: no visible global function definition for 'as.formula'
paf: no visible global function definition for 'model.response'
paf: no visible global function definition for 'model.frame'
paf: no visible global function definition for 'model.matrix'
plot.paf: no visible global function definition for 'plot'
plot.paf: no visible global function definition for 'lines'
Undefined global functions or variables:
  as.formula lines model.frame model.matrix model.response plot
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
GOpredict: no visible global function definition for 'fisher.test'
KEGGpredict: no visible global function definition for 'fisher.test'
ProteinCluster: no visible global function definition for 'ecdf'
ProteinCluster: no visible global function definition for 'as.hclust'
ProteinCluster: no visible global function definition for
  'as.dendrogram'
ProteinCluster : addE: no visible global function definition for
  'is.leaf'
ProteinCluster: no visible global function definition for 'plot'
SignificantSubcluster: no visible global function definition for
  'order.dendrogram'
SignificantSubcluster: no visible global function definition for
  'fisher.test'
SignificantSubcluster: no visible global function definition for 'plot'
Undefined global functions or variables:
  as.dendrogram as.hclust ecdf fisher.test is.leaf order.dendrogram
  plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "as.dendrogram", "as.hclust", "ecdf",
             "fisher.test", "is.leaf", "order.dendrogram")
to your NAMESPACE file.
adalasso: no visible global function definition for 'predict'
lm.ridge.univariate: no visible global function definition for 'sd'
mylars: no visible global function definition for 'predict'
mylars: no visible binding for global variable 'var'
performance.pcor: no visible global function definition for
  'ggm.test.edges'
performance.pcor: no visible global function definition for 'var'
ridge.cv: no visible global function definition for 'coef'
ridge.cv: no visible global function definition for 'plot'
Undefined global functions or variables:
  coef ggm.test.edges plot predict sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "predict", "sd", "var")
to your NAMESPACE file.
draw.pcaBootPlot: no visible global function definition for 'plot'
draw.pcaBootPlot: no visible global function definition for 'grid'
draw.pcaBootPlot: no visible global function definition for 'points'
draw.pcaBootPlot: no visible global function definition for 'symbols'
draw.pcaBootPlot: no visible global function definition for 'legend'
pcaBootPlot: no visible global function definition for 'prcomp'
pcaBootPlot: no visible global function definition for 'cor'
pcaBootPlot: no visible global function definition for 'quantile'
pcaBootPlot: no visible global function definition for 'pdf'
pcaBootPlot: no visible global function definition for 'dev.off'
Undefined global functions or variables:
  cor dev.off grid legend pdf plot points prcomp quantile symbols
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "grid", "legend", "plot", "points", "symbols")
  importFrom("stats", "cor", "prcomp", "quantile")
to your NAMESPACE file.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.3Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  13.2Mb
peacf: no visible global function definition for 'is.ts'
peacf: no visible global function definition for 'cycle'
peacf: no visible global function definition for 'ts.intersect'
peacf: no visible global function definition for 'lag'
peacf: no visible global function definition for 'ts'
peacf: no visible global function definition for 'pchisq'
peacf.plot: no visible global function definition for 'plot'
peacf.plot: no visible global function definition for 'segments'
peacf.plot: no visible global function definition for 'title'
pear: no visible global function definition for 'cycle'
pear: no visible global function definition for 'pchisq'
peboxplot: no visible global function definition for 'cycle'
peboxplot: no visible global function definition for 'boxplot'
peboxplot: no visible global function definition for 'title'
peplot: no visible global function definition for 'par'
peplot: no visible global function definition for 'cycle'
peplot: no visible global function definition for 'plot'
peplot: no visible global function definition for 'identify'
peplot: no visible global function definition for 'mtext'
Undefined global functions or variables:
  boxplot cycle identify is.ts lag mtext par pchisq plot segments title
  ts ts.intersect
Consider adding
  importFrom("graphics", "boxplot", "identify", "mtext", "par", "plot",
             "segments", "title")
  importFrom("stats", "cycle", "is.ts", "lag", "pchisq", "ts",
             "ts.intersect")
to your NAMESPACE file.
PearsonICA: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'rnorm'
PearsonICAdemo: no visible global function definition for 'dev.new'
PearsonICAdemo: no visible global function definition for 'par'
PearsonICAdemo: no visible global function definition for 'plot'
PearsonICAdemo: no visible global function definition for 'axis'
PearsonICAdemo: no visible global function definition for 'title'
PearsonICAdemo: no visible global function definition for 'lines'
Undefined global functions or variables:
  axis dev.new lines par plot rnorm title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "axis", "lines", "par", "plot", "title")
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11090 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11090 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/phateR.Rcheck/00install.out' for details.
fox: no visible binding for global variable 'sd'
fox: no visible global function definition for 'cor'
fox: no visible global function definition for 'interaction.plot'
fox: no visible global function definition for 'reorder'
fox: no visible global function definition for 'plot'
kang: no visible global function definition for 'var'
kang: no visible binding for global variable 'sd'
kang: no visible global function definition for 'cor'
kang: no visible global function definition for 'interaction.plot'
kang: no visible global function definition for 'reorder'
kang: no visible global function definition for 'plot'
nahu: no visible global function definition for 'interaction.plot'
nahu: no visible global function definition for 'reorder'
nahu: no visible global function definition for 'plot'
thsu: no visible global function definition for 'median'
thsu: no visible binding for global variable 'sd'
thsu: no visible global function definition for 'cor'
thsu: no visible global function definition for 'interaction.plot'
thsu: no visible global function definition for 'reorder'
thsu: no visible global function definition for 'plot'
Undefined global functions or variables:
  cor interaction.plot median plot reorder sd var
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cor", "interaction.plot", "median", "reorder",
             "sd", "var")
to your NAMESPACE file.
Running 'testthat.R' [39s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenocamapi)
  Loading required package: data.table
  Loading required package: rjson
  Loading required package: RCurl
  > library(data.table)
  > 
  > test_check("phenocamapi")
  trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  Content type 'application/octet-stream' length 205436 bytes (200 KB)
  ==================================================
  downloaded 200 KB
  
  -- 1. Failure: test getting awb data (@testphenocamapi.R#42)  ------------------
  `wb` not equal to "LIKELY_NO".
  target is NULL, current is character
  
  == testthat results  ===========================================================
  [ OK: 5 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: test getting awb data (@testphenocamapi.R#42) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting_started_phenocam_api.Rmd' using rmarkdown
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 205436 bytes (200 KB)
==================================================
downloaded 200 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/2013/05/dukehw_2013_05_31_150331.jpg'
Content type 'image/jpeg' length 470270 bytes (459 KB)
==================================================
downloaded 459 KB

Quitting from lines 282-298 (getting_started_phenocam_api.Rmd) 
Error: processing vignette 'getting_started_phenocam_api.Rmd' failed with diagnostics:
a character vector argument expected
--- failed re-building 'getting_started_phenocam_api.Rmd'

--- re-building 'phenocam_data_fusion.Rmd' using rmarkdown
Loading required package: rjson
Loading required package: RCurl
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 205436 bytes (200 KB)
==================================================
downloaded 200 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/oregonMP/ROI/oregonMP_EN_1000_3day.csv'
Content type 'application/octet-stream' length 271464 bytes (265 KB)
==================================================
downloaded 265 KB

--- finished re-building 'phenocam_data_fusion.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.0Mb
    libs      1.5Mb
plotAuto: no visible global function definition for 'window'
plotAuto: no visible global function definition for 'title'
plotAuto: no visible global function definition for 'axis'
plotAuto: no visible global function definition for 'box'
plotCumu: no visible global function definition for 'title'
plotCumu: no visible global function definition for 'axis'
plotCumu: no visible global function definition for 'box'
plotDens : panel.dens: no visible global function definition for 'var'
plotDens : panel.dens: no visible global function definition for
  'quantile'
plotDens : panel.dens: no visible global function definition for
  'median'
plotDens: no visible global function definition for 'tail'
plotQuant: no visible global function definition for 'par'
plotQuant: no visible binding for global variable 'quantile'
plotQuant: no visible global function definition for 'plot'
plotQuant: no visible global function definition for 'lines'
plotQuant: no visible global function definition for 'bxp'
plotQuant: no visible global function definition for 'matplot'
plotQuant: no visible global function definition for 'axis'
plotQuant: no visible global function definition for 'box'
plotQuant: no visible global function definition for 'title'
plotSplom: no visible global function definition for 'pairs'
plotTrace : panel.trace: no visible global function definition for
  'var'
plotTrace : panel.trace: no visible global function definition for
  'median'
plotTrace: no visible global function definition for 'tail'
Undefined global functions or variables:
  axis box bxp lines matplot median pairs par plot quantile tail title
  var window
Consider adding
  importFrom("graphics", "axis", "box", "bxp", "lines", "matplot",
             "pairs", "par", "plot", "title")
  importFrom("stats", "median", "quantile", "var", "window")
  importFrom("utils", "tail")
to your NAMESPACE file.
.MCM: no visible global function definition for 'runif'
.MCM: no visible global function definition for 'rmultinom'
.MCM: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'optimize'
.MCM : f: no visible global function definition for 'mahalanobis'
.MCM: no visible global function definition for 'alarm'
.igpark: no visible global function definition for 'kmeans'
.loglik: no visible global function definition for 'mahalanobis'
.plot.gpcm: no visible global function definition for 'plot'
.plot.gpcm: no visible global function definition for 'lines'
.plot.gpcm: no visible global function definition for 'legend'
.rwgpar: no visible global function definition for 'rexp'
.weights: no visible global function definition for 'mahalanobis'
Undefined global functions or variables:
  alarm kmeans legend lines mahalanobis optimize plot rexp rmultinom
  runif
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "kmeans", "mahalanobis", "optimize", "rexp",
             "rmultinom", "runif")
  importFrom("utils", "alarm")
to your NAMESPACE file.
plot.sigma: no visible global function definition for 'plot'
smooth: no visible global function definition for 'genoud'
Undefined global functions or variables:
  genoud plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R      6.8Mb
    data   4.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
fnfam: no visible global function definition for 'qnorm'
fx: no visible global function definition for 'qnorm'
normplot : <local> : replot: no visible global function definition for
  'qnorm'
normplot : <local> : replot: no visible global function definition for
  'pnorm'
normplot : <local> : replot: no visible global function definition for
  'plot'
normplot : <local> : replot: no visible global function definition for
  'dnorm'
normplot : <local> : replot: no visible global function definition for
  'points'
normplot : <local> : replot: no visible global function definition for
  'lines'
normplot : <local> : regen: no visible global function definition for
  'rnorm'
normplot : <local> : regen: no visible global function definition for
  'rexp'
nsibs: no visible global function definition for 'qnorm'
ntdt: no visible global function definition for 'uniroot'
plotDom: no visible global function definition for 'plot'
plotNsibs: no visible global function definition for 'plot'
plotNtdt: no visible global function definition for 'plot'
plotNtdt: no visible global function definition for 'lines'
plotNtdt: no visible global function definition for 'legend'
ptdt: no visible global function definition for 'optimize'
ptdt: no visible global function definition for 'uniroot'
ptdt: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  dnorm legend lines optimize plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/3.6/PPRL.Rcheck/00install.out' for details.
LDA.Tree : Find.proj: no visible binding for global variable 'var'
LDA.Tree : Find.proj: no visible binding for global variable 'IQR'
LDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'var'
PDA.Tree : Find.proj: no visible binding for global variable 'median'
PDA.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.Tree : Find.proj: no visible binding for global variable 'var'
PP.Tree : Find.proj: no visible binding for global variable 'median'
PP.Tree : Find.proj: no visible binding for global variable 'IQR'
PP.optimize.Huber: no visible binding for global variable 'sd'
PP.optimize.anneal: no visible binding for global variable 'sd'
PP.optimize.plot: no visible binding for global variable 'sd'
PP.optimize.plot: no visible global function definition for 'hist'
PP.optimize.plot: no visible global function definition for 'text'
PP.optimize.plot: no visible global function definition for 'par'
PP.optimize.plot: no visible global function definition for 'plot'
PP.optimize.plot: no visible global function definition for 'colors'
PP.optimize.plot: no visible global function definition for 'pairs'
PP.optimize.random: no visible binding for global variable 'sd'
Undefined global functions or variables:
  IQR colors hist median pairs par plot sd text var
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "hist", "pairs", "par", "plot", "text")
  importFrom("stats", "IQR", "median", "sd", "var")
to your NAMESPACE file.
basisplot: no visible global function definition for 'plot'
basisplot: no visible global function definition for 'abline'
basisplot: no visible global function definition for 'text'
basisplot: no visible global function definition for 'par'
plot.prinsimp: no visible global function definition for 'screeplot'
plot.simpart: no visible global function definition for 'par'
position_text: no visible global function definition for 'par'
position_text: no visible global function definition for 'strwidth'
simpart.formula: no visible global function definition for 'terms'
simpart.formula: no visible global function definition for
  'model.matrix'
varperc: no visible global function definition for 'plot'
varperc: no visible global function definition for 'lines'
varperc: no visible global function definition for 'text'
varsimp: no visible global function definition for 'plot'
varsimp: no visible global function definition for 'points'
varsimp: no visible global function definition for 'text'
varsimp: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline lines model.matrix par plot points screeplot strwidth terms
  text
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points",
             "strwidth", "text")
  importFrom("stats", "model.matrix", "screeplot", "terms")
to your NAMESPACE file.
.pfda.fstep: no visible global function definition for 'dist'
.pfda.main: no visible global function definition for 'plot'
.pfda.mstep: no visible global function definition for 'cov'
Undefined global functions or variables:
  cov dist plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "cov", "dist")
to your NAMESPACE file.
GPois: no visible global function definition for 'dnorm'
GPois: no visible binding for global variable 'poisson'
GPois: no visible global function definition for 'predict'
GPois: no visible global function definition for 'fitted'
GPois: no visible global function definition for 'residuals'
GPois: no visible global function definition for 'smooth.spline'
ProDenICA: no visible global function definition for 'rnorm'
d.gaussmix: no visible global function definition for 'dnorm'
djordan: no visible global function definition for 'dt'
djordan: no visible global function definition for 'dunif'
mixmat: no visible global function definition for 'rnorm'
mixmat: no visible global function definition for 'runif'
plot.ProDenICA: no visible global function definition for 'plot'
r.gaussmix: no visible global function definition for 'rmultinom'
r.gaussmix: no visible global function definition for 'rnorm'
rjordan: no visible global function definition for 'rt'
rjordan: no visible global function definition for 'runif'
rmix.dexp: no visible global function definition for 'runif'
Undefined global functions or variables:
  dnorm dt dunif fitted plot poisson predict residuals rmultinom rnorm
  rt runif smooth.spline
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dnorm", "dt", "dunif", "fitted", "poisson",
             "predict", "residuals", "rmultinom", "rnorm", "rt", "runif",
             "smooth.spline")
to your NAMESPACE file.
addpi: no visible global function definition for 'lines'
genPerms: no visible global function definition for 'combn'
getVar: no visible global function definition for 'glm'
getVar: no visible global function definition for 'binomial'
getVar: no visible global function definition for 'var'
pba: no visible global function definition for 'glm'
pba: no visible global function definition for 'binomial'
pba: no visible global function definition for 'predict'
pba: no visible global function definition for 'rbinom'
pcr: no visible global function definition for 'quantile'
plotpi: no visible global function definition for 'plot'
plotpi: no visible global function definition for 'axis'
plotpi: no visible global function definition for 'abline'
plotpi: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline axis binomial combn glm lines plot predict quantile rbinom var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "plot")
  importFrom("stats", "binomial", "glm", "predict", "quantile", "rbinom",
             "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
    libs   1.8Mb
addcircle: no visible global function definition for 'lines'
addclassifierboundary: no visible global function definition for 'par'
addclassifierboundary: no visible global function definition for
  'contour'
plot.protoclass: no visible global function definition for 'plot'
plot.protoclass: no visible global function definition for 'box'
plot.protoclass: no visible global function definition for 'rgb2hsv'
plot.protoclass: no visible global function definition for 'col2rgb'
plot.protoclass: no visible global function definition for 'points'
plot.protoclass: no visible global function definition for 'hsv'
predict.protoclass: no visible global function definition for 'knn1'
Undefined global functions or variables:
  box col2rgb contour hsv knn1 lines par plot points rgb2hsv
Consider adding
  importFrom("grDevices", "col2rgb", "hsv", "rgb2hsv")
  importFrom("graphics", "box", "contour", "lines", "par", "plot",
             "points")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
PurBayes: no visible global function definition for 'update'
PurBayes: no visible global function definition for 'sd'
plot.PurBayes: no visible global function definition for 'plot'
plot.PurBayes: no visible global function definition for 'quantile'
plot.PurBayes: no visible global function definition for 'lines'
summary.PurBayes : <anonymous>: no visible global function definition
  for 'quantile'
Undefined global functions or variables:
  lines plot quantile sd update
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "quantile", "sd", "update")
to your NAMESPACE file.
csQCAbinTest: no visible global function definition for 'p.adjust'
fsQCApermTest: no visible global function definition for 'p.adjust'
mvQCAbinTest: no visible global function definition for 'p.adjust'
p.threshold.adjust: no visible global function definition for
  'p.adjust'
plot.fsQCApt: no visible global function definition for 'dev.cur'
plot.fsQCApt: no visible global function definition for 'dev.new'
plot.fsQCApt: no visible global function definition for 'par'
plot.fsQCApt: no visible global function definition for 'plot'
plot.fsQCApt: no visible global function definition for 'density'
plot.fsQCApt: no visible global function definition for 'axis'
plot.fsQCApt: no visible global function definition for 'polygon'
plot.fsQCApt: no visible global function definition for 'points'
plot.fsQCApt: no visible global function definition for 'hist'
summary.csQCAbt: no visible global function definition for
  'printCoefmat'
summary.fsQCApt: no visible global function definition for
  'printCoefmat'
summary.mvQCAbt: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  axis density dev.cur dev.new hist p.adjust par plot points polygon
  printCoefmat
Consider adding
  importFrom("grDevices", "dev.cur", "dev.new")
  importFrom("graphics", "axis", "hist", "par", "plot", "points",
             "polygon")
  importFrom("stats", "density", "p.adjust", "printCoefmat")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
alphaf: no visible global function definition for 'pchisq'
alphaf: no visible global function definition for 'dbinom'
conout: no visible global function definition for 'sd'
ibgaout: no visible global function definition for 'qnorm'
ibgaout: no visible global function definition for 'pnorm'
plot.qualint: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'rnorm'
powerval: no visible global function definition for 'qnorm'
powerval: no visible global function definition for 'pnorm'
print.expplot: no visible global function definition for 'gray'
print.expplot: no visible binding for global variable 'coef'
print.outplot: no visible global function definition for 'gray'
print.outplot: no visible binding for global variable 'coef'
qualint: no visible global function definition for 'qnorm'
qualint: no visible global function definition for 'plot'
qualval: no visible global function definition for 'qnorm'
qualval: no visible global function definition for 'plot'
surout: no visible global function definition for 'tail'
surout: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef dbinom gray pchisq plot pnorm qnorm rnorm sd tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "plot")
  importFrom("stats", "coef", "dbinom", "pchisq", "pnorm", "qnorm",
             "rnorm", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   2.5Mb
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
getsonde: no visible global function definition for 'read.table'
plotsonde: no visible global function definition for 'par'
plotwind: no visible global function definition for 'plot'
plotwind: no visible global function definition for 'mtext'
plotwind: no visible global function definition for 'abline'
skewt.axis: no visible global function definition for 'par'
skewt.axis: no visible global function definition for 'plot'
skewt.axis: no visible global function definition for 'axis'
skewt.axis: no visible global function definition for 'mtext'
skewt.axis: no visible global function definition for 'segments'
skewt.axis: no visible global function definition for 'text'
skewt.axis: no visible global function definition for 'lines'
skewt.lines: no visible global function definition for 'lines'
skewt.points: no visible global function definition for 'points'
station.symbol: no visible global function definition for 'sd'
station.symbol: no visible global function definition for 'par'
station.symbol: no visible global function definition for 'lines'
station.symbol: no visible global function definition for 'polygon'
station.symbol: no visible global function definition for 'text'
station.symbol: no visible global function definition for 'segments'
Undefined global functions or variables:
  abline axis lines mtext par plot points polygon read.table sd
  segments text
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "plot", "points", "polygon", "segments", "text")
  importFrom("stats", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/randstr.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   3.8Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/Rblpapi.Rcheck/00install.out' for details.
brewer.pal: no visible global function definition for 'rgb'
display.brewer.all: no visible global function definition for 'par'
display.brewer.all: no visible global function definition for 'plot'
display.brewer.all: no visible global function definition for 'rect'
display.brewer.all: no visible global function definition for 'text'
display.brewer.pal: no visible global function definition for 'image'
Undefined global functions or variables:
  image par plot rect rgb text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "image", "par", "plot", "rect", "text")
to your NAMESPACE file.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       3.9Mb
    libs      2.9Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      1.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      2.0Mb
CUR: no visible global function definition for 'runif'
CUR: no visible global function definition for 'new'
plotLeverage,CURobj: no visible global function definition for 'plot'
plotLeverage,CURobj: no visible global function definition for 'points'
plotLeverage,CURobj: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline new plot points runif
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("methods", "new")
  importFrom("stats", "runif")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
distimage: no visible binding for global variable 'terrain.colors'
distimage: no visible global function definition for 'filled.contour'
distimage: no visible global function definition for 'title'
distimage: no visible global function definition for 'axis'
distimage: no visible global function definition for 'lines'
drawkpc: no visible global function definition for 'plot'
drawkpc: no visible global function definition for 'segments'
drawkpc: no visible global function definition for 'lines'
modelimage: no visible binding for global variable 'topo.colors'
modelimage: no visible global function definition for 'filled.contour'
modelimage: no visible global function definition for 'title'
modelimage: no visible global function definition for 'axis'
modelimage: no visible global function definition for 'lines'
sincdata: no visible global function definition for 'runif'
sincdata: no visible global function definition for 'rnorm'
Undefined global functions or variables:
  axis filled.contour lines plot rnorm runif segments terrain.colors
  title topo.colors
Consider adding
  importFrom("grDevices", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "filled.contour", "lines", "plot",
             "segments", "title")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/readr.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.7Mb
AutoCorrelationLRtest: no visible global function definition for
  'logLik'
AutoCorrelationLRtest: no visible global function definition for
  'pchisq'
REEMtree: no visible global function definition for 'terms'
REEMtree: no visible binding for global variable 'SubsetVector'
REEMtree: no visible global function definition for 'predict'
REEMtree: no visible global function definition for 'logLik'
fitted.REEMtree: no visible global function definition for 'fitted'
plot.REEMtree: no visible global function definition for 'plot'
predict.REEMtree: no visible global function definition for 'predict'
residuals.REEMtree: no visible global function definition for
  'residuals'
Undefined global functions or variables:
  SubsetVector fitted logLik pchisq plot predict residuals terms
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "fitted", "logLik", "pchisq", "predict",
             "residuals", "terms")
to your NAMESPACE file.
CapDistSlope: no visible global function definition for 'coef'
CapDistSlope: no visible global function definition for 'lm'
EnergyEntropyDecomp: no visible global function definition for 'legend'
FernholzDecomp: no visible global function definition for 'legend'
Invest: no visible global function definition for 'par'
Invest: no visible global function definition for 'legend'
SimMarketModel: no visible global function definition for 'rnorm'
plot.capdist: no visible global function definition for 'plot'
plot.capdist: no visible global function definition for 'abline'
plot.capdist: no visible global function definition for 'lm'
plot.toymkt: no visible global function definition for 'par'
plot.toymkt: no visible global function definition for 'plot'
plot.toymkt: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline coef legend lm par plot rnorm
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "coef", "lm", "rnorm")
to your NAMESPACE file.
RearrangeData: no visible global function definition for 'rainbow'
RearrangeData: no visible global function definition for 'hclust'
RearrangeData: no visible global function definition for
  'as.dendrogram'
RearrangeData: no visible global function definition for 'heatmap'
RearrangeData: no visible global function definition for 'pdf'
RearrangeData: no visible global function definition for
  'colorRampPalette'
RearrangeData: no visible global function definition for 'legend'
RearrangeData: no visible global function definition for 'dev.off'
RearrangeJoseph: no visible global function definition for
  'write.table'
RearrangeJoseph: no visible global function definition for
  'as.dendrogram'
RearrangeJoseph: no visible global function definition for
  'order.dendrogram'
colorDendClass : colLab: no visible global function definition for
  'is.leaf'
colorDendClass: no visible global function definition for 'dendrapply'
colorDendClass: no visible global function definition for 'plot'
testData1: no visible global function definition for 'runif'
testData1: no visible global function definition for 'image'
testData2: no visible global function definition for 'runif'
testData2: no visible global function definition for 'image'
Undefined global functions or variables:
  as.dendrogram colorRampPalette dendrapply dev.off hclust heatmap
  image is.leaf legend order.dendrogram pdf plot rainbow runif
  write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off", "pdf",
             "rainbow")
  importFrom("graphics", "image", "legend", "plot")
  importFrom("stats", "as.dendrogram", "dendrapply", "hclust", "heatmap",
             "is.leaf", "order.dendrogram", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file.
plot.reweight: no visible global function definition for 'par'
plot.reweight: no visible global function definition for 'plot'
plot.reweight: no visible global function definition for 'density'
plot.reweight: no visible global function definition for 'rug'
reweight: no visible global function definition for 'aggregate'
search.best.h: no visible global function definition for 'quantile'
Undefined global functions or variables:
  aggregate density par plot quantile rug
Consider adding
  importFrom("graphics", "par", "plot", "rug")
  importFrom("stats", "aggregate", "density", "quantile")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'RFmerge-RainfallExample-minimal.Rmd' using rmarkdown

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Loading required package: sp
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: D:/temp/RtmpsJo0uf/RLIBS_1e5446cf0209b/rgdal/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: D:/temp/RtmpsJo0uf/RLIBS_1e5446cf0209b/rgdal/proj
 Linking to sp version: 1.4-1 
(C) 2019 M. Zambrano-Bigiarini and Oscar M. Baez-Villanueva (GPL >=3 license)
Type 'citation('RFmerge')' to see how to cite this package
Quitting from lines 268-274 (RFmerge-RainfallExample-minimal.Rmd) 
Error: processing vignette 'RFmerge-RainfallExample-minimal.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building 'RFmerge-RainfallExample-minimal.Rmd'

SUMMARY: processing the following file failed:
  'RFmerge-RainfallExample-minimal.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   2.8Mb
    libs      6.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rglpk.Rcheck/00install.out' for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.5Mb
    libs    2.1Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.7Mb
    libs   5.1Mb
R2ngon: no visible global function definition for 'approx'
plotR2pre: no visible global function definition for 'plot'
plotR2pre: no visible global function definition for 'points'
plotR2pre: no visible global function definition for 'gray'
plotR2pre: no visible global function definition for 'legend'
plotR2pre: no visible global function definition for 'rainbow'
Undefined global functions or variables:
  approx gray legend plot points rainbow
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "legend", "plot", "points")
  importFrom("stats", "approx")
to your NAMESPACE file.
plot.ijzip: no visible global function definition for 'plot'
plot.ijzip : <anonymous>: no visible global function definition for
  'plot'
plot.ijzip: no visible global function definition for 'axis'
read.ijzip: no visible global function definition for 'unzip'
Undefined global functions or variables:
  axis plot unzip
Consider adding
  importFrom("graphics", "axis", "plot")
  importFrom("utils", "unzip")
to your NAMESPACE file.
KM.plot: no visible global function definition for 'plot'
KM.plot: no visible global function definition for 'lines'
SchoenSmooth: no visible global function definition for 'lm'
llCoxReg: no visible binding for global variable 'time'
risksetAUC: no visible global function definition for 'abline'
risksetROC: no visible global function definition for 'abline'
weightedKM: no visible binding for global variable 'time'
Undefined global functions or variables:
  abline lines lm plot time
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "lm", "time")
to your NAMESPACE file.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.6/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.6/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
cv.coef: no visible global function definition for 'sd'
normalize.softmax: no visible global function definition for 'plogis'
plot.rknnBeg: no visible global function definition for 'plot'
plot.rknnBel: no visible global function definition for 'plot'
plot.rknnSupport: no visible global function definition for 'dotchart'
predicted: no visible global function definition for 'influence'
predicted: no visible global function definition for 'fitted'
predicted: no visible global function definition for 'resid'
pressresid: no visible global function definition for 'influence'
pressresid: no visible global function definition for 'resid'
Undefined global functions or variables:
  dotchart fitted influence plogis plot resid sd
Consider adding
  importFrom("graphics", "dotchart", "plot")
  importFrom("stats", "fitted", "influence", "plogis", "resid", "sd")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rmagic.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.1Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.6Mb
GIC: no visible global function definition for 'integrate'
QM.poisson: no visible global function definition for 'ppois'
QM.poisson: no visible global function definition for 'dpois'
cplot.robustgam: no visible global function definition for 'plot'
expect.poisson: no visible global function definition for 'dpois'
expect.poisson: no visible global function definition for 'ppois'
pred.robustgam: no visible global function definition for
  'Predict.matrix'
robust.sigma: no visible global function definition for 'median'
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.GIC.optim: no visible global function definition for 'optim'
robustgam.crossval : w.fun: no visible global function definition for
  'covMcd'
robustgam.crossval: no visible global function definition for
  'integrate'
smooth.construct.tr.smooth.spec: no visible global function definition
  for 'quantile'
w.binomial: no visible global function definition for 'pbinom'
w.poisson: no visible global function definition for 'ppois'
Undefined global functions or variables:
  Predict.matrix covMcd dpois integrate median optim pbinom plot ppois
  quantile s smooth.construct.cr.smooth.spec
  smooth.construct.ps.smooth.spec smooth.construct.tp.smooth.spec
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dpois", "integrate", "median", "optim", "pbinom",
             "ppois", "quantile")
to your NAMESPACE file.
ROSE.eval: no visible global function definition for 'methods'
ROSE.eval: no visible binding for global variable 'model.frame'
ROSE.eval: no visible binding for global variable 'predict'
adj.formula: no visible global function definition for 'terms'
adj.formula: no visible global function definition for 'as.formula'
omnibus.balancing: no visible binding for global variable 'model.frame'
ou.sampl: no visible global function definition for 'rbinom'
over.sampl: no visible global function definition for 'rbinom'
plot.roc.inner: no visible global function definition for 'plot'
roc.curve: no visible global function definition for 'lines'
roc.curve: no visible global function definition for 'abline'
rose.real: no visible binding for global variable 'sd'
rose.real: no visible global function definition for 'sd'
rose.real: no visible global function definition for 'rnorm'
rose.sampl: no visible global function definition for 'rbinom'
under.sampl: no visible global function definition for 'rbinom'
Undefined global functions or variables:
  abline as.formula lines methods model.frame plot predict rbinom rnorm
  sd terms
Consider adding
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "as.formula", "model.frame", "predict", "rbinom",
             "rnorm", "sd", "terms")
  importFrom("utils", "methods")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.7Mb
    libs   2.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    libs    1.8Mb
    tests   1.3Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
.computekappa: no visible global function definition for 'pnorm'
.computekappa: no visible global function definition for 'dnorm'
.initmethod : <anonymous>: no visible global function definition for
  'median'
.initmethod: no visible global function definition for 'model.matrix'
.mspe: no visible global function definition for 'rnorm'
.mspe : <anonymous>: no visible global function definition for 'rnorm'
makedata: no visible global function definition for 'rnorm'
makedata : addraneff: no visible global function definition for 'rnorm'
plot.meanssaemodel: no visible global function definition for 'par'
plot.meanssaemodel: no visible global function definition for 'plot'
plot.meanssaemodel: no visible global function definition for 'lines'
plot.meanssaemodel: no visible global function definition for 'axis'
plot.meanssaemodel: no visible global function definition for 'grid'
plot.meanssaemodel: no visible global function definition for 'box'
plot.meanssaemodel: no visible global function definition for 'legend'
plot.meanssaemodel: no visible global function definition for 'arrows'
saemodel: no visible global function definition for 'model.frame'
saemodel: no visible global function definition for 'model.response'
saemodel: no visible global function definition for 'model.matrix'
summary.fitsaemodel: no visible global function definition for 'pt'
summary.fitsaemodel: no visible global function definition for
  'printCoefmat'
Undefined global functions or variables:
  arrows axis box dnorm grid legend lines median model.frame
  model.matrix model.response par plot pnorm printCoefmat pt rnorm
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "grid", "legend",
             "lines", "par", "plot")
  importFrom("stats", "dnorm", "median", "model.frame", "model.matrix",
             "model.response", "pnorm", "printCoefmat", "pt", "rnorm")
to your NAMESPACE file.
convexhull: no visible global function definition for 'chull'
convexhull: no visible global function definition for 'rnorm'
drawcompletegraph: no visible global function definition for 'plot'
drawcompletegraph: no visible global function definition for 'segments'
getbag: no visible global function definition for 'plot'
getbag: no visible global function definition for 'chull'
getbag: no visible global function definition for 'polygon'
getbag: no visible global function definition for 'points'
inflate: no visible global function definition for 'rnorm'
rsmed: no visible global function definition for 'runif'
rsplot: no visible global function definition for 'plot'
rsplot: no visible global function definition for 'chull'
rsplot: no visible global function definition for 'polygon'
rsplot: no visible global function definition for 'points'
rsrings: no visible global function definition for 'plot'
rsrings: no visible global function definition for 'chull'
rsrings: no visible global function definition for 'polygon'
rsrings: no visible global function definition for 'points'
rstinterval: no visible global function definition for 'plot'
rstinterval: no visible global function definition for 'runif'
rstinterval: no visible global function definition for 'rnorm'
rstinterval: no visible global function definition for 'chull'
rstinterval: no visible global function definition for 'polygon'
Undefined global functions or variables:
  chull plot points polygon rnorm runif segments
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "plot", "points", "polygon", "segments")
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.6/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.6/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.6/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
addNoisyCopies: no visible global function definition for 'rnorm'
eta: no visible global function definition for 'var'
gaussClassifier: no visible global function definition for 'runif'
getSigma: no visible global function definition for 'sd'
getSigma: no visible binding for global variable 'sd'
sfaClassify: no visible global function definition for 'rainbow'
sfaClassify: no visible global function definition for 'par'
sfaClassify: no visible global function definition for 'plot'
sfaClassify: no visible global function definition for 'points'
sfaClassify: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines par plot points rainbow rnorm runif sd var
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Name: SolrList-class
> ### Title: SolrList
> ### Aliases: class:SolrList SolrList-class length,SolrList-method
> ###   names,SolrList-method [<-,SolrList,ANY,ANY,ANY-method
> ###   [[,SolrList,ANY-method [,SolrList-method [[,SolrList-method
> ###   [[<-,SolrList-method unique,SolrList-method searchDocs
> ###   searchDocs,Solr SolrList coerce,Solr,SolrList-method
> ###   coerce,SolrList,DocCollection-method show,SolrList-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  4.07 0.16 4.33 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    4.4Mb
    libs  17.8Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/rstap.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.2Mb
barplot.rtconnect: no visible global function definition for 'rainbow'
barplot.rtconnect: no visible global function definition for 'text'
plot.rtconnect: no visible global function definition for 'par'
plot.rtconnect: no visible global function definition for 'plot'
plot.rtconnect: no visible global function definition for 'axis.Date'
rtconnect: no visible global function definition for 'read.table'
Undefined global functions or variables:
  axis.Date par plot rainbow read.table text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis.Date", "par", "plot", "text")
  importFrom("utils", "read.table")
to your NAMESPACE file.
plotGLCM: no visible global function definition for 'plot'
plotGLCM: no visible global function definition for 'points'
Undefined global functions or variables:
  plot points
Consider adding
  importFrom("graphics", "plot", "points")
to your NAMESPACE file.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   1.8Mb
RWBP.default: no visible global function definition for 'na.omit'
RWBP.default: no visible global function definition for 'kmeans'
RWBP.formula: no visible global function definition for 'model.extract'
plot.RWBP: no visible global function definition for 'plot'
predict.RWBP: no visible global function definition for 'head'
Undefined global functions or variables:
  head kmeans model.extract na.omit plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "kmeans", "model.extract", "na.omit")
  importFrom("utils", "head")
to your NAMESPACE file.
.dwt: no visible global function definition for 'median'
.udwt: no visible global function definition for 'median'
plotSignalTransformation: no visible global function definition for
  'plot'
plotSignalTransformation: no visible global function definition for
  'box'
plotSignalTransformation: no visible global function definition for
  'axis'
plotSignalTransformation: no visible global function definition for
  'lines'
plotSignalTransformation: no visible global function definition for
  'legend'
Undefined global functions or variables:
  axis box legend lines median plot
Consider adding
  importFrom("graphics", "axis", "box", "legend", "lines", "plot")
  importFrom("stats", "median")
to your NAMESPACE file.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
fit.saery.AR1: no visible global function definition for 'qnorm'
fit.saery.MA1: no visible global function definition for 'qnorm'
fit.saery.indep: no visible global function definition for 'qnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.AR1.typeII: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeI: no visible global function definition for
  'write.table'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'rnorm'
mse.saery.boot.MA1.typeII: no visible global function definition for
  'write.table'
plot.saery: no visible global function definition for 'devAskNewPage'
plot.saery: no visible global function definition for 'par'
plot.saery: no visible global function definition for 'plot'
plot.saery: no visible global function definition for 'abline'
plot.saery: no visible global function definition for 'title'
plot.saery: no visible global function definition for 'axis'
plot.saery: no visible global function definition for 'lines'
plot.saery: no visible global function definition for 'legend'
pvalue: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  abline axis devAskNewPage legend lines par plot pnorm qnorm rnorm
  title write.table
Consider adding
  importFrom("grDevices", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "legend", "lines", "par",
             "plot", "title")
  importFrom("stats", "pnorm", "qnorm", "rnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   1.9Mb
plot.scair: no visible global function definition for 'par'
plot.scair: no visible global function definition for 'plot'
plot.scair: no visible global function definition for 'points'
plot.scar: no visible global function definition for 'par'
plot.scar: no visible global function definition for 'plot'
plot.scar: no visible global function definition for 'points'
predict.scair: no visible global function definition for 'approx'
predict.scar: no visible global function definition for 'approx'
scair: no visible global function definition for 'gaussian'
scair: no visible global function definition for 'runif'
scair: no visible global function definition for 'rnorm'
scar: no visible global function definition for 'gaussian'
scar: no visible global function definition for 'glm.fit'
scar: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx gaussian glm.fit par plot points rnorm runif
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.5Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
adx: no visible global function definition for 'abline'
adx: no visible global function definition for 'legend'
dx: no visible global function definition for 'abline'
dx: no visible global function definition for 'legend'
maxd: no visible global function definition for 'abline'
maxd: no visible global function definition for 'legend'
pc: no visible global function definition for 'rainbow'
pc: no visible global function definition for 'plot'
pc: no visible global function definition for 'abline'
pc: no visible global function definition for 'legend'
pc: no visible global function definition for 'points'
pcu: no visible global function definition for 'rainbow'
pcu: no visible global function definition for 'plot'
pcu: no visible global function definition for 'abline'
pcu: no visible global function definition for 'legend'
pcu: no visible global function definition for 'points'
rmsd: no visible global function definition for 'abline'
rmsd: no visible global function definition for 'legend'
rsd: no visible global function definition for 'abline'
rsd: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend plot points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "plot", "points")
to your NAMESPACE file.
SEchart: no visible global function definition for 'plot'
SEchart: no visible global function definition for 'rect'
SEchart: no visible global function definition for 'par'
SEchart: no visible global function definition for 'grid'
SEchart: no visible global function definition for 'axis'
SEchart: no visible global function definition for 'text'
SEchart: no visible global function definition for 'lines'
SEchart: no visible global function definition for 'heat.colors'
SEchart: no visible global function definition for 'topo.colors'
SEchart: no visible global function definition for 'cm.colors'
SEchart: no visible global function definition for 'terrain.colors'
SEchart: no visible global function definition for 'gray.colors'
SEchart: no visible global function definition for 'rainbow'
SEchart: no visible global function definition for 'points'
SEchart: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par plot
  points rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "points", "rect", "text")
to your NAMESPACE file.
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'
getbinPost: no visible binding for global variable 'dbeta'
getbinPost: no visible binding for global variable 'pbeta'
getbinPost : fu: no visible global function definition for 'dbinom'
getbinPost : fu: no visible global function definition for 'predict'
getbinPost: no visible global function definition for 'integrate'
getbinPost: no visible global function definition for 'splinefun'
int.funct: no visible global function definition for 'integrate'
int.funct2: no visible global function definition for 'integrate'
min.abs: no visible global function definition for 'uniroot'
plot.SEL: no visible global function definition for 'plot'
print.SEL: no visible global function definition for 'integrate'
print.summary.SEL : foo1: no visible global function definition for
  'predict'
print.summary.SEL : foo2: no visible global function definition for
  'predict'
print.summary.SEL: no visible global function definition for
  'integrate'
quantSEL: no visible global function definition for 'predict'
quantSEL: no visible global function definition for 'splinefun'
rvSEL: no visible global function definition for 'runif'
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
plotenz : addmark: no visible global function definition for 'par'
plotenz : addmark: no visible global function definition for 'plot'
plotenz : addmark: no visible global function definition for 'text'
plotenz : addmark: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'segments'
plotenz : addband: no visible global function definition for 'text'
plotenz: no visible global function definition for 'layout'
plotenz: no visible global function definition for 'text'
plotenz: no visible global function definition for 'dev.new'
Undefined global functions or variables:
  dev.new layout par plot segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "plot", "segments", "text")
to your NAMESPACE file.
filter.PCA.default: no visible global function definition for
  'princomp'
filter.mRMR.default: no visible global function definition for
  'discretize'
gaussian.default: no visible global function definition for 'cov'
gaussian.default: no visible global function definition for
  'cov.shrink'
plot.verify.cv: no visible global function definition for 'plot'
plot.verify.cv: no visible global function definition for 'points'
plot.verify.ho: no visible global function definition for 'plot'
plot.verify.ho: no visible global function definition for 'points'
plot.verify.loo: no visible global function definition for 'plot'
plot.verify.loo: no visible global function definition for 'points'
predict.dpa1: no visible global function definition for 'cor'
predict.filter.PCA: no visible global function definition for 'predict'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'is.struct'
predict.filter.RegressionTreeFilter: no visible global function
  definition for 'var'
simulator.Simple1: no visible global function definition for 'rnorm'
verify.ho.default: no visible global function definition for 'predict'
verify.loo.default: no visible global function definition for 'predict'
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct plot points predict princomp
  rnorm var
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
plot.SII: no visible global function definition for 'plot'
plot.SII: no visible global function definition for 'lines'
plot.SII: no visible global function definition for 'abline'
plot.SII: no visible global function definition for 'legend'
sii : approx.l: no visible global function definition for 'approx'
sii.excel: no visible global function definition for 'predict'
sii.excel : approx.l: no visible global function definition for
  'approx'
Undefined global functions or variables:
  abline approx legend lines plot predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
cumallcausehr: no visible global function definition for 'integrate'
plotbe: no visible global function definition for 'plot'
plotbe: no visible global function definition for 'lines'
plotbe: no visible global function definition for 'legend'
plotcph: no visible global function definition for 'confint'
plotcph: no visible global function definition for 'plot'
plotcph: no visible global function definition for 'abline'
plotcph: no visible global function definition for 'axis'
plotcph: no visible global function definition for 'polygon'
plotcph: no visible global function definition for 'lines'
plotnae: no visible global function definition for 'plot'
simCR: no visible global function definition for 'rnorm'
simEBMT: no visible global function definition for 'model.matrix'
simexit: no visible global function definition for 'runif'
simexitinner: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix plot polygon
  rnorm runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
             "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
Simpsons: no visible global function definition for 'Mclust'
Simpsons: no visible global function definition for 'lm'
Simpsons: no visible global function definition for 'plot'
Simpsons: no visible global function definition for 'abline'
Simpsons: no visible global function definition for 'par'
Simpsons: no visible global function definition for 'legend'
Simpsons: no visible global function definition for 'txtProgressBar'
Simpsons: no visible global function definition for 'setTxtProgressBar'
Simpsons: no visible global function definition for 'quantile'
plot.Simpson: no visible global function definition for 'plot'
plot.Simpson: no visible global function definition for 'lm'
plot.Simpson: no visible global function definition for 'abline'
plot.Simpson: no visible global function definition for 'par'
plot.Simpson: no visible global function definition for 'legend'
Undefined global functions or variables:
  Mclust abline legend lm par plot quantile setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
slcestimates: no visible global function definition for 'par'
slcestimates: no visible global function definition for 'plot'
slcestimates: no visible global function definition for 'abline'
slcestimates: no visible global function definition for 'lines'
slcestimates: no visible global function definition for 'axis'
slcestimates: no visible global function definition for 'points'
slcestimates: no visible global function definition for 'title'
Undefined global functions or variables:
  abline axis lines par plot points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "title")
to your NAMESPACE file.
em: no visible global function definition for 'coxph'
em: no visible global function definition for 'optim'
plotpredictsmcure: no visible global function definition for 'plot'
plotpredictsmcure: no visible global function definition for 'matplot'
plotpredictsmcure: no visible global function definition for 'lines'
smcure: no visible binding for global variable 'na.omit'
smcure: no visible global function definition for 'model.frame'
smcure: no visible global function definition for 'model.extract'
smcure: no visible global function definition for 'model.matrix'
smcure: no visible global function definition for 'coxph'
smcure: no visible global function definition for 'survreg'
smcure: no visible binding for global variable 'var'
smcure: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim plot pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot", "plot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
Grad.sph: no visible global function definition for 'dist'
IMDS: no visible global function definition for 'cmdscale'
IMDS: no visible global function definition for 'as.dist'
IMDS: no visible global function definition for 'runif'
IMDS: no visible global function definition for 'optim'
idistSph: no visible global function definition for 'dist'
obj.sph: no visible global function definition for 'dist'
plot.imds: no visible binding for global variable 'lines'
plot.imds: no visible global function definition for 'plot'
plot.imds: no visible global function definition for 'text'
plot.imds: no visible global function definition for 'rect'
Undefined global functions or variables:
  as.dist cmdscale dist lines optim plot rect runif text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
lines.SmithWilsonYieldCurve: no visible global function definition for
  'lines'
plot.SmithWilsonYieldCurve: no visible global function definition for
  'plot'
points.SmithWilsonYieldCurve: no visible global function definition for
  'points'
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
plot.soma: no visible global function definition for 'plot'
soma: no visible global function definition for 'runif'
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building 'SongEvo.Rmd' using rmarkdown
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/3.6/SongEvo.Rcheck/
vign_test/SongEvo/vignettes/SongEvo_files/figure-latex/Examine\%20population\%2
0size\%20over\%20time-1.pdf' not found.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/3.6/SongEvo.Rcheck/vign_test/SongEvo/vignettes/SongEvo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SongEvo.log for more info.
--- failed re-building 'SongEvo.Rmd'

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

Error: Vignette re-building failed.
Execution halted
analyzeSP23Design: no visible global function definition for 'plot'
exploreSP23Design: no visible global function definition for
  'txtProgressBar'
exploreSP23Design: no visible global function definition for
  'setTxtProgressBar'
generateClinicalTrialData : <anonymous>: no visible global function
  definition for 'runif'
generateClinicalTrialData: no visible global function definition for
  'rbinom'
generateClinicalTrialData: no visible global function definition for
  'rexp'
mHP.b : crossingProbDiff: no visible global function definition for
  'pnorm'
mHP.b : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.b: no visible global function definition for 'qnorm'
mHP.b: no visible global function definition for 'uniroot'
mHP.c : crossingProbDiff: no visible global function definition for
  'Miwa'
mHP.c: no visible global function definition for 'uniroot'
mHP.c: no visible global function definition for 'qnorm'
performInterimLook: no visible global function definition for 'optim'
performInterimLook: no visible global function definition for
  'constrOptim'
performInterimLook: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  Miwa constrOptim optim plot pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   6.3Mb
Ell.Theta: no visible global function definition for 'ell.theta'
confid.int.theta: no visible global function definition for 'qchisq'
confid.int.theta : sim.c: no visible global function definition for
  'runif'
confid.int.theta: no visible global function definition for 'quantile'
dd.est: no visible global function definition for 'ecdf'
ks.sporm : Simul: no visible global function definition for 'runif'
ks.stat: no visible global function definition for 'ecdf'
plotor: no visible global function definition for 'ecdf'
plotor: no visible global function definition for 'plot'
test.theta: no visible global function definition for 'ecdf'
test.theta : sim: no visible global function definition for 'runif'
Undefined global functions or variables:
  ecdf ell.theta plot qchisq quantile runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
plot.SPRT: no visible global function definition for 'par'
plot.SPRT: no visible global function definition for 'plot'
plot.SPRT: no visible global function definition for 'abline'
print.SPRT: no visible global function definition for 'head'
Undefined global functions or variables:
  abline head par plot
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("utils", "head")
to your NAMESPACE file.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   5.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
genericPlot: no visible global function definition for 'dev.new'
genericPlot: no visible global function definition for 'par'
genericPlot: no visible global function definition for 'rainbow'
genericPlot: no visible global function definition for 'plot'
genericPlot: no visible global function definition for 'lines'
genericPlot: no visible global function definition for 'legend'
genericPlot: no visible global function definition for 'dev.copy2pdf'
genericPlot: no visible global function definition for 'dev.copy2eps'
genericPlot: no visible global function definition for 'dev.print'
genericPlot: no visible binding for global variable 'png'
genericPlot: no visible binding for global variable 'tiff'
plotStrains: no visible global function definition for 'rainbow'
plotStrains: no visible global function definition for 'dev.new'
plotStrains: no visible global function definition for 'par'
plotStrains: no visible global function definition for 'plot'
plotStrains: no visible global function definition for 'lines'
plotStrains: no visible global function definition for 'legend'
plotStrains: no visible global function definition for 'dev.copy2pdf'
plotStrains: no visible global function definition for 'dev.copy2eps'
plotStrains: no visible global function definition for 'dev.print'
plotStrains: no visible binding for global variable 'png'
plotStrains: no visible binding for global variable 'tiff'
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
actvspred: no visible global function definition for 'quantile'
actvspred: no visible global function definition for 'aggregate'
actvspred: no visible global function definition for 'par'
actvspred: no visible global function definition for 'plot'
actvspred: no visible global function definition for 'lines'
auc: no visible global function definition for 'par'
auc: no visible global function definition for 'plot'
decile: no visible global function definition for 'quantile'
dqcontinuous : numoutliers: no visible global function definition for
  'quantile'
dqcontinuous : <anonymous>: no visible global function definition for
  'sd'
dqcontinuous : <anonymous>: no visible global function definition for
  'quantile'
gini: no visible global function definition for 'par'
gini: no visible global function definition for 'plot'
gini: no visible global function definition for 'abline'
iv: no visible global function definition for 'quantile'
iv: no visible global function definition for 'aggregate'
ks: no visible global function definition for 'aggregate'
ks: no visible global function definition for 'par'
ks: no visible global function definition for 'plot'
ks: no visible global function definition for 'lines'
outliers: no visible global function definition for 'quantile'
outliers: no visible global function definition for 'na.omit'
pentile: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline aggregate lines na.omit par plot quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
getStp: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'plot'
plot.steeptest: no visible global function definition for 'axis'
plot.steeptest: no visible global function definition for 'box'
plot.steeptest: no visible global function definition for 'lm'
plot.steeptest: no visible global function definition for 'abline'
plot.steeptest: no visible global function definition for 'legend'
plot.steeptest: no visible global function definition for
  'as.graphicsAnnot'
steeptest: no visible global function definition for 'lm'
summary.steeptest: no visible global function definition for 'var'
summary.steeptest: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm plot quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend", "plot")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.8Mb
identifyGraph: no visible global function definition for 'phyper'
mytriangle: no visible global function definition for 'symbols'
plotGraph: no visible global function definition for 'par'
plotGraph: no visible global function definition for 'plot'
updateOrgEnvir: no visible global function definition for 'read.table'
Undefined global functions or variables:
  par phyper plot read.table symbols
Consider adding
  importFrom("graphics", "par", "plot", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
playSudoku : replot: no visible global function definition for 'par'
playSudoku : replot: no visible global function definition for 'plot'
playSudoku : replot: no visible global function definition for
  'segments'
playSudoku : replot: no visible global function definition for 'text'
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
  'getGraphicsEvent'
playSudoku: no visible global function definition for 'tkbind'
playSudoku: no visible global function definition for 'tkwait.window'
Undefined global functions or variables:
  getGraphicsEvent par plot segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "plot", "segments", "text")
to your NAMESPACE file.
SUE.fitted.values: no visible global function definition for
  'model.frame'
SUE.lm: no visible global function definition for 'model.frame'
SUE.lm: no visible global function definition for 'lm'
SUE.lm: no visible global function definition for 'anova'
SUE.plot: no visible global function definition for 'plot'
SUE.residuals: no visible global function definition for 'model.frame'
parameters : para2: no visible global function definition for 'uniroot'
parameters: no visible global function definition for 'optimize'
parameters: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  anova lm model.frame optimize plot uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for 'plot'
plot.survAUC: no visible global function definition for 'lines'
plot.survErr: no visible global function definition for 'plot'
plot.survErr: no visible global function definition for 'lines'
schemper: no visible global function definition for 'predict'
schemper: no visible global function definition for 'survfit'
schemper: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx lines plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
pearson: no visible global function definition for 'cor'
plot.survcorr: no visible global function definition for 'pnorm'
plot.survcorr: no visible global function definition for 'par'
plot.survcorr: no visible global function definition for 'plot'
plot.survcorr: no visible global function definition for 'points'
survcorr: no visible global function definition for 'model.frame'
survcorr: no visible global function definition for 'qnorm'
survcorr: no visible global function definition for 'runif'
survcorr: no visible global function definition for 'pnorm'
survcorr: no visible global function definition for 'var'
survcorr: no visible global function definition for 'qt'
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
Est.HR.FUN: no visible global function definition for 'coxph'
Est.HR.FUN: no visible global function definition for 'basehaz'
Est.HR.FUN: no visible global function definition for 'approx'
Ghat.FUN: no visible global function definition for 'survfit'
IDI.INF: no visible global function definition for 'kmcens'
IDI.INF: no visible global function definition for 'quantile'
IDI.INF.GRAPH: no visible global function definition for 'plot'
IDI.INF.GRAPH: no visible global function definition for 'lines'
IDI.INF.GRAPH: no visible global function definition for 'abline'
IDI.INF.GRAPH: no visible global function definition for 'points'
IDI.INF.GRAPH: no visible global function definition for 'title'
PTB.IDI.FUN: no visible global function definition for 'rexp'
shade: no visible global function definition for 'polygon'
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines plot points polygon quantile
  rexp survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points", "polygon",
             "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
svycox.calibrate: no visible global function definition for 'quantile'
svycox.calibrate: no visible binding for global variable 'median'
svycox.calibrate: no visible global function definition for
  'as.formula'
svycox.calibrate: no visible global function definition for 'plot'
svycox.calibrate: no visible global function definition for 'arrows'
svycox.calibrate: no visible global function definition for 'abline'
svycox.nomogram: no visible global function definition for 'predict'
svycox.nomogram: no visible global function definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'as.formula'
svycox.validate : internal.validate.func: no visible global function
  definition for 'formula'
Undefined global functions or variables:
  abline arrows as.formula formula median plot predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows", "plot")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
mainNetFunction: no visible global function definition for 'png'
mainNetFunction: no visible global function definition for 'plot'
mainNetFunction: no visible global function definition for 'lines'
mainNetFunction: no visible global function definition for 'legend'
mainNetFunction: no visible global function definition for 'dev.off'
plotPR: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'plot'
plotROC: no visible global function definition for 'lines'
simulatedData: no visible global function definition for 'rpois'
simulatedData : <anonymous>: no visible global function definition for
  'rpois'
simulatedData : rlognormpois: no visible global function definition for
  'rnorm'
simulatedData : rlognormpois: no visible global function definition for
  'rpois'
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
BootTree: no visible global function definition for 'hclust'
BootTree: no visible global function definition for 'dist'
BootTree: no visible global function definition for 'as.dist'
BootTree: no visible global function definition for 'cor'
BootTree: no visible binding for global variable 'var'
Pgpd: no visible global function definition for 'optim'
Pgpd : <anonymous>: no visible global function definition for 'optim'
Pgpd: no visible global function definition for 'var'
Pgpd: no visible global function definition for 'rnorm'
Pgpd: no visible global function definition for 'quantile'
Pvalue: no visible global function definition for 'rnorm'
SigTree: no visible global function definition for 'data'
TreeStat: no visible global function definition for 'hclust'
TreeStat: no visible global function definition for 'as.dist'
TreeStat: no visible global function definition for 'dist'
TreeStat: no visible global function definition for 'cor'
plot.best: no visible global function definition for 'hclust'
plot.best: no visible global function definition for 'as.dist'
plot.best: no visible global function definition for 'dist'
plot.best: no visible global function definition for 'cor'
plot.best: no visible global function definition for 'plot'
treetext: no visible global function definition for 'par'
treetext: no visible global function definition for 'text'
Undefined global functions or variables:
  as.dist cor data dist hclust optim par plot quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is 83.1Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    gdal   3.8Mb
    libs  71.8Mb
    proj   5.0Mb
phyper_right: no visible global function definition for 'dhyper'
progression: no visible global function definition for 'density'
progression: no visible global function definition for 'plot'
progression: no visible global function definition for 'points'
progression: no visible global function definition for 'legend'
progression: no visible global function definition for 'text'
specificities.distribution.plot: no visible global function definition
  for 'dhyper'
specificities.distribution.plot: no visible global function definition
  for 'plot'
specificities.distribution.plot: no visible global function definition
  for 'Axis'
specificities.distribution.plot: no visible global function definition
  for 'arrows'
specificities.distribution.plot: no visible global function definition
  for 'text'
specificities.distribution.plot: no visible global function definition
  for 'title'
specificities.probabilities.vector: no visible global function
  definition for 'phyper'
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
coef_traceplot: no visible global function definition for 'rainbow'
coef_traceplot: no visible global function definition for 'plot'
coef_traceplot: no visible global function definition for 'abline'
coef_traceplot : <anonymous>: no visible global function definition for
  'lines'
coef_traceplot: no visible global function definition for 'text'
ee.GEE.aux : <anonymous>: no visible global function definition for
  'combn'
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/tibble.Rcheck/00install.out' for details.
drawGraph: no visible global function definition for 'pdf'
drawGraph: no visible global function definition for 'par'
drawGraph: no visible global function definition for 'plot'
drawGraph: no visible global function definition for 'segments'
drawGraph: no visible global function definition for 'lines'
drawGraph: no visible global function definition for 'text'
drawGraph: no visible global function definition for 'dev.off'
drugRank: no visible global function definition for 'aggregate'
floating2: no visible global function definition for 'cor'
timma: no visible global function definition for 'median'
timma: no visible global function definition for 'write.table'
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
tipom.car: no visible global function definition for 'abline'
tipom.car: no visible global function definition for 'axis'
tipom.heat: no visible global function definition for 'image'
tipom.heat: no visible global function definition for 'gray'
tipom.lw: no visible global function definition for 'plot'
tipom.lw: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import 'sf::st_make_valid' by 'lwgeom::st_make_valid' when loading 'tmap'
See 'd:/Rcompile/CRANpkg/local/3.6/tmap.Rcheck/00install.out' for details.
ConfA: no visible global function definition for 'qf'
EstM2Sn: no visible global function definition for 'nlm'
EstM2Sn: no visible global function definition for 'qnorm'
TV.model: no visible global function definition for 'dev.new'
TV.model: no visible global function definition for 'points'
betaBino: no visible global function definition for 'pbinom'
doseD: no visible global function definition for 'lm'
doseD: no visible global function definition for 'dev.new'
doseD: no visible global function definition for 'par'
doseD: no visible global function definition for 'plot'
doseD: no visible global function definition for 'axTicks'
doseD: no visible global function definition for 'axis'
doseD: no visible global function definition for 'lines'
doseD: no visible global function definition for 'abline'
doseD: no visible global function definition for 'legend'
setD: no visible global function definition for 'dev.new'
setD: no visible global function definition for 'par'
setD: no visible global function definition for 'pbinom'
setD: no visible global function definition for 'abline'
setD: no visible global function definition for 'axis'
setD: no visible global function definition for 'rect'
setD: no visible global function definition for 'lines'
setD: no visible global function definition for 'text'
setD: no visible global function definition for 'axTicks'
setD: no visible global function definition for 'legend'
spoD : spoD_A: no visible global function definition for 'chisq.test'
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
LikAge: no visible global function definition for 'read.table'
bd.ME.optim: no visible global function definition for 'optim'
bd.ME.optim.rho: no visible global function definition for 'optim'
bd.ME.optim.rho.all: no visible global function definition for 'optim'
bd.MEyule.optim: no visible global function definition for 'optimize'
bd.MEyule.optim: no visible global function definition for 'optim'
bd.age.optim.matlab: no visible global function definition for
  'read.table'
bd.groups.conf: no visible global function definition for 'uniroot'
bd.shifts.plot: no visible global function definition for 'plot'
bd.shifts.plot: no visible global function definition for 'lines'
bdsky.stt.optim: no visible global function definition for 'optim'
create.mat: no visible global function definition for 'write.table'
Undefined global functions or variables:
  lines optim optimize plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  11.5Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tricolore)
  > 
  > test_check('tricolore')
  -- 1. Error: NA, Inf, NaNs in input return NA in output (@test-global.R#82)  ---
  "plot.title.position" is not a valid theme element name.
  Backtrace:
   1. tricolore::Tricolore(P, "a", "b", "c", breaks = Inf)
   2. tricolore:::ColorKeyTricolore(...)
   3. tricolore:::BasicKey(...)
   4. ggtern:::`+.gg`(...)
   5. ggtern:::add_ggplot(e1, e2, e2name)
   6. ggtern:::update_theme(p$theme, object)
   9. base::mapply(validate_element, elements, names(elements))
  
  == testthat results  ===========================================================
  [ OK: 33 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: NA, Inf, NaNs in input return NA in output (@test-global.R#82) 
  
  Error: testthat unit tests failed
  Execution halted
HtoGp: no visible global function definition for 'odd'
HtoGp: no visible global function definition for 'even'
plot.pirls.gam: no visible global function definition for 'par'
plot.pirls.gam: no visible global function definition for 'plot'
plot.pirls.gam: no visible global function definition for 'title'
plot.pirls.gam: no visible global function definition for 'lines'
plot.pirls.gam: no visible global function definition for 'rug'
plot.pirls.gam: no visible global function definition for 'mtext'
test.trioGxE: no visible global function definition for 'write.table'
trioGxE: no visible global function definition for 'quantile'
trioGxE: no visible global function definition for 'qtnorm'
trioplot: no visible global function definition for 'quantile'
trioplot: no visible global function definition for 'formula'
trioplot: no visible global function definition for 'gam'
trioplot: no visible global function definition for 'binomial'
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
cdens: no visible global function definition for 'head'
dplot: no visible global function definition for 'knots'
dplot: no visible global function definition for 'median'
dplot: no visible global function definition for 'par'
dplot: no visible global function definition for 'plot.stepfun'
dplot: no visible global function definition for 'abline'
edf: no visible global function definition for 'approxfun'
mctest : rdist: no visible global function definition for 'runif'
mctest : S: no visible global function definition for 'optim'
qplot: no visible global function definition for 'plot'
qplot: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline approxfun head knots median optim par plot plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
dLag : dlag.f: no visible global function definition for
  'complete.cases'
distmat: no visible global function definition for 'dist'
fitCity: no visible global function definition for 'glm.control'
fitCity: no visible global function definition for 'terms'
ldmvnorm: no visible global function definition for 'mahalanobis'
lspline: no visible global function definition for 'quantile'
plot.tsdecomp: no visible global function definition for 'par'
plot.tsdecomp: no visible global function definition for 'plot'
setupFormula: no visible global function definition for 'as.formula'
spatialgibbs: no visible global function definition for 'rnorm'
spatialgibbs: no visible global function definition for 'rgamma'
spatialgibbs: no visible global function definition for 'runif'
tsdecomp: no visible global function definition for 'fft'
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
Crm: no visible global function definition for 'integrate'
Crm : <anonymous>: no visible global function definition for
  'integrate'
Crm: no visible global function definition for 'optimize'
ail1: no visible global function definition for 'uniroot'
ail2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ail2: no visible global function definition for 'uniroot'
aip : fu : <anonymous>: no visible global function definition for
  'integrate'
aip: no visible global function definition for 'uniroot'
ait1: no visible global function definition for 'uniroot'
ait2 : fu : <anonymous>: no visible global function definition for
  'integrate'
ait2: no visible global function definition for 'uniroot'
sim3p3: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'rbinom'
simCrm: no visible global function definition for 'palette'
simCrm: no visible global function definition for 'gray'
simCrm: no visible global function definition for 'plot'
simCrm: no visible global function definition for 'abline'
simCrm: no visible global function definition for 'lines'
ssim3p3: no visible global function definition for 'txtProgressBar'
ssim3p3: no visible global function definition for 'setTxtProgressBar'
ssimCrm: no visible global function definition for 'txtProgressBar'
ssimCrm: no visible global function definition for 'setTxtProgressBar'
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
installed size is 82.4Mb
  sub-directories of 1Mb or more:
    data      2.0Mb
    extdata   2.3Mb
    gdal      3.8Mb
    libs     69.0Mb
    proj      5.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.6Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/vader.Rcheck/00install.out' for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
Mammen: no visible global function definition for 'runif'
PR2: no visible global function definition for 'ar.burg'
PR2: no visible global function definition for 'pt'
PR2: no visible global function definition for 'pf'
PR3: no visible global function definition for 'ar.burg'
PR3: no visible global function definition for 'pt'
PR3: no visible global function definition for 'pf'
VAR.FOR: no visible global function definition for 'qnorm'
VAR.ForeB: no visible global function definition for 'runif'
VAR.LRtest: no visible global function definition for 'pchisq'
VAR.LRtest: no visible global function definition for 'pf'
VAR.PI: no visible global function definition for 'quantile'
VAR.Waldtest: no visible global function definition for 'pf'
VAR.irf: no visible global function definition for 'par'
VAR.irf: no visible global function definition for 'plot'
VAR.irf: no visible global function definition for 'abline'
VAR1.sim: no visible global function definition for 'rnorm'
resamp: no visible global function definition for 'runif'
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Compare2FDS: no visible global function definition for 'runif'
Compare2FDS: no visible global function definition for 'lm'
Compare2FDS: no visible global function definition for 'model.matrix'
Compare2FDS: no visible global function definition for 'plot'
Compare2FDS: no visible global function definition for 'abline'
Compare2FDS: no visible global function definition for 'lines'
Compare2FDS: no visible global function definition for 'text'
Compare2Vdg: no visible global function definition for 'par'
Compare2Vdg: no visible global function definition for 'plot'
Compare2Vdg: no visible global function definition for 'lines'
Compare2Vdg: no visible global function definition for 'legend'
FDSPlot: no visible global function definition for 'runif'
FDSPlot: no visible global function definition for 'lm'
FDSPlot: no visible global function definition for 'model.matrix'
FDSPlot: no visible global function definition for 'plot'
FDSPlot: no visible global function definition for 'abline'
Vdgraph: no visible global function definition for 'par'
Vdgraph: no visible global function definition for 'plot'
Vdgraph: no visible global function definition for 'lines'
Vdgraph: no visible global function definition for 'legend'
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   3.9Mb
Decile.Plot: no visible global function definition for 'barplot'
Decile.Plot: no visible global function definition for 'axis'
Sliding.Window: no visible global function definition for 'plot'
Sliding.Window: no visible global function definition for 'lines'
Sliding.Window: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Error(s) in re-building vignettes:
--- re-building 'wCorrArguments.Rmd' using rmarkdown
Loading required package: knitr
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/3.6/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrArguments_files/figure-latex/ML\%20RMSE\%20plot-1.
pdf' not found.

Error: processing vignette 'wCorrArguments.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/3.6/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrArguments.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrArguments.log for more info.
--- failed re-building 'wCorrArguments.Rmd'

--- re-building 'wCorrFormulas.Rmd' using rmarkdown
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/3.6/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrFormulas_files/figure-latex/bias\%20Versus\%20rho-
1.pdf' not found.

Error: processing vignette 'wCorrFormulas.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/3.6/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrFormulas.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrFormulas.log for more info.
--- failed re-building 'wCorrFormulas.Rmd'

SUMMARY: processing the following files failed:
  'wCorrArguments.Rmd' 'wCorrFormulas.Rmd'

Error: Vignette re-building failed.
Execution halted
plotTrait: no visible global function definition for 'plot'
plotTrait: no visible global function definition for 'points'
plotTrait: no visible global function definition for 'legend'
test.windex: no visible global function definition for 'hist'
test.windex: no visible global function definition for 'abline'
test.windex: no visible global function definition for 'legend'
windex: no visible global function definition for 'sd'
windex: no visible global function definition for 'var'
windex: no visible global function definition for 'dist'
windex: no visible global function definition for 'quantile'
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for 'lm'
plotfit,Leader: no visible global function definition for 'par'
plotfit,Leader: no visible global function definition for 'plot'
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
simul.wsvm: no visible binding for global variable 'mixture.example'
wsvm.boost: no visible global function definition for 'plot'
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/x13binary.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    libs          4.2Mb
Error(s) in re-building vignettes:
--- re-building ‘aaSEA_Documentation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

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

Warning in normalizePath(f2) :
  path[1]="webshot3f472895632b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot3f472895632b.png': No such file or directory
Quitting from lines 90-91 (aaSEA_Documentation.Rmd) 
Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘aaSEA_Documentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/abcdeFBA.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘httr’ ‘progress’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.7Mb
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/adamethods.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘adapt_demo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'adapt_demo.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘adapt_demo.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'WGCNA', 'DeconRNASeq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
No protocol specified
No protocol specified
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ade4TkGUI.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
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No protocol specified
No protocol specified
No protocol specified
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No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
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No protocol specified
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘amigaDiskFiles.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'amigaDiskFiles.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘amigaDiskFiles.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/adiv.Rcheck/00install.out’ for details.
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘HiTC’
Package unavailable to check Rd xrefs: ‘HiTC’
Error(s) in re-building vignettes:
  ...
--- re-building ‘adpss_ex.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'adpss_ex.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘adpss_ex.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/afCEC.Rcheck/00install.out’ for details.
Running examples in ‘agridat-Ex.R’ failed
The error most likely occurred in:

> ### Name: baker.wheat.uniformity
> ### Title: Uniformity trial of wheat
> ### Aliases: baker.wheat.uniformity
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(baker.wheat.uniformity)
> dat <- baker.wheat.uniformity
> 
> require(desplot)
Loading required package: desplot
Error: package or namespace load failed for ‘desplot’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘stringi’
> desplot(yield ~ col*row, dat,
+         flip=TRUE, aspect=1,
+         main="baker.wheat.uniformity")
Error in desplot(yield ~ col * row, dat, flip = TRUE, aspect = 1, main = "baker.wheat.uniformity") : 
  could not find function "desplot"
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘agridat_data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'agridat_data.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘agridat_data.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘agridat_data.Rmd’ ‘agridat_examples.Rmd’ ‘agridat_papadakis.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ahn.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ahn.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Biostrings’
Packages unavailable to check Rd xrefs: ‘Biostrings’, ‘Starr’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/AIG.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggseas’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/akmedoids.Rcheck/00install.out’ for details.
Package required but not available: ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘allelic/libs/allelic.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/alphashape3d.Rcheck/00install.out’ for details.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘amen.Rnw’ using knitr
Loading required package: network
network: Classes for Relational Data
Version 1.15 created on 2019-04-01.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


Execution halted
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/analogueExtra.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/AnalyzeFMRI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/animalTrack.Rcheck/00install.out’ for details.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    25.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘antaresH5.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 51-85 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘antaresH5.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Anthropometry.Rcheck/00install.out’ for details.
installed size is 163.3Mb
  sub-directories of 1Mb or more:
    libs  162.9Mb
Packages suggested but not available for checking: 'Biostrings', 'kebabs'
Running examples in ‘aplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: insert_left
> ### Title: plot-insertion
> ### Aliases: insert_left insert_right insert_top insert_bottom
> 
> ### ** Examples
> 
> library(ggplot2)
> library(aplot)
> 
> p <- ggplot(mtcars, aes(mpg, disp)) + geom_point()
> p2 <- ggplot(mtcars, aes(mpg)) + 
+     geom_density(fill='steelblue', alpha=.5) + 
+         ggtree::theme_dendrogram()
Error: 'theme_dendrogram' is not an exported object from 'namespace:ggtree'
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
Packages suggested but not available for checking:
  'RGtk2', 'gWidgetsRGtk2', 'cairoDevice'
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/aqr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/archiDART.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘argparse.Rrst’ using knitr
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'argparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
--- failed re-building ‘argparse.Rrst’

SUMMARY: processing the following file failed:
  ‘argparse.Rrst’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.2Mb
    testScripts   1.1Mb
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Package suggested but not available for checking: ‘GLAD’
Packages suggested but not available for checking:
  'GLAD', 'sfit', 'expectile', 'HaarSeg', 'mpcbs'
Package unavailable to check Rd xrefs: ‘GLAD’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Arothron.Rcheck/00install.out’ for details.
installed size is 37.9Mb
  sub-directories of 1Mb or more:
    R      3.2Mb
    libs  34.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.3Mb
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/asbio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  au.c:375:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int)') with an expression of type 'au_instance_t *(SEXP, float, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int)') [-Wincompatible-pointer-types]
  au.c:376:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int, int)') with an expression of type 'au_instance_t *(SEXP, float, int, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int, int)') [-Wincompatible-pointer-types]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/audio.Rcheck/00install.out’ for details.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Packages required but not available:
  'org.Hs.eg.db', 'ConsensusClusterPlus', 'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/babel.Rcheck/00install.out’ for details.
Running examples in ‘babette-Ex.R’ failed
The error most likely occurred in:

> ### Name: prepare_file_creation
> ### Title: Prepare for 'BEAST2' creating files
> ### Aliases: prepare_file_creation
> 
> ### ** Examples
> 
> library(testthat)
> 
> # For a test inference model, the files can be prepared
> inference_model <- create_test_inference_model()
> beast2_options <- create_beast2_options()
> expect_silent(prepare_file_creation(inference_model, beast2_options))
Error in prepare_file_creation(inference_model, beast2_options) : 
  Cannot create file '/Users/urbanek/Library/Caches/beast2_83cf1ce29b8.xml.state'. 
Maybe no permissions to write there?
Calls: expect_silent ... withCallingHandlers -> withVisible -> eval_bare -> prepare_file_creation
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BACA.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.3Mb
    libs   2.8Mb
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
installed size is 67.8Mb
  sub-directories of 1Mb or more:
    libs  66.7Mb
Running ‘test-all.R’ [1s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Need at least two classes to do classification.
  1: samme(activity ~ ., train, test, 3, ntree = 5, trace = F) at /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bagRboostR.Rcheck/bagRboostR/tests/test_samme.R:6
  2: randomForest(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  3: randomForest.formula(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  4: randomForest.default(m, y, ...)
  5: stop("Need at least two classes to do classification.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 39 SKIPPED: 0 FAILED: 1
  1. Error: samme returns a character vector of predicted classes (@test_samme.R#6) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
Package suggested but not available for checking: ‘philr’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BALCONY.Rcheck/00install.out’ for details.
No protocol specified
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BALLI.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bapred.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   3.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.0Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/baseflow.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘article2-vignette.Rnw’ using knitr

Execution halted
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BAT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BAwiR.Rcheck/00install.out’ for details.
installed size is 53.4Mb
  sub-directories of 1Mb or more:
    libs  51.5Mb
Package required but not available: ‘mritc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 54.1Mb
  sub-directories of 1Mb or more:
    libs  53.3Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  12.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  17.8Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  13.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   3.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BayesXsrc.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.1Mb
Found the following significant warnings:
  sparseFactor.cpp:33:10: warning: explicitly assigning value of variable of type 'Rcpp::IntegerVector' (aka 'Vector<13>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BClustLonG.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘DNAcopy’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bcROCsurface.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'beadarrayExampleData', 'lumi'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/beadarrayFilter.Rcheck/00install.out’ for details.
Package required but not available: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 69.3Mb
  sub-directories of 1Mb or more:
    libs  67.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘beanz_vignettes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Execution halted
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
installed size is 131.4Mb
  sub-directories of 1Mb or more:
    include  131.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   7.4Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BIGL.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
No protocol specified
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="webshot142971fec70e2.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot142971fec70e2.png': No such file or directory
Quitting from lines 245-248 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Rmpi’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      2.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      8.2Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
Package required but not available: ‘csaw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bioacoustics.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘BioCircos.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘BioCircos.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'BiocStyle', 'BiocVersion'
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Biocomb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BiodiversityR.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.1Mb
Packages required but not available: 'ChemmineR', 'fmcsR', 'org.Hs.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bios2mds.Rcheck/00install.out’ for details.
Package required but not available: ‘rpanel’

Package suggested but not available for checking: ‘soilphysics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘colorspace’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘deldir’ ‘rgl’ ‘tcltk’ ‘tcltk2’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking: 'GO.db', 'org.Hs.eg.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BiSEp.Rcheck/00install.out’ for details.
installed size is 53.5Mb
  sub-directories of 1Mb or more:
    libs  51.7Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
Found the following executable file:
  inst/extdata/awt.gri
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is 36.8Mb
  sub-directories of 1Mb or more:
    libs  36.5Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Packages suggested but not available for checking:
  'graph', 'Rgraphviz', 'gRain'
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Package suggested but not available for checking: ‘sangerseqR’
installed size is 335.3Mb
  sub-directories of 1Mb or more:
    include    8.5Mb
    lib      326.4Mb
installed size is 75.9Mb
  sub-directories of 1Mb or more:
    libs  75.4Mb
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bootsPLS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘qvalue’
Package unavailable to check Rd xrefs: ‘qvalue’
Running examples in ‘Boptbd-Ex.R’ failed
The error most likely occurred in:

> ### Name: graphoptBbd
> ### Title: Creates the graphical layout of resultant optimal design
> ### Aliases: graphoptBbd
> ### Keywords: Graphical layout
> 
> ### ** Examples
> 
>     ##To create the graphical layout of the D-optimal block design
>     ##obtained using the treatment exchange algorithm for 
>     trt.N <- 10  #Number of treatments
>     blk.N <- 10  #Number of blocks
>     alpha <- 0.1 #alpha value 
>     beta  <- 0.1 #beta value 
>     OptdesF <- rbind(1:10, c(2:10,1)) #Bayesian A-optimal block design (loop design)
> 
>     graphoptBbd(trt.N = 10, blk.N = 10, alpha = 0.1, beta = 0.1, OptdesF, Optcrit = "A")
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "font".
Calls: graphoptBbd ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bpca.Rcheck/00install.out’ for details.
Running examples in ‘bqror-Ex.R’ failed
The error most likely occurred in:

> ### Name: deviance3
> ### Title: Deviance Information Criteria for Ordinal Models with 3 outcomes
> ### Aliases: deviance3
> 
> ### ** Examples
> 
> set.seed(101)
> data("data25j3")
> x <- data25j3$x
> y <- data25j3$y
> p <- 0.25
> ans <- quan_reg3(y, x, mc = 50, p)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: quan_reg3 ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
No protocol specified

(R:60058): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brainKCCA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/brainR.Rcheck/00install.out’ for details.
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
Packages suggested but not available for checking:
  'vsn', 'DESeq2', 'pasilla'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Brundle.Rcheck/00install.out’ for details.
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  28.1Mb
installed size is 94.6Mb
  sub-directories of 1Mb or more:
    libs  93.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘simple_plotting.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Removed 4550 rows containing missing values (geom_path).
Quitting from lines 173-174 (simple_plotting.Rmd) 
Error: processing vignette 'simple_plotting.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘simple_plotting.Rmd’

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

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'c3'

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

    %>%

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

    grid, legend

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshote6846e017576.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshote6846e017576.png': No such file or directory
Quitting from lines 53-62 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘cairoDevice/R/zzz.R’:
  .onLoad calls:
    message("R session is headless; GTK+ not initialized.")

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

No protocol specified
Running examples in ‘cairoDevice-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cairo
> ### Title: The Cairo Graphics Device
> ### Aliases: Cairo Cairo_pdf Cairo_ps Cairo_svg Cairo_png
> ### Keywords: device
> 
> ### ** Examples
> 
> Cairo()

(R:91377): Gdk-CRITICAL **: gdk_screen_get_width: assertion `GDK_IS_SCREEN (screen)' failed

(R:91377): Gdk-CRITICAL **: gdk_screen_get_width_mm: assertion `GDK_IS_SCREEN (screen)' failed

(R:91377): Gdk-CRITICAL **: gdk_screen_get_height: assertion `GDK_IS_SCREEN (screen)' failed

(R:91377): Gdk-CRITICAL **: gdk_screen_get_height_mm: assertion `GDK_IS_SCREEN (screen)' failed

(R:91377): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:91377): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:91377): Gtk-CRITICAL **: gtk_window_set_default_size: assertion `width >= -1' failed

(R:91377): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:91377): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:91377): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:91377): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:91377): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:91377): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:91377): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

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

Traceback:
 1: Cairo()
An irrecoverable exception occurred. R is aborting now ...
Packages suggested but not available for checking:
  'GenomicRanges', 'IRanges', 'S4Vectors'
Package unavailable to check Rd xrefs: ‘GenomicRanges’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.2Mb
Package required and available but unsuitable version: ‘reticulate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘limma’
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘GenomeInfoDbData’
Calls: stat.DESeq ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CaRpools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 1875-1881 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
there is no package called 'GenomeInfoDbData'
--- failed re-building ‘CaRpools.Rmd’

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

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning in normalizePath(f2) :
  path[1]="webshot87bf53b79c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot87bf53b79c.png': No such file or directory
Quitting from lines 451-480 (cartograflow.Rmd) 
Error: processing vignette 'cartograflow.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘cartograflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/cati.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.2Mb
installed size is 120.7Mb
  sub-directories of 1Mb or more:
    libs  120.4Mb
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘plot’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘plot’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
Package suggested but not available for checking: ‘graph’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   5.9Mb
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/changepoint.np.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pbdMPI’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ChaosGame.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘multtest’
Packages suggested but not available for checking:
  'GenomicInteractions', 'Gviz', 'countreg'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘Visualising_Interactions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-105 (Visualising_Interactions.Rmd) 
Error: processing vignette 'Visualising_Interactions.Rmd' failed with diagnostics:
there is no package called 'GenomicInteractions'
--- failed re-building ‘Visualising_Interactions.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ComplexHeatmap’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.1Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/CleanBSequences.Rcheck/00install.out’ for details.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘getstarted.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'http://weather.uwyo.edu/cgi-bin/sounding?region=europe&TYPE=TEXT%3ALIST&YEAR=2020&MONTH=03&FROM=2300&TO=2300&STNM=12120'
Content type 'text/html; charset=UTF-8' length 7894 bytes
==================================================
downloaded 7894 bytes

Quitting from lines 128-144 (getstarted.Rmd) 
Error: processing vignette 'getstarted.Rmd' failed with diagnostics:
cannot open the connection to 'https://dane.imgw.pl/data/dane_pomiarowo_obserwacyjne/dane_meteorologiczne/miesieczne/synop/s_m_d_format.txt'
--- failed re-building ‘getstarted.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/clpAPI.Rcheck/00install.out’ for details.
Package required but not available: ‘IsoGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/clusterSim.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package suggested but not available for checking: ‘SingleCellExperiment’
Packages suggested but not available for checking:
  'Biobase', 'annotate', 'GO.db', 'moe430a.db'
Package unavailable to check Rd xrefs: ‘Biobase’
Error(s) in re-building vignettes:
  ...
--- re-building ‘clValid.Rnw’ using Sweave
Loading required package: cluster
Read 7 items
Loading required package: Biobase
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Biobase’
Loading required package: RankAggreg
Error: processing vignette 'clValid.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./clValid-022.pdf): PDF inclusion: required page 
does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘clValid.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'InteractionSet', 'GenomicInteractions',
  'BSgenome.Hsapiens.UCSC.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.4Mb
Package suggested but not available for checking: ‘limma’
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  14.9Mb
Running ‘testthat.R’ [40s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  33: withOneRestart(expr, restarts[[1L]])
  34: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  35: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        reporter$start_file(basename(path))        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        reporter$.end_context()        reporter$end_file()    })
  36: FUN(X[[i]], ...)
  37: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  38: force(code)
  39: doWithOneRestart(return(expr), restart)
  40: withOneRestart(expr, restarts[[1L]])
  41: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  42: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  43: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  44: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  45: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  46: test_check("collapse")
  An irrecoverable exception occurred. R is aborting now ...
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   2.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/colourvision.Rcheck/00install.out’ for details.
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  28.7Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
Packages suggested but not available for checking:
  'inSilicoDb', 'mogene10sttranscriptcluster.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/CONDOP.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [15s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 96 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 12 ]
  1. Error: embed_images() works for non-ASCII dir (@test-embed-images.R#52) 
  2. Error: confluence_settings can be set from front-matter (@test-front-matter.R#38) 
  3. Error: confluence_settings$title is prior to title (@test-front-matter.R#92) 
  4. Error: confluence_settings can be specified partially (@test-front-matter.R#135) 
  5. Error: supported_syntax_highlighting can be set via option (@test-front-matter.R#149) 
  6. Error: confluence_settings raise an error when any of mandatory parameters are missing (@test-front-matter.R#167) 
  7. Error: confluence_settings are accepted for backward-compatibility (@test-front-matter.R#192) 
  8. Failure: confluence_document() stops early (@test-invalid-credential.R#24) 
  9. Failure: rmarkdown::render() works when no space_key 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   11. pins::board_pin_store(...)
   13. pins:::board_pin_create.local(...)
   14. pins:::pin_registry_update(name = name, component = board$name)
   15. pins:::pin_registry_save_entries(entries, component)
   16. yaml::write_yaml(entries, pin_registry_config(component))
   17. base::file(file, "w", encoding = fileEncoding)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 22 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: tbl pin is created w/o error (@test-pins.R#16) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ConsRank.Rcheck/00install.out’ for details.
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    libs  50.0Mb
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ConvergenceConcepts.Rcheck/00install.out’ for details.
Running examples in ‘ConvergenceConcepts-Ex.R’ failed
The error most likely occurred in:

> ### Name: investigate
> ### Title: Investigate examples and exercises from the paper
> ### Aliases: investigate
> ### Keywords: dplot iplot distribution htest
> 
> ### ** Examples
> 
> investigate()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: investigate ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/CoopGame.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/cops.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.0Mb
Package suggested but not available for checking: ‘ProData’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/corregp.Rcheck/00install.out’ for details.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘dplyr’ ‘ggridges’ ‘markdown’ ‘shinyjs’ ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/CovTools.Rcheck/00install.out’ for details.
No protocol specified
prepare_Rd: RGL: unable to open X11 display
prepare_Rd: 'rgl_init' failed, running with rgl.useNULL = TRUE
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/cplexAPI.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 399-421 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/crs.Rcheck/00install.out’ for details.
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  23.4Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
Running examples in ‘ctDNAtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_mutations_read_counts
> ### Title: Counts ref and alt reads for a set of mutations
> ### Aliases: get_mutations_read_counts
> 
> ### ** Examples
> 
> data("mutations", package = "ctDNAtools")
> bamT1 <- system.file("extdata", "T1.bam", package = "ctDNAtools")
> get_mutations_read_counts(mutations = mutations[1:3, ], bam = bamT1)
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘GenomeInfoDbData’
Calls: get_mutations_read_counts ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    5. base::getNamespace(ns)
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   12. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   13. base:::withOneRestart(expr, restarts[[1L]])
   14. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: (unknown) (@test-ctDNAtest.R#3) 
  2. Error: (unknown) (@test-fragment_size.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ctDNAtools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 42-69 (ctDNAtools.Rmd) 
Error: processing vignette 'ctDNAtools.Rmd' failed with diagnostics:
there is no package called 'BSgenome.Hsapiens.UCSC.hg19'
--- failed re-building ‘ctDNAtools.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 93.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs  90.8Mb
Package which this enhances but not available for checking: ‘pbdMPI’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/cubing.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/curvHDR.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘RGtk2’
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    doc    1.2Mb
    help   1.0Mb
    libs   4.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cycling_data_analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘cycling_data_analysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/dartR.Rcheck/00install.out’ for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   3.5Mb
Package required but not available: ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘get_started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 60.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  57.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘applications.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘applications.Rmd’

--- re-building ‘data.tree.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot157e81cd7762b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot157e81cd7762b.png': No such file or directory
Quitting from lines 513-516 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘data.tree.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘gWidgetsRGtk2’
Package required but not available: ‘SDD’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 42.4Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
Error(s) in re-building vignettes:
--- re-building ‘RC_units.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘RC_units.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘delayed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 97-98 (delayed.Rmd) 
Error: processing vignette 'delayed.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘delayed.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 66.2Mb
  sub-directories of 1Mb or more:
    libs  63.6Mb
Package unavailable to check Rd xrefs: ‘WGCNA’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/depth.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.5Mb
    libs   3.1Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rsymphony'
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.6Mb
installed size is 52.9Mb
  sub-directories of 1Mb or more:
    libs  52.5Mb
Package required but not available: ‘ALL’

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

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

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

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DGVM3D.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DiceView.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DiffusionRgqd.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DiffusionRimp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DiffusionRjgqd.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘Part_1_Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Part_1_Introduction.Rmd’

--- re-building ‘Part_2_Transition_Densities.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 176-185 (Part_2_Transition_Densities.Rmd) 
Error: processing vignette 'Part_2_Transition_Densities.Rmd' failed with diagnostics:
there is no package called 'DiffusionRgqd'
--- failed re-building ‘Part_2_Transition_Densities.Rmd’

--- re-building ‘Part_3_Bivariate_Diffusions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Part_3_Bivariate_Diffusions.Rmd’

--- re-building ‘DiffusionRjgqd_Paper.pdf.asis’ using asis
--- finished re-building ‘DiffusionRjgqd_Paper.pdf.asis’

--- re-building ‘DiffusionRjgqd_RepMaterials.html.asis’ using asis
--- finished re-building ‘DiffusionRjgqd_RepMaterials.html.asis’

--- re-building ‘Part_4_Likelihood_Inference.html.asis’ using asis
--- finished re-building ‘Part_4_Likelihood_Inference.html.asis’

SUMMARY: processing the following file failed:
  ‘Part_2_Transition_Densities.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Package suggested but not available for checking: ‘pcaL1’
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Directional.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/directPA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DirichletReg.Rcheck/00install.out’ for details.
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Error(s) in re-building vignettes:
--- re-building ‘brt.Rnw’ using Sweave
Loading required package: raster
Loading required package: sp
Loading required namespace: gbm
fitting final gbm model with a fixed number of 600 trees for Angaus
fitting final gbm model with a fixed number of 1800 trees for Angaus
gbm.simplify - version 2.9 
simplifying gbm.step model for Angaus with 11 predictors and 1000 observations 
original deviance = 0.6743(0.0269)
a fixed number of 5 drops will be tested
creating initial models...
dropping predictor: 1 2 3 4 5
processing final dropping of variables with full data
1-DSDam
2-SegLowFlow
3-USAvgT
4-SegTSeas
5-DSMaxSlope
fitting final gbm model with a fixed number of 1300 trees for Angaus
gbm.interactions - version 2.9
Cross tabulating interactions for gbm model with 11 predictors
1 2 3 4 5 6 7 8 9 10 
maximum value = 0.58


Error: processing vignette 'brt.Rnw' failed with diagnostics:
 chunk 12 (label = dismo-10) 
Error in library(gbm) : there is no package called ‘gbm’

--- failed re-building ‘brt.Rnw’

--- re-building ‘sdm.Rnw’ using Sweave
Loading required package: raster
Loading required package: sp
Checking rgeos availability: TRUE
Loading required namespace: XML
REQUEST_DENIED:Ayacucho+P.+Huamanga+Minas+Ckucho,Peru
REQUEST_DENIED:Ayacucho+P.+Huamanga+Minas+Ckucho,Peru
REQUEST_DENIED:Ayacucho+P.+Huamanga+Minas+Ckucho,Peru
REQUEST_DENIED:Ayacucho+P.+Huamanga+Minas+Ckucho,Peru
Loading required namespace: rgeos
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Warning in randomForest.default(m, y, ...) :
  The response has five or fewer unique values.  Are you sure you want to do regression?

Attaching package: ‘kernlab’

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

    buffer, rotated

Loading required namespace: gstat
Loading required namespace: deldir
--- finished re-building ‘sdm.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Biobase’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DiversityOccupancy.Rcheck/00install.out’ for details.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  16.2Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   3.6Mb
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DNLC.Rcheck/00install.out’ for details.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   9.2Mb
Package unavailable to check Rd xrefs: ‘doMPI’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/dpcR.Rcheck/00install.out’ for details.
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DRomics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/drugCombo.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘userGuide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
No protocol specified
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot219036569873.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot219036569873.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘userGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/dti.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.8Mb
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  23.3Mb
Running ‘testthat.R’ [36s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ── 2. Error: Perform dimred dm_destiny  ────────────────────────────────────────
  Please install the following packages: 
    "destiny"
  Backtrace:
   1. dyndimred:::method_fun(small_expr)
   2. dynutils::install_packages("destiny")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 191 | SKIPPED: 0 | WARNINGS: 5 | FAILED: 2 ]
  1. Error: Perform dimred dm_destiny 
  2. Error: Perform dimred dm_destiny 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.5Mb
    libs   2.8Mb
Package suggested but not available for checking: ‘dyndimred’
Package unavailable to check Rd xrefs: ‘dyndimred’
Running ‘testthat.R’ [87s/86s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   3. base::getExportedValue(pkg, name)
   4. base::asNamespace(ns)
   5. base::getNamespace(ns)
   6. base::loadNamespace(name)
   7. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8. base:::withOneRestart(expr, restarts[[1L]])
   9. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1269 | SKIPPED: 1 | WARNINGS: 6 | FAILED: 2 ]
  1. Error: Testing add_dimred including calculation of dimred (@test-wrap_add_dimred.R#110) 
  2. Error: Test get_dimred (@test-wrap_add_dimred.R#278) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs        8.4Mb
    shiny_app   1.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs   3.9Mb
Running examples in ‘ebirdst-Ex.R’ failed
The error most likely occurred in:

> ### Name: compute_ppms
> ### Title: Computes the Predictive Performance Metrics for a spatiotemporal
> ###   extent
> ### Aliases: compute_ppms
> 
> ### ** Examples
> 
> # download and load example data
> sp_path <- ebirdst_download("example_data", tifs_only = FALSE)
Warning in dir.create(path, recursive = TRUE) :
  cannot create dir '/Users/urbanek/Library/Application Support/ebirdst', reason 'Read-only file system'
Warning in utils::download.file(s3_files$s3_path[i], s3_files$local_path[i],  :
  URL https://ebirdst-data.s3.amazonaws.com/yebsap-ERD2018-EBIRD_SCIENCE-20191030-3abe59ca-example/data/yebsap-ERD2018-EBIRD_SCIENCE-20191030-3abe59ca-example_srd_raster_template.tif: cannot open destfile '/Users/urbanek/Library/Application Support/ebirdst/yebsap-ERD2018-EBIRD_SCIENCE-20191030-3abe59ca-example/data/yebsap-ERD2018-EBIRD_SCIENCE-20191030-3abe59ca-example_srd_raster_template.tif', reason 'No such file or directory'
Warning in utils::download.file(s3_files$s3_path[i], s3_files$local_path[i],  :
  download had nonzero exit status
Error in ebirdst_download("example_data", tifs_only = FALSE) : 
  Error downloading files from AWS S3
Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   1. ebirdst::ebirdst_download("example_data", tifs_only = FALSE)
  
  ── 3. Error: (unknown) (@test_ppms.R#3)  ───────────────────────────────────────
  Error downloading files from AWS S3
  Backtrace:
   1. ebirdst::ebirdst_download("example_data", tifs_only = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 1 | WARNINGS: 9 | FAILED: 3 ]
  1. Error: (unknown) (@test_loading.R#3) 
  2. Error: (unknown) (@test_plotting.R#3) 
  3. Error: (unknown) (@test_ppms.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/edgeRun.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/edrGraphicalTools.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/eegkit.Rcheck/00install.out’ for details.
installed size is 75.5Mb
  sub-directories of 1Mb or more:
    libs  74.9Mb
Package suggested but not available for checking: ‘BiocStyle’
Error(s) in re-building vignettes:
--- re-building ‘EHRtemporalVariability.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "diagcode1"
Warning: Column `diagcode1` joining factor and character vector, coercing into character vector
# Missing values: 0 cases ( 0%)
# External causes codes: 0 cases ( 0%)
# V codes not mapped: 74330 cases ( 22.82%)
# Total ICD9-CM codes mapped: 146262 cases ( 44.9%)
# Unique ICD9-CM codes mapped: 3020
# Total PheWAS codes: 757
# ICD9 codes not mapped: 105180 cases ( 32.29%)
Quitting from lines 317-322 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘EHRtemporalVariability.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  44.9Mb
Running examples in ‘elementR-Ex.R’ failed
The error most likely occurred in:

> ### Name: elementR_project
> ### Title: Object elementR_project
> ### Aliases: elementR_project
> 
> ### ** Examples
> 
> ## create a new elementR_repStandard object based on the "filePath" 
> ## from a folder containing sample replicate
> 
> filePath <- system.file("Example_Session", package="elementR")
> 
> exampleProject <- elementR_project$new(filePath)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: <Anonymous> ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Packages suggested but not available for checking:
  'hgu133plus2.db', 'lumi', 'GO.db'
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  11.2Mb
Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

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

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> data("qs_factor")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> 
> cinp.daily.file <- qs_factor
> cinp.weekly     <- list(mon=1, tue=.83, wed=.83, thu=.83, fri=1, sat=1.25, sun=1.25)  
> # factors average to 1
> cinp.seasonal   <- list(jan=.79, feb=.79, mar=1.15, apr=1.15, may=1.15, jun=1.15,
+                         jul=1.15, aug=1.15, sep=1.15, oct=1.15, nov=.79, dec=.79) 
> # factors average to 1
> ts1 <- CInp2TS(cinp, prec, cinp.daily.file, cinp.weekly, cinp.seasonal)
Error in `[.xts`(cinp.ts.deltap, 1:nrow(P1), ) : subscript out of bounds
Calls: CInp2TS -> [ -> [.xts
Execution halted
Package suggested but not available for checking: ‘taxadb’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/EMMIXcskew.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/empiricalFDR.DESeq2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/emstreeR.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘epicontacts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshotb53a10875b16.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotb53a10875b16.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘epicontacts.Rmd’

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

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

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

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EpiReport_Vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 367-368 (EpiReport_Vignette.Rmd) 
Error: processing vignette 'EpiReport_Vignette.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
--- failed re-building ‘EpiReport_Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   1.8Mb
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Errors in running code in vignettes:
when running code in ‘ESEA.Rnw’
  ...

> PathwayNetwork <- Results[[2]][[1]]

> SavePathway2File(PathwayNetwork, layout = layout.circle, 
+     file = "Graph")
[1] "...writing to file"

  When sourcing ‘ESEA.R’:
Error: there is no package called ‘graph’
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ESEA.Rnw’ using Sweave
Loading required package: igraph

Attaching package: ‘igraph’

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

    decompose, spectrum

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

    union

Loading required package: XML
Loading required package: parmigene

Error: processing vignette 'ESEA.Rnw' failed with diagnostics:
 chunk 11 
Error in loadNamespace(name) : there is no package called ‘graph’

--- failed re-building ‘ESEA.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/etasFLP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Evomorph.Rcheck/00install.out’ for details.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    exiftool  13.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ExomeDepth.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.4Mb
Running ‘runit.R’ [35s/68s]
Running the tests in ‘tests/runit.R’ failed.
Last 13 lines of output:
  test_touch: (1 checks) ... OK (2.01 seconds)
  --------------------------- 
  Test file: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fakemake.Rcheck/fakemake/runit_tests/runit-throw.R 
  test_exception: (1 checks) ... OK (0 seconds)
  --------------------------- 
  Test file: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fakemake.Rcheck/fakemake/runit_tests/runit-xmake.R 
  test_make_full_tree: (4 checks) ... OK (0.03 seconds)
  test_make_missing: (2 checks) ... OK (0.03 seconds)
  test_make_newer: (2 checks) ... OK (1.03 seconds)
  test_make_phony: (3 checks) ... OK (2.04 seconds)
  test_make_prerequisite: (3 checks) ... OK (1.04 seconds)
  test_make_sink: (2 checks) ... OK (0.01 seconds)
  test_make_source_files: (0 checks) ... OK (0 seconds)
  Error: RUnit failed.
  Execution halted
Found the following significant warnings:
  Warning: ‘i’ is used uninitialized in this function [-Wuninitialized]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fAsianOptions.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.1Mb
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    libs  42.1Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  16.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      6.9Mb
Packages suggested but not available for checking: 'DESeq2', 'destiny'
Error(s) in re-building vignettes:
  ...
--- re-building ‘FateID.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 141-142 (FateID.Rmd) 
Error: processing vignette 'FateID.Rmd' failed with diagnostics:
there is no package called 'destiny'
--- failed re-building ‘FateID.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/FcircSEC.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 39.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  36.3Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fdasrvf.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: rainbow
Loading required package: MASS
Loading required package: pcaPP
Loading required package: RCurl
Loading required package: bitops

Execution halted
Running ‘test-as-dgCMatrix.R’ [2s/2s]
  Running ‘test-empty_array.R’ [2s/2s]
  Running ‘test-existence_collision.R’ [2s/2s]
  Running ‘test-hash.mapping.R’ [2s/2s]
  Running ‘test-hashing.R’ [2s/2s]
Running the tests in ‘tests/test-hashing.R’ failed.
Last 13 lines of output:
  +     if (class(e)[1] != "std::invalid_argument") stop(e)
  +     if (conditionMessage(e) != "Failed to find the column:PlAnT") stop(e)
  +   })
  +   
  +   m <- hashed.model.matrix(~ Plant:Type:Treatment, CO2, create.mapping = TRUE, signed.hash = TRUE)
  +   map <- hash.mapping(m)
  +   map <- map[grepl("\\w+:\\w+:\\w+", names(map))]
  +   checkTrue(all(hashed.interaction.value(names(map)) %% (2^18) + 1== map),
  +             "The hashed.interaction.value gives inconsistent result of hashed.model.matrix")
  + }
  Loading required package: RUnit
  Error in .hashed.model.matrix.dataframe(tf, data, hash.size, transpose,  : 
    c++ exception (unknown reason)
  Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/feature.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/FieldSim.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘EML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fingerPro.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘quick_charts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning in normalizePath(f2) :
  path[1]="webshot114e76fe61b6d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot114e76fe61b6d.png': No such file or directory
Quitting from lines 125-134 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘quick_charts.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lifeExpectancy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 76-77 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘lifeExpectancy.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.5Mb
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fit4NM.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:7928): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
'library' or 'require' calls to packages already attached by Depends:
  ‘RGtk2’ ‘cairoDevice’ ‘gWidgets’ ‘gWidgetsRGtk2’ ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:7936): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
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No protocol specified

(R:7944): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:7952): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
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No protocol specified

(R:8012): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:8020): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
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(R:8028): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
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(R:8036): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
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No protocol specified

(R:8050): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘fit4NM-Ex.R’ failed
The error most likely occurred in:

> ### Name: fit4NM
> ### Title: Platform for NONMEM
> ### Aliases: fit4NM
> ### Keywords: utilities
> 
> ### ** Examples
> 
> fit4NM()

(R:8075): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:8075): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:8075): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:8075): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:8075): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:8075): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:8075): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:8075): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:8075): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

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

Traceback:
 1: .RGtkCall("S_gtk_widget_show", object, PACKAGE = "RGtk2")
 2: method(obj, ...)
 3: window$Show()
 4: .gwindow(toolkit, title, visible, width, height, parent, handler,     action, ...)
 5: .gwindow(toolkit, title, visible, width, height, parent, handler,     action, ...)
 6: gwindow("GUI for NONMEM", width = 850, height = 300)
 7: fit4NM()
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
--- failed re-building ‘fitbitScraper-examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   2.9Mb
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/float.Rcheck/00install.out’ for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
installed size is 48.0Mb
  sub-directories of 1Mb or more:
    libs  46.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_fontHind.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 38-49 (Using_fontHind.Rmd) 
Error: processing vignette 'Using_fontHind.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Using_fontHind.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_fontMPlus.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 56-67 (Using_fontMPlus.Rmd) 
Error: processing vignette 'Using_fontMPlus.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Using_fontMPlus.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/foodweb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ForImp.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘formattable-data-frame.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘formattable-data-frame.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-formulaic.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-132 (Introduction-to-formulaic.Rmd) 
Error: processing vignette 'Introduction-to-formulaic.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Introduction-to-formulaic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘seasonal’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   4.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Found the following significant warnings:
  c_hd_mf.cpp:157:12: warning: explicitly assigning value of variable of type 'Eigen::VectorXd' (aka 'Matrix<double, Dynamic, 1>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/FRegSigCom.Rcheck/00install.out’ for details.
installed size is 61.7Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs  59.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   6.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.4Mb
Package unavailable to check Rd xrefs: ‘frm’
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    libs  40.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/frontiles.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fsbrain.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 69 | SKIPPED: 15 | WARNINGS: 2553 | FAILED: 37 ]
  1. Error: A label can be extracted from a region of a loaded annotation (@test-atlas.R#3) 
  2. Error: A label can be extracted from a region of an annotation file (@test-atlas.R#31) 
  3. Error: Labels can be extracted from a region of an annotation file for a group of subjects (@test-atlas.R#43) 
  4. Error: Loading of native space whole brain morph data on group level works (@test-fsdir-abstraction-group.R#3) 
  5. Error: Loading of native space whole brain morph data restricted to the cortex on group level works (@test-fsdir-abstraction-group.R#29) 
  6. Error: Loading of standard space whole brain morph data on group level works (@test-fsdir-abstraction-group.R#57) 
  7. Error: Label data can be read on group level (@test-fsdir-abstraction-group.R#79) 
  8. Error: Annotation data can be read on group level (@test-fsdir-abstraction-group.R#97) 
  9. Error: Loading of native space whole brain morph data on subject level works (@test-fsdir-abstraction-subject.R#3) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Error(s) in re-building vignettes:
--- re-building ‘format_columns.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: /tmp/RtmpVYe8Du/file1e4357d8891f: Permission denied
Quitting from lines 28-36 (format_columns.Rmd) 
Error: processing vignette 'format_columns.Rmd' failed with diagnostics:
lexical error: invalid char in json text.
                                       NA
                     (right here) ------^

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fulltext.Rcheck/00install.out’ for details.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘futureheatwaves.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘futureheatwaves.Rmd’

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

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ArrayBin’
Package which this enhances but not available for checking: ‘doMPI’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.9Mb
installed size is 79.9Mb
  sub-directories of 1Mb or more:
    libs  79.5Mb
installed size is 58.9Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     55.6Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  14.9Mb
Packages suggested but not available for checking:
  'classGraph', 'graph', 'Rgraphviz'
installed size is 170.2Mb
  sub-directories of 1Mb or more:
    L8NY18    2.2Mb
    libs    166.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/gdimap.Rcheck/00install.out’ for details.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Running ‘testthat.R’ [6s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("genBaRcode")
  ── 1. Error: (unknown) (@test_raw_data_functions.R#3)  ─────────────────────────
  package 'GenomeInfoDb' could not be loaded
  Backtrace:
   1. base::library(ShortRead)
   2. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
   3. base::library(...)
   4. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 17 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test_raw_data_functions.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘genBaRcode_GUI_Vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘genBaRcode_GUI_Vignette.Rmd’

--- re-building ‘genBaRcode_Vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 155-176 (genBaRcode_Vignette.Rmd) 
Error: processing vignette 'genBaRcode_Vignette.Rmd' failed with diagnostics:
there is no package called 'GenomeInfoDbData'
--- failed re-building ‘genBaRcode_Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [9s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] "clustering genes from baseline samples normalized to mean..."
  [1] "clustering genes from all samples normalized to mean..."
  [1] "clustering genes from all samples normalized to baseline..."
  [1] "clustering genes from baseline samples normalized to mean..."
  [1] "clustering genes from baseline samples normalized to controls..."
  [1] "clustering genes from all samples normalized to mean..."
  [1] "clustering genes from all samples normalized to controls..."
  [1] "clustering genes from all samples normalized to baseline..."
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 134 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 2 ]
  1. Error: genModelResults outputs correctly for one comparison (@test_genModelResults.R#64) 
  2. Error: genModelResults outputs correctly for multiple comparisons (@test_genModelResults.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GENEAsphere.Rcheck/00install.out’ for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/geno2proteo.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'KEGG.db', 'reactome.db', 'AnnotationDbi'
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/gensphere.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘sf’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/geoelectrics.Rcheck/00install.out’ for details.
Output for data("sinkhole", package = "geoelectrics"):
  Warning messages:
  1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
  2: 'rgl_init' failed, running with rgl.useNULL = TRUE
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   3.9Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R         8.8Mb
    extdata   1.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/geomorph.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.9Mb
Running ‘testthat.R’ [33s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(getCRUCLdata)
  > 
  > test_check("getCRUCLdata")
  ── 1. Failure: cache directory is created if necessary (@test_caching.R#29)  ───
  dir.exists(manage_cache$cache_path_get()) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 23 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: cache directory is created if necessary (@test_caching.R#29) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘RGtk2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘IntroductionToGFD.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 106-107 (IntroductionToGFD.Rmd) 
Error: processing vignette 'IntroductionToGFD.Rmd' failed with diagnostics:
there is no package called 'RGtk2'
--- failed re-building ‘IntroductionToGFD.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespace in Imports field not imported from: ‘corrr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GGEBiplotGUI.Rcheck/00install.out’ for details.
Running examples in ‘GGEBiplotGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: GGEBiplot
> ### Title: GGEBiplotGUI: Interactive GGE Biplots in R
> ### Aliases: GGEBiplot
> 
> ### ** Examples
> 
> data(Ontario)
> GGEBiplot(Data = Ontario)
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: GGEBiplot ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Switching to 'nipals' method.
  Missing values detected: (3%)
  Missing values detected: (3%)
  Switching to 'nipals' method.
  Missing values detected: (3%)
  Switching to 'nipals' method.
  ── 1. Failure: rgl works (@test_gge.R#162)  ────────────────────────────────────
  `{ ... }` produced warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Failure: rgl works (@test_gge.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  18.7Mb
Error(s) in re-building vignettes:
--- re-building ‘ggPredict.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra

Attaching package: 'ggiraphExtra'

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

    addLabelDf, getMapping

Loading required package: plyr
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot8a65240e95b5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot8a65240e95b5.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

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

Attaching package: 'gglogo'

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

    fortify

Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Quitting from lines 45-52 (gglogo-alphabet.Rmd) 
Error: processing vignette 'gglogo-alphabet.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building ‘gglogo-alphabet.Rmd’

SUMMARY: processing the following file failed:
  ‘gglogo-alphabet.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.2Mb
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: Matrix
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 185-186 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.2Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is 64.5Mb
  sub-directories of 1Mb or more:
    libs  63.4Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    libs  40.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rnw’ using knitr
--- finished re-building ‘intro.Rnw’

--- re-building ‘parallel.Rnw’ using knitr

Execution halted
SUMMARY: processing the following file failed:
  ‘parallel.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
installed size is 63.8Mb
  sub-directories of 1Mb or more:
    doc         1.2Mb
    libs       60.3Mb
    test_data   1.2Mb
glmulti,character-character-ANY-ANY: no visible global function
  definition for ‘regsubsets’
Undefined global functions or variables:
  regsubsets
Running examples in ‘gluvarpro-Ex.R’ failed
The error most likely occurred in:

> ### Name: preprocessgvp
> ### Title: preprocessing raw data from continuous glucose monitoring
> ### Aliases: preprocessgvp
> 
> ### ** Examples
> 
> data("datagvp4")
> preprocessgvp(datagvp4)
Error in preprocessgvp(datagvp4) : 
  Variable date and time must have yyyy/mm/dd and hh:mm:ss format.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GMMAT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/gMOIP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/gnmf.Rcheck/00install.out’ for details.
File ‘gnmf/libs/gnmf.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘WGCNA’

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GPareto.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GPGame.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GPoM.FDLyapu.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GPoM.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘gprofiler2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 239-240 (gprofiler2.Rmd) 
Error: processing vignette 'gprofiler2.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘gprofiler2.Rmd’

SUMMARY: processing the following file failed:
  ‘gprofiler2.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 49.0Mb
  sub-directories of 1Mb or more:
    libs  46.4Mb
Running ‘testthat.R’ [68s/77s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 3096 | SKIPPED: 309 | WARNINGS: 0 | FAILED: 25 ]
  1. Error: gpuMatrix Double Precision Matrix-Vector multiplication (@test_gpuMatrix_algebra.R#840) 
  2. Error: gpuMatrix Integer Precision Sum (@test_gpuMatrix_row_col.R#41) 
  3. Error: gpuMatrix Double Precision Sum (@test_gpuMatrix_row_col.R#67) 
  4. Error: gpuMatrix Double Precision Block Sum (@test_gpuMatrix_row_col.R#400) 
  5. Error: gpuVector Double precision tcrossprod (@test_gpuVector_algebra.R#607) 
  6. Error: Switching GPUs vclMatrix Double Precision Matrix Multiplication (@test_switch_gpu_vclMatrix_algebra.R#480) 
  7. Error: Switching GPUs vclMatrix Double Precision Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#507) 
  8. Error: Switching GPUs vclMatrix Double Precision Scalar Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#535) 
  9. Error: Switching GPUs vclMatrix Double Precision Unary Scalar Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#567) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   2.9Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/graphscan.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GSAgm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘impute’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/gsl.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error: package or namespace load failed for 'testthat' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
   there is no package called 'rlang'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-34 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
package or namespace load failed for 'ggplot2' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'rlang'
--- failed re-building ‘profiling.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘interval’
Package suggested but not available for checking: ‘gt’
Error(s) in re-building vignettes:
--- re-building ‘gunsales.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: line 1: 13995 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/x13ashtml /tmp/RtmpZhJtlI/x1336a159a99349/iofile -n -s 2> /dev/null
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x1251da579
#1  0x1251d9945
#2  0x7fff9ae44529
Quitting from lines 33-34 (gunsales.Rmd) 
Error: processing vignette 'gunsales.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
--- failed re-building ‘gunsales.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘run-tests.R’ [1s/1s]
Running the tests in ‘tests/run-tests.R’ failed.
Last 13 lines of output:
  > f <- Filter(function(x) !grepl("html", x), f)
  > 
  > sapply(f, function(i) {
  +   message("testing ", i)
  +   source(i)
  + })
  testing /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/gWidgets2/tests/button.R
  Loading required package: gWidgets2RGtk2
  Loading required package: memoise
  Loading required package: RGtk2
  No protocol specified
  R session is headless; GTK+ not initialized.
  Error in guiToolkit() : Can't load RGtk2
  Calls: sapply ... withVisible -> eval -> eval -> gwindow -> guiToolkit
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.5Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 40-43 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [1s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("hail")
  ── 1. Error: hail_hydra works (@test.R#4)  ─────────────────────────────────────
  cannot open the connection to 'https://or.water.usgs.gov/precip/walmart_ecoroof.rain'
  1: hail_hydra("Walmart Eco Roof") at testthat/test.R:4
  2: hydra_base(station_data$urls, station_data$stations)
  3: readLines(url)
  4: file(con, "r")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: hail_hydra works (@test.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Basic_use.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hchinamap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://czxb.github.io/br/chinadf.rda'
Content type 'application/octet-stream' length 3992 bytes
==================================================
downloaded 3992 bytes

Quitting from lines 50-58 (hchinamap.Rmd) 
Error: processing vignette 'hchinamap.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘hchinamap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    CWrappers_1.10.2   2.6Mb
    CWrappers_1.10.3   2.6Mb
    CWrappers_1.12.0   2.9Mb
    libs               6.5Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Error(s) in re-building vignettes:
--- re-building ‘heatmaply.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 1.1.0

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

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

No protocol specified
Quitting from lines 108-110 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘heatmaply.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'rgl', 'FRB'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HeritSeq.Rcheck/00install.out’ for details.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs  15.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hetGP_vignette.Rnw’ using knitr
Quitting from lines 434-443 (hetGP_vignette.Rnw) 
Error: processing vignette 'hetGP_vignette.Rnw' failed with diagnostics:
invalid 'z' limits
--- failed re-building ‘hetGP_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HiCfeat.Rcheck/00install.out’ for details.
Unexported objects imported by ':::' calls:
  ‘ggplot2:::build_guides’ ‘ggplot2:::guide_axis’
  ‘ggplot2:::scales_list’
  See the note in ?`:::` about the use of this operator.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HierO.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
    libs   1.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        8.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/hiPOD.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.2Mb
Package suggested but not available for checking: ‘trackr’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HiveR.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   3.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/hmgm.Rcheck/00install.out’ for details.
No protocol specified
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘methods’ ‘rgl’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/hoardeR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'iheatmapr', 'ropls'
Error(s) in re-building vignettes:
  ...
--- re-building ‘simulating-data.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 25-31 (simulating-data.Rmd) 
Error: processing vignette 'simulating-data.Rmd' failed with diagnostics:
there is no package called 'ropls'
--- failed re-building ‘simulating-data.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/homals.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hpackedbubble.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 35-49 (hpackedbubble.Rmd) 
Error: processing vignette 'hpackedbubble.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘hpackedbubble.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
File ‘hpa/libs/hpa.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Objects: ‘hpaBinary.o’, ‘hpaML.o’, ‘hpaSelection.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified

(R:8058): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
installed size is 48.9Mb
  sub-directories of 1Mb or more:
    libs  48.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
Running ‘testthat.R’ [53s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   18. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   20. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   22. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   23. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   24. base:::withOneRestart(expr, restarts[[1L]])
   25. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 102 | SKIPPED: 18 | WARNINGS: 3 | FAILED: 3 ]
  1. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2) 
  2. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15) 
  3. Error: HRSIP runs with default (@test-HRSIP.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HUM.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 161-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hwordcloud.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-53 (hwordcloud.Rmd) 
Error: processing vignette 'hwordcloud.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘hwordcloud.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/hyper.fit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/hypervolume.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ibmsunburst.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ibmsunburst.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.1000genomes.hs37d5',
  'BSgenome.Hsapiens.UCSC.hg38', 'BSgenome.Mmusculus.UCSC.mm10'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ICAMS.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 84-88 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
argument of length 0
--- failed re-building ‘example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   5.9Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Package suggested but not available for checking: ‘mixAK’
Running examples in ‘iClick-Ex.R’ failed
The error most likely occurred in:

> ### Name: iClick.ARIMA
> ### Title: iClick GUI for ARIMA
> ### Aliases: iClick.ARIMA
> 
> ### ** Examples
> 
> 
> ##External data
> data("world20")
> y=na.omit(diff(log(world20[,1])))
> 
> ## Simulation data
> #dat=rnorm(200,5,1)
> #y=ts(dat, start = c(1970, 1), frequency = 12)
> 
> iClick.ARIMA(y)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: iClick.ARIMA ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/icosa.Rcheck/00install.out’ for details.
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  27.7Mb
Error(s) in re-building vignettes:
--- re-building ‘model_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 25-32 (model_details.Rmd) 
Error: processing vignette 'model_details.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘model_details.Rmd’

--- re-building ‘parameter_details.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-31 (parameter_details.Rmd) 
Error: processing vignette 'parameter_details.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘parameter_details.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.2Mb
    libs  14.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.0Mb
    include   3.0Mb
    libs     18.7Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Found the following significant warnings:
  IM4ECpp.cpp:24:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:22:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:32:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Immigrate.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Packages suggested but not available for checking: 'rsprng', 'Rmpi'
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
sh: line 1: 52038 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/x13ashtml /tmp/RtmpIbZ5DU/x13cb3e1fb9e948/iofile -n -s 2> /dev/null
Warning in system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE) :
  running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/x13ashtml /tmp/RtmpIbZ5DU/x13cb3e1fb9e948/iofile -n -s 2>/dev/null' had status 133
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x12b311579
#1  0x12b310945
#2  0x7fff98106529
Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Packages suggested but not available for checking:
  'MLP', 'org.Hs.eg.db', 'a4Base'
Error(s) in re-building vignettes:
--- re-building ‘IntGraphTutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: DiagrammeR
Loading required package: DiagrammeRsvg
Loading required package: rsvg
Loading required package: gtools
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot15a63ac4ea79.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot15a63ac4ea79.png': No such file or directory
Quitting from lines 32-34 (IntGraphTutorial.Rmd) 
Error: processing vignette 'IntGraphTutorial.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘IntGraphTutorial.Rmd’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
.nndsvd.internal: no visible global function definition for ‘runif’
nmf.mnnals: no visible global function definition for ‘runif’
nmf.opt.k: no visible global function definition for ‘flush.console’
nmf.opt.k: no visible global function definition for ‘points’
nmf.opt.k: no visible global function definition for ‘lines’
nmf.opt.k: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  flush.console lines mtext points runif
Consider adding
  importFrom("graphics", "lines", "mtext", "points")
  importFrom("stats", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ionflows.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘coda’ ‘lattice’
  All declared Imports should be used.
Running examples in ‘IRATER-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
sh: admb: command not found
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘getting-started-with-irg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
ndvi                    package:irg                    R Documentation

_R_a_w _N_D_V_I _T_i_m_e _S_e_r_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

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

_F_o_r_m_a_t:

     A data.table with 2530 rows and 5 variables:

        • id - individual identifier

        • yr - year of sample

        • DayOfYear - julian day/day of year of sample

        • NDVI - sampled value

        • SummaryQA - Summary quality assessment value

     SummaryQA details:

        • 0 - Good data, use with confidence

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

        • 2 - Pixel covered with snow/ice

        • 3 - Pixel is cloudy

_E_x_a_m_p_l_e_s:

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

Quitting from lines 99-153 (getting-started-with-irg.Rmd) 
Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘getting-started-with-irg.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.3Mb
Packages suggested but not available for checking: 'pcalg', 'Rgraphviz'
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

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

    isFALSE

Loading required package: rngtools
Loading required package: cluster
# NOTE - CRAN check detected: limiting maximum number of cores [2/8]
NMF - BioConductor layer [NO: missing Biobase] | Shared memory capabilities [OK] | Cores 2/2 | CRAN check
  To enable the Bioconductor layer, try: install.extras('
NMF
') [with Bioconductor repository enabled]
Quitting from lines 94-99 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'pcalg'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          15.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/JFE.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.6Mb
Found the following significant warnings:
  jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/jomo.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.7Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Missing or unexported object: ‘tidyr::unnest_legacy’
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/kerastuneR.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/kernhaz.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘org.Hs.eg.db’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/KernSmoothIRT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/kmcudaR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/kml3d.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/kml.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/kmlShape.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘kstIO.Rnw’ using Sweave
Loading required package: pks
Loading required package: sets
Loading required package: MASS
Loading required package: stringr

Attaching package: ‘stringr’

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

    %>%

Loading required package: relations

Error: processing vignette 'kstIO.Rnw' failed with diagnostics:
 chunk 1 
Error in library("kst") : there is no package called ‘kst’

--- failed re-building ‘kstIO.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Rgraphviz’
Error(s) in re-building vignettes:
--- re-building ‘kst.Rnw’ using Sweave
Loading required package: proxy

Attaching package: ‘proxy’

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

    as.dist, dist

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

    as.matrix

Loading required package: relations
Loading required package: sets
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Error: processing vignette 'kst.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'kst.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./kst-012.pdf): PDF inclusion: required page does
 not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘kst.Rnw’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LambertW.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LANDD.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
installed size is 144.2Mb
  sub-directories of 1Mb or more:
    libs  142.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_to_lavaanPlot.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-42 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Intro_to_lavaanPlot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/lba.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./lda_svi.h:1:9: warning: '_lda_svi_guard' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/lda.svi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/leapp.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      6.4Mb
Packages suggested but not available for checking: 'gWidgetsRGtk2', 'RGtk2'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Understanding_lime.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 262-263 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Understanding_lime.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘linkspotterVignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘linkspotterVignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   9.1Mb
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      21.8Mb
    testdata   1.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LMERConvenienceFunctions.Rcheck/00install.out’ for details.
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

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

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

Error: Vignette re-building failed.
Execution halted
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/longitudinalData.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RDRToolbox’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/loon.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LoopRig.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [13s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("loose.rock")
  ── 1. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/")` did not produce any warnings.
  
  ── 2. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/daca")` did not produce any warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 147 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#29) 
  2. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LOST.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LSAfun.Rcheck/00install.out’ for details.
installed size is 51.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  49.3Mb
Running examples in ‘LTRCtrees-Ex.R’ failed
The error most likely occurred in:

> ### Name: ICtree
> ### Title: Fit a survival tree for interval-censored survival data
> ### Aliases: ICtree
> 
> ### ** Examples
> 
> library(interval)
Error in library(interval) : there is no package called ‘interval’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LTRCtrees.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in min(diff(sort(ux))) :
  no non-missing arguments to min; returning Inf
Quitting from lines 199-207 (LTRCtrees.Rmd) 
Error: processing vignette 'LTRCtrees.Rmd' failed with diagnostics:
there is no package called 'interval'
--- failed re-building ‘LTRCtrees.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LUCIDus-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 63-64 (LUCIDus-vignette.Rmd) 
Error: processing vignette 'LUCIDus-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘LUCIDus-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.1Mb
    libs   1.7Mb
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Maeswrap.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 12 ]
  1. Error: interactive_blur (@test_interactive_blur.R#6) 
  2. Error: interactive_canny (@test_interactive_canny.R#5) 
  3. Error: interactive_charcoal (@test_interactive_charcoal.R#6) 
  4. Error: interactive_composite (@test_interactive_composite.R#5) 
  5. Error: interactive_despeckle (@test_interactive_despeckle.R#6) 
  6. Error: interactive_emboss (@test_interactive_emboss.R#6) 
  7. Error: interactive_implode (@test_interactive_implode.R#6) 
  8. Error: interactive_modulate (@test_interactive_modulate.R#6) 
  9. Error: interactive_oilpaint (@test_interactive_oilpaint.R#6) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 80.1Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  72.8Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  19.2Mb
Error(s) in re-building vignettes:
--- re-building ‘manhattanly.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshotd4a14dcd902a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotd4a14dcd902a.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘manhattanly.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘manipulateWidgets.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot9723ea5db42.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot9723ea5db42.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘manipulateWidgets.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/maotai.Rcheck/00install.out’ for details.
prepare_Rd: RGL: unable to open X11 display
prepare_Rd: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    data          1.3Mb
    doc           1.2Mb
    htmlwidgets   1.8Mb
    libs         14.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mapmisc.Rnw’ using knitr
Loading required package: sp
Loading required package: raster
map images will be cached in  /tmp/Rtmpvjscv5/mapmiscCache
--- finished re-building ‘mapmisc.Rnw’

--- re-building ‘north.Rmd’ using docco_linear
Quitting from lines 221-238 (north.Rmd) 
Error: processing vignette 'north.Rmd' failed with diagnostics:
unable to find an inherited method for function 'coordinates' for signature '"numeric"'
--- failed re-building ‘north.Rmd’

pandoc --self-contained --to=html5 --css=http://diseasemapping.r-forge.r-project.org/webpage.css --output=north.html north.md	
make: pandoc: No such file or directory
make: *** [north.html] Error 1
Error in tools:::buildVignettes(dir = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mapmisc.Rcheck/vign_test/mapmisc",  : 
  running 'make' failed
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-100 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.6Mb
Package suggested but not available for checking: ‘ASGSCA’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mcca.Rcheck/00install.out’ for details.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   9.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MDSMap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mdsOpt.Rcheck/00install.out’ for details.
Found the following significant warnings:
  lightextinction.cpp:74:63: warning: explicitly assigning value of variable of type 'Rcpp::String' to itself [-Wself-assign-overloaded]
  lightextinction.cpp:85:64: warning: explicitly assigning value of variable of type 'Rcpp::String' to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/medfate.Rcheck/00install.out’ for details.
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs  20.5Mb
Packages suggested but not available for checking:
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'org.Hs.eg.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Mega2R.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.6Mb
installed size is 76.9Mb
  sub-directories of 1Mb or more:
    libs  76.5Mb
Package required but not available: ‘GO.db’

Packages suggested but not available for checking: 'clpAPI', 'ctc'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MetaIntegrator.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 29-30 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘MetaIntegrator.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'org.Hs.eg.db', 'annaffy', 'hgu133plus2.db', 'hgu133a.db',
  'hgu95av2.db'
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MetaPath.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'GEOquery', 'affy', 'hgu133plus2.db', 'doSMP', 'impute'
Packages suggested but not available for checking:
  'HTSFilter', 'DESeq', 'DESeq2'
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
  ...

> options(width = 60)

> library(metaRNASeq)

> library(DESeq2)

  When sourcing ‘metaRNASeq.R’:
Error: there is no package called ‘DESeq2’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘metaRNASeq.Rnw’ using Sweave

Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
 chunk 2 (label = loadparameters) 
Error in library(DESeq2) : there is no package called ‘DESeq2’

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

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.1Mb
    libs  18.6Mb
    misc   1.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MFHD.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mgcViz.Rcheck/00install.out’ for details.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  21.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgwrsar-basic_examples.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘mgwrsar-basic_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Package suggested but not available for checking: ‘biotools’
Package unavailable to check Rd xrefs: ‘biotools’
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
sROC 0.1-2 loaded
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running ‘testthat.R’ [20s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  subscript out of bounds
  1: assumptions(mic1a) at testthat/test_micomp.R:281
  2: assumptions.micomp(mic1a)
  3: lapply(obj, function(x) assumptions(x))
  4: FUN(X[[i]], ...)
  5: assumptions(x)
  6: assumptions.cmpoutput(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 363 SKIPPED: 0 FAILED: 2
  1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R#214) 
  2. Error: micomp assumptions have the correct properties (@test_micomp.R#281) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘paper.Rnw’ using knitr
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette 'paper.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘paper.Rnw’

--- re-building ‘tolatex-examples.Rnw’ using knitr
Warning in wilcox.test.default(x = c(-2.17390550005803e-11, -2.17097451127302e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(2.13309370167281e-11, 2.12594386539422e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.99236183107132e-11, 1.97388771994156e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.00897068477934e-12, 1.02406971791424e-12,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(8.95727936267576e-13, 8.4909856923332e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.80548975348938e-13, 8.81072992342524e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(5.90887339058099e-11, 6.09077233093558e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.97119053991469e-15, 9.92695509127728e-15,  :
  cannot compute exact p-value with ties
--- finished re-building ‘tolatex-examples.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘gWidgets2RGtk2’
Error(s) in re-building vignettes:
--- re-building ‘milr-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.8390.
trying URL 'http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz'
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
The penalty term is selected automatically with 100 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 3.2909.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.

Execution halted
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.9Mb
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Package unavailable to check Rd xrefs: ‘mixAK’
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/missDeaths.Rcheck/00install.out’ for details.
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
Running examples in ‘MixSIAR-Ex.R’ failed
The error most likely occurred in:

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

        If installing GTK+ continues to be problematic, consider using the
        script version of MixSIAR. See manual for help and examples.
Execution halted
Package suggested but not available for checking: ‘IlluminaHumanMethylation450kmanifest’
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in png::readPNG(path, native = TRUE, info = TRUE) :
  libpng warning: iCCP: CRC error
Quitting from lines 172-173 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MMDai.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ALL’
Running examples in ‘MMDvariance-Ex.R’ failed
The error most likely occurred in:

> ### Name: gsMMD.v
> ### Title: Gene selection based on variances by using a mixture of marginal
> ###   distributions
> ### Aliases: gsMMD.v
> ### Keywords: classif
> 
> ### ** Examples
> 
>       t1 = proc.time()
>       library(ALL)
Error in library(ALL) : there is no package called ‘ALL’
Execution halted
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Error(s) in re-building vignettes:
--- re-building ‘mnlogit.Rnw’ using Sweave
Package: mnlogit
Version: 1.2.6
Multinomial Logit Choice Models.
Scientific Computing Group, Sentrana Inc.
Loading required package: Formula
Loading required package: zoo

Attaching package: 'zoo'

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

    index

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

    as.Date, as.Date.numeric

Loading required package: lmtest

Attaching package: 'mlogit'

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

    hmftest, scoretest
Package suggested but not available for checking: ‘doMPI’

Package which this enhances but not available for checking: ‘MoBPSmaps’
Package required but not available: ‘doMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/molaR.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   4.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/morphomap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Morpho.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   6.4Mb
Error(s) in re-building vignettes:
--- re-building ‘tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 342-344 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
The model needs too many iterations to provide reliable parameter estimates !
--- failed re-building ‘tutorial.Rmd’

--- re-building ‘modelling.Snw’ using Sweave
--- finished re-building ‘modelling.Snw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘rhdf5’
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

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

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

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

Error: Vignette re-building failed.
Execution halted
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  38.9Mb
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  45.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘msir.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot127825d88bea8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot127825d88bea8.png': No such file or directory
Quitting from lines 102-104 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MSIseq.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MSQC.Rcheck/00install.out’ for details.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  16.2Mb
Running examples in ‘mssqlR-Ex.R’ failed
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mtk.Rcheck/00install.out’ for details.
Packages required but not available:
  'org.Hs.eg.db', 'org.Mm.eg.db', 'org.Ce.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 83.5Mb
  sub-directories of 1Mb or more:
    libs  83.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running examples in ‘multistateutils-Ex.R’ failed
The error most likely occurred in:

> ### Name: cohort_simulation
> ### Title: Runs a cohort discrete event simulation
> ### Aliases: cohort_simulation
> 
> ### ** Examples
> 
> library(multistateutils)
> library(mstate)
Loading required package: survival
> library(flexsurv)
> 
> # Convert data to long
> data(ebmt3)
> tmat <- trans.illdeath()
> long <- msprep(time=c(NA, 'prtime', 'rfstime'),
+                status=c(NA, 'prstat', 'rfsstat'),
+                data=ebmt3,
+                trans=tmat,
+                keep=c('age', 'dissub'))
> 
> # Fit parametric models
> models <- lapply(1:3, function(i) {
+     flexsurvreg(Surv(time, status) ~ age + dissub, data=long, dist='weibull')
+ })
> 
> sim <- cohort_simulation(models, ebmt3, tmat)

 *** caught illegal operation ***
address 0x10e8f7042, cause 'illegal opcode'

Traceback:
 1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states -     1, tcovs)
 2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat,     start_times, start_states - 1, tcovs))
 3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times,     start_states)
 4: state_occupancy(models, trans_mat, newdata, tcovs, start_time,     start_state, ci, M, agelimit, agecol, agescale)
 5: cohort_simulation(models, ebmt3, tmat)
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  32: withOneRestart(expr, restarts[[1L]])
  33: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  34: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        reporter$start_file(basename(path))        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        reporter$.end_context()        reporter$end_file()    })
  35: FUN(X[[i]], ...)
  36: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  37: force(code)
  38: doWithOneRestart(return(expr), restart)
  39: withOneRestart(expr, restarts[[1L]])
  40: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  41: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  42: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  43: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  44: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  45: test_check("multistateutils")
  An irrecoverable exception occurred. R is aborting now ...
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    libs  42.0Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("mustashe")
  ── 1. Failure: stashing works (@test-stash.R#28)  ──────────────────────────────
  file_time(file.path(target_dir, "a.rds")) == old_rds_time isn't false.
  
  ── 2. Failure: stashing works (@test-stash.R#29)  ──────────────────────────────
  file_time(file.path(target_dir, "a.hash")) == old_hash_time isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 54 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: stashing works (@test-stash.R#28) 
  2. Failure: stashing works (@test-stash.R#29) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mvmesh.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_mvord2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘vignette_mvord2.Rmd’

--- re-building ‘vignette_mvord.Rnw’ using Sweave
Loading required package: minqa
Loading required package: BB
Loading required package: ucminf
Loading required package: dfoptim
Error: processing vignette 'vignette_mvord.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'vignette_mvord.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'vignette_mvord.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nat.nblast.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nat.templatebrains.Rcheck/00install.out’ for details.
Package required but not available: ‘sSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NeatMap.Rcheck/00install.out’ for details.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘ConsensusClusterPlus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing or unexported object: ‘reticulate::use_miniconda’
Error(s) in re-building vignettes:
  ...
--- re-building ‘netgsa.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 86-89 (netgsa.Rmd) 
Error: processing vignette 'netgsa.Rmd' failed with diagnostics:
error creating directory: /Users/urbanek/Library/Caches/graphite-bioc/12
--- failed re-building ‘netgsa.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.4Mb
Packages suggested but not available for checking:
  'limma', 'DESeq2', 'edgeR', 'org.Hs.eg.db'
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/neuroim.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Error(s) in re-building vignettes:
--- re-building ‘NFP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: graphite
Quitting from lines 135-143 (NFP.Rmd) 
Error: processing vignette 'NFP.Rmd' failed with diagnostics:
error creating directory: /Users/urbanek/Library/Caches/graphite-bioc/12
--- failed re-building ‘NFP.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              6.0Mb
    classic-bugs   1.5Mb
    include        5.5Mb
    libs          19.0Mb
    tests          1.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NIPTeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nlcv.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘geocode.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘geocode.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Found the following significant warnings:
  clang-7: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
  DIRsubrout.c:505:10: warning: explicitly assigning value of variable of type 'integer' (aka 'int') to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nloptr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NNS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nonlinearTseries.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NPCirc.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘PMA’
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs  16.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.0Mb
File ‘obliclus/libs/obliclus.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘readODS’ ‘xlsx’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OceanView.Rcheck/00install.out’ for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    doc    2.3Mb
    help   2.8Mb
    libs   3.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OCNet.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ── 2. Failure: OLC encoding throws an error with odd-numbered requested lengths 
  `x` threw an error with unexpected message.
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 1 FAILED: 2
  1. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#20) 
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
comp.freq: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/onemap.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ontologyPlot’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OpenCL.Rcheck/00install.out’ for details.
installed size is 74.7Mb
  sub-directories of 1Mb or more:
    libs   64.9Mb
    share   9.7Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   6.0Mb
Error(s) in re-building vignettes:
--- re-building ‘openland_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://zenodo.org/record/3685230/files/SaoLourencoBasin.rda?download=1'
Content type 'application/octet-stream' length 5309066 bytes (5.1 MB)
==================================================
downloaded 5.1 MB

Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Warning: `expand_scale()` is deprecated; use `expansion()` instead.
Quitting from lines 264-269 (openland_vignette.Rmd) 
Error: processing vignette 'openland_vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘openland_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 189.4Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    libs    179.3Mb
    models    4.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OpenRepGrid.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      4.1Mb
Packages suggested but not available for checking: 'gurobi', 'Rsymphony'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Packages suggested but not available for checking:
  'GO.db', 'org.At.tair.db'
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/optiSel.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.7Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/optiSolve.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘optparse.Rrst’ using knitr
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
--- failed re-building ‘optparse.Rrst’

SUMMARY: processing the following file failed:
  ‘optparse.Rrst’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘graph’
Packages suggested but not available for checking: 'IsoGene', 'Biobase'
File ‘OriGen/libs/OriGen.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/orthoDr.Rcheck/00install.out’ for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   5.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.9Mb
Error(s) in re-building vignettes:
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Rcpp_API.Rmd’

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

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

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

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

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

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

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 196-217 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘progressive_packing.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PACVr.Rcheck/00install.out’ for details.
Package required but not available: ‘GO.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘evals.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-19 (evals.Rmd) 
Error: processing vignette 'evals.Rmd' failed with diagnostics:
package or namespace load failed for 'futile.logger' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'formatR'
--- failed re-building ‘evals.Rmd’

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

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

Attaching package: 'Hmisc'

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

    format.pval, units

--- finished re-building ‘pander.Rmd’

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

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

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

> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)

Attaching package: ‘bnlearn’

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

    sigma

> library(pcalg)
Error in library(pcalg) : there is no package called ‘pcalg’
Execution halted
Package suggested but not available for checking: ‘M3C’
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parcoords-.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-30 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction-to-parcoords-.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘parmigene/libs/parmigene.so’:
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/patternize.Rcheck/00install.out’ for details.
Packages required but not available: 'jetset', 'Mfuzz', 'WGCNA'

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pbdPROF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pbdZMQ.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pca3d.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   2.7Mb
    libs      2.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pcaL1.Rcheck/00install.out’ for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   7.0Mb
installed size is 100.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  97.2Mb
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PCGSE.Rcheck/00install.out’ for details.
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
Found the following significant warnings:
  Warning: 'rgl.init' failed, running with 'rgl.useNULL = TRUE'.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PCRedux.Rcheck/00install.out’ for details.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs    6.5Mb
    share  11.9Mb
Package suggested but not available for checking: ‘globaltest’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/permGPU.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data       2.3Mb
    examples   2.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
Found the following significant warnings:
  phreeqcpp/transport.cpp:794:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/phreeqc.Rcheck/00install.out’ for details.
installed size is 37.1Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘phybreak_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Execution halted
Error(s) in re-building vignettes:
--- re-building ‘Advanced_Usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshotc4dc454c7107.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotc4dc454c7107.png': No such file or directory
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Advanced_Usage.Rmd’

--- re-building ‘Basic_Use.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 30-32 (Basic_Use.Rmd) 
Error: processing vignette 'Basic_Use.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Basic_Use.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/phylocurve.Rcheck/00install.out’ for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   9.3Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Package required but not available: ‘rggobi’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PlasmaMutationDetector.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘S4Vectors’
No protocol specified

(R:89682): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:89690): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:89698): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified

(R:89706): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:89732): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:89760): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:89768): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:89776): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:89784): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:89798): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/plot3Drgl.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_plotdap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 138-146 (using_plotdap.Rmd) 
Error: processing vignette 'using_plotdap.Rmd' failed with diagnostics:
Failed to open file /Users/urbanek/Library/Caches/R/rerddap/d3691d4726dcf37b41ff22352dc3ac7e.nc.
--- failed re-building ‘using_plotdap.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.7Mb
Package suggested but not available for checking: ‘mixOmics’
Running examples in ‘PLSbiplot1-Ex.R’ failed
The error most likely occurred in:

> ### Name: Mag.Bmat.plot
> ### Title: Magnitude of the Partial Least Squares Regression (PLSR)
> ###   coefficients matrix
> ### Aliases: Mag.Bmat.plot
> 
> ### ** Examples
> 
> if(require(pls))
+ data(oliveoil, package="pls")
Loading required package: pls

Attaching package: ‘pls’

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

    loadings

> X = as.matrix(oliveoil$chemical, ncol=5)
> dimnames(X) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Acidity","Peroxide","K232","K270","DK")))
> Y = as.matrix(oliveoil$sensory, ncol=6)
> dimnames(Y) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Yellow","Green","Brown","Glossy","Transp","Syrup")))
> Mag.Bmat.plot(X, Y, algorithm=mod.SIMPLS, A=2)
> 
> #nutrimouse data
> if(require(mixOmics))
+ data(nutrimouse, package="mixOmics")
Loading required package: mixOmics
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mixOmics’
> X1 = as.matrix(nutrimouse$lipid, ncol=21)
Error in as.matrix(nutrimouse$lipid, ncol = 21) : 
  object 'nutrimouse' not found
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/plsVarSel.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘pmc_tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ape
Loading required package: subplex

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda

Execution halted
Package which this enhances but not available for checking: ‘gt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘OpenCPU.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘OpenCPU.Rmd’

--- re-building ‘vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
... activating corpus: GERMAPARLMINI
... activating corpus: REUTERS
Quitting from lines 140-141 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R      6.8Mb
    data   4.0Mb
No protocol specified
Namespace in Imports field not imported from: ‘combinat’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘polynomials.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'polynomials.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘polynomials.Rmd’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PPQplan.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPQnote.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘PPQnote.Rmd’

--- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
No protocol specified
Warning in normalizePath(f2) :
  path[1]="webshot83bd39d2f15.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot83bd39d2f15.png': No such file or directory
Quitting from lines 135-136 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PPQplan-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted