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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette1.Rnw’ using knitr
Quitting from lines 59-61 (vignette1.Rnw) 
Error: processing vignette 'vignette1.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette1.Rnw’

SUMMARY: processing the following file failed:
  ‘vignette1.Rnw’

Error: Vignette re-building failed.
Execution halted
.snqProfitImposeConvexityStEr: no visible global function definition
  for ‘runif’
predict.snqProfitEst: no visible global function definition for
  ‘model.matrix’
predict.snqProfitEst: no visible global function definition for ‘qt’
predict.snqProfitEst: no visible global function definition for
  ‘df.residual’
predict.snqProfitEst: no visible global function definition for
  ‘residuals’
snqProfitCoef: no visible global function definition for ‘pt’
snqProfitEla: no visible global function definition for ‘pt’
snqProfitEst: no visible global function definition for ‘as.formula’
snqProfitEst: no visible global function definition for ‘coef’
snqProfitEst: no visible global function definition for ‘vcov’
snqProfitEst: no visible global function definition for ‘fitted’
snqProfitEst: no visible global function definition for ‘df.residual’
snqProfitImposeConvexity: no visible global function definition for
  ‘optim’
snqProfitSystem: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula coef df.residual fitted model.matrix optim pt qt residuals
  runif vcov
Consider adding
  importFrom("stats", "as.formula", "coef", "df.residual", "fitted",
             "model.matrix", "optim", "pt", "qt", "residuals", "runif",
             "vcov")
to your NAMESPACE file.
Running examples in ‘microbenchmark-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.microbenchmark
> ### Title: Autoplot method for microbenchmark objects: Prettier graphs for
> ###   microbenchmark using ggplot2
> ### Aliases: autoplot.microbenchmark
> 
> ### ** Examples
> 
> if (requireNamespace("ggplot2")) {
+ 
+ tm <- microbenchmark(rchisq(100, 0),
+                      rchisq(100, 1),
+                      rchisq(100, 2),
+                      rchisq(100, 3),
+                      rchisq(100, 5), times=1000L)
+ ggplot2::autoplot(tm)
+ }
Loading required namespace: ggplot2
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Package suggested but not available for checking: ‘microcontax.data’
Package unavailable to check Rd xrefs: ‘microcontax.data’
Running examples in ‘micromap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lmgroupedplot
> ### Title: Linked Micromaps
> ### Aliases: lmgroupedplot lmplot mmgroupedplot mmplot lmplot mmgroupedplot
> ###   lmgroupedplot mmplot.SpatialPolygonsDataFrame mmplot.default
> ### Keywords: hplot
> 
> ### ** Examples
> 
> # initial example
> 
> data("USstates")
> head(USstates@data)
  ST    ST_NAME   AREA_KM  PERIM_KM
0 AK     Alaska 1506038.1 60260.638
1 AL    Alabama  133761.0  2354.600
2 AR   Arkansas  137733.7  2172.208
3 AZ    Arizona  295267.5  2395.409
4 CA California  409603.3  5682.304
5 CO   Colorado  269599.9  2100.092
> statePolys <- create_map_table(USstates, 'ST')
> head(statePolys)
  ID region poly coordsx coordsy hole plotorder plug
1 AK      1    1       2       5    0         1    0
2 AK      1    1       7      10    0         1    0
3 AK      1    1       4      12    0         1    0
4 AK      1    1       7      15    0         1    0
5 AK      1    1       4      15    0         1    0
6 AK      1    1       4      17    0         1    0
> 
> data("edPov")
> 
> # basic figure 1
> lmplot(stat.data = edPov,
+   	map.data = statePolys,
+ 	panel.types = c('labels', 'dot', 'dot','map'),
+ 	panel.data = list('state','pov','ed', NA),
+ 	ord.by = 'pov',   
+ 	grouping = 5, median.row = TRUE,
+ 	map.link = c('StateAb','ID'))
Coordinate system already present. Adding new coordinate system, which will replace the existing one.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: lmplot -> mmplot -> mmplot.default -> print -> print.mm
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_Guide.Rnw’ using Sweave
Loading required package: maptools
Loading required package: sp
Checking rgeos availability: TRUE
Loading required package: RColorBrewer
Loading required package: rgdal
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
 Path to GDAL shared files: /usr/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: 1.3-1 
Coordinate system already present. Adding new coordinate system, which will replace the existing one.

Error: processing vignette 'Introduction_Guide.Rnw' failed with diagnostics:
 chunk 5 (label = fig1) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: theme_collapse
> ### Title: Set the 'ggplot2' theme to remove all marginal space.
> ### Aliases: theme_collapse
> ### Keywords: ggplot2
> 
> ### ** Examples
> 
> theme_collapse()
List of 61
 $ line                 :List of 6
  ..$ colour       : chr "black"
  ..$ size         : num 0.5
  ..$ linetype     : num 1
  ..$ lineend      : chr "butt"
  ..$ arrow        : logi FALSE
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_line" "element"
 $ rect                 :List of 5
  ..$ fill         : chr "white"
  ..$ colour       : chr "black"
  ..$ size         : num 0.5
  ..$ linetype     : num 1
  ..$ inherit.blank: logi TRUE
  ..- attr(*, "class")= chr [1:2] "element_rect" "element"
 $ text                 :List of 11
  ..$ family       : chr ""
  ..$ face         : chr "plain"
  ..$ colour       : chr "black"
  ..$ size         : num 11
  ..$ hjust        : num 0.5
  ..$ vjust        : num 0.5
  ..$ angle        : num 0
  ..$ lineheight   : num 0.9
  ..$ margin       :Error in x[[3]] : subscript out of bounds
Calls: <Anonymous> ... format.fun -> format -> format.unit -> vapply -> FUN
Execution halted
Running examples in ‘microsamplingDesign-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: construct2CompModel
> ### Title: construct a 2 compartmental 'PkModel-class' by providing
> ###   parameters and dosing info
> ### Aliases: construct2CompModel
> 
> ### ** Examples
> 
>   dosingInfo              <-  data.frame( time = 0 , dose = 1 )
>   dataParametersFile      <-  system.file(  "extData",
+  "examplePkParameters.csv" ,   package = "microsamplingDesign" )
>   exampleParameters       <-  read.csv( dataParametersFile ,
+  stringsAsFactors = FALSE , na.strings = NULL )
>   pkModel                 <-  construct2CompModel( exampleParameters , dosingInfo ) 
>   plotObject( pkModel , times = seq( 0, 5 , 0.1) , nSamplesIntegration = 12 )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘microsamplingDesign.Rmd’ using rmarkdown
Loading required package: Rcpp
Quitting from lines 387-392 (microsamplingDesign.Rmd) 
Error: processing vignette 'microsamplingDesign.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘microsamplingDesign.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Non-standard file/directory found at top level:
  ‘MicroStrategyR-Ex.R’
'library' or 'require' call to ‘gWidgetsRGtk2’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘gWidgetsRGtk2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  migrate.c:179:30: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:186:26: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:199:28: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:286:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:312:29: warning: ‘%d’ directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:559:31: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:595:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:603:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MigClim.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘SDMTools’ ‘raster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MigClim.genClust: no visible global function definition for ‘raster’
MigClim.migrate: no visible global function definition for ‘raster’
MigClim.migrate: no visible global function definition for
  ‘dataframe2asc’
MigClim.migrate: no visible global function definition for
  ‘writeRaster’
MigClim.migrate: no visible global function definition for ‘cellStats’
MigClim.migrate: no visible global function definition for ‘read.table’
MigClim.migrate: no visible global function definition for
  ‘write.table’
MigClim.plot: no visible global function definition for ‘raster’
MigClim.plot: no visible global function definition for ‘rainbow’
MigClim.plot: no visible global function definition for ‘jpeg’
MigClim.plot: no visible global function definition for ‘ymax’
MigClim.plot: no visible global function definition for ‘ymin’
MigClim.plot: no visible global function definition for ‘xmax’
MigClim.plot: no visible global function definition for ‘xmin’
MigClim.plot: no visible global function definition for ‘image’
MigClim.plot: no visible global function definition for ‘dev.off’
MigClim.plot: no visible global function definition for ‘png’
MigClim.plot: no visible global function definition for ‘dev.new’
MigClim.plot: no visible global function definition for ‘plot’
Undefined global functions or variables:
  cellStats dataframe2asc dev.new dev.off image jpeg plot png rainbow
  raster read.table write.table writeRaster xmax xmin ymax ymin
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "jpeg", "png", "rainbow")
  importFrom("graphics", "image", "plot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
File ‘MigClim/libs/MigClim.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’, ‘src_cell.o’, ‘validate.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
.default_model: no visible global function definition for ‘is’
.guess_type: no visible global function definition for ‘is.ts’
.parse_trans: no visible binding for global variable ‘qnorm’
do_get_data_from_disk: no visible global function definition for
  ‘read.csv’
do_get_data_from_mi: no visible global function definition for ‘data’
do_get_data_from_r : <anonymous>: no visible global function definition
  for ‘is’
do_parametric_eval : <anonymous>: no visible global function definition
  for ‘dev.off’
do_parametric_eval : <anonymous>: no visible global function definition
  for ‘title’
do_var_options : varHandler2: no visible global function definition for
  ‘is’
do_var_options : varHandler3: no visible global function definition for
  ‘getClass’
do_var_options : varHandler3: no visible global function definition for
  ‘is’
do_var_options : changeHandler: no visible global function definition
  for ‘is’
do_var_options : <anonymous>: no visible global function definition for
  ‘title’
do_var_options: no visible global function definition for ‘getClass’
do_var_options: no visible global function definition for ‘is’
helpHandler: no visible global function definition for ‘browseURL’
is.method_in_mi: no visible global function definition for
  ‘selectMethod’
is.method_in_mi: no visible global function definition for ‘signature’
Undefined global functions or variables:
  browseURL data dev.off getClass is is.ts qnorm read.csv selectMethod
  signature title
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "title")
  importFrom("methods", "getClass", "is", "selectMethod", "signature")
  importFrom("stats", "is.ts", "qnorm")
  importFrom("utils", "browseURL", "data", "read.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
nat_hist: no visible global function definition for ‘data’
nat_hist: no visible binding for global variable ‘current.other’
t_mal: no visible global function definition for ‘uniroot’
t_prog: no visible global function definition for ‘rlnorm’
tdeath_lung: no visible global function definition for ‘data’
tdeath_lung: no visible binding for global variable ‘ci.lung’
tdeath_lung: no visible binding for global variable ‘current.other’
tdeath_lung: no visible binding for global variable ‘former.other’
tdeath_lung: no visible binding for global variable ‘never.other’
tdeath_other: no visible global function definition for ‘data’
tdeath_other: no visible binding for global variable ‘ci.lung’
tdeath_other: no visible binding for global variable ‘current.other’
tdeath_other: no visible binding for global variable ‘former.other’
tdeath_other: no visible binding for global variable ‘never.other’
Undefined global functions or variables:
  ci.lung current.other data former.other never.other rlnorm uniroot
Consider adding
  importFrom("stats", "rlnorm", "uniroot")
  importFrom("utils", "data")
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")
Quitting from lines 634-643 (milr-intro.Rmd) 
Error: processing vignette 'milr-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘milr-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
MImix.default: no visible binding for global variable ‘coef’
MImix.default: no visible binding for global variable ‘vcov’
MImix.one: no visible global function definition for ‘qnorm’
MImix.one: no visible global function definition for ‘uniroot’
mixcdf.target: no visible global function definition for ‘pnorm’
print.MImixresult: no visible global function definition for ‘coef’
print.MImixresult: no visible global function definition for ‘vcov’
summary.MImixresult: no visible global function definition for ‘coef’
summary.MImixresult: no visible global function definition for ‘vcov’
summary.MImixresult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  coef pnorm qnorm qt uniroot vcov
Consider adding
  importFrom("stats", "coef", "pnorm", "qnorm", "qt", "uniroot", "vcov")
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.
rminimax: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
read_design: no visible global function definition for ‘model.frame’
read_design: no visible global function definition for ‘read.table’
read_design: no visible global function definition for ‘model.matrix’
read_response: no visible global function definition for ‘read.table’
update_beta: no visible global function definition for ‘update’
update_beta: no visible global function definition for ‘glm’
update_beta: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  glm model.frame model.matrix poisson read.table update
Consider adding
  importFrom("stats", "glm", "model.frame", "model.matrix", "poisson",
             "update")
  importFrom("utils", "read.table")
to your NAMESPACE file.
minxent.multiple: no visible global function definition for ‘cov.wt’
minxent.single: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  cov.wt optimize
Consider adding
  importFrom("stats", "cov.wt", "optimize")
to your NAMESPACE file.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.

Found the following calls to attach():
File ‘MIPHENO/R/cdf.pval.R’:
  attach(sample.cdf)
See section ‘Good practice’ in ‘?attach’.
.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.
Running examples in ‘MiRAnorm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: miranorm
> ### Title: Adaptive algorithm to identify normalization genes.
> ### Aliases: miranorm
> 
> ### ** Examples
> 
> dat = simData(n.trt=15, n.ctrl=15, n.gene=30, n.err=10, sigma.error = c(1, 0.3), mean.sample = 2,
+ sigma.sample = 1.88 , sigma.gene = 0.1, n.big.effect = 5, n.small.effect = 10, mean.big.effect = 2,
+ mean.small.effect = 1.2)$sim
> 
> obj = miranorm(data = dat, group = dat$Group, method="simple")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: miranorm ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
fisher.combination: no visible global function definition for ‘pchisq’
gs.test: no visible global function definition for ‘ks.test’
gs.test: no visible global function definition for ‘wilcox.test’
gs.test: no visible global function definition for ‘fisher.test’
inverse.normal.combination: no visible global function definition for
  ‘qnorm’
inverse.normal.combination: no visible global function definition for
  ‘pnorm’
limma.one.sided: no visible global function definition for ‘pt’
Undefined global functions or variables:
  fisher.test ks.test pchisq pnorm pt qnorm wilcox.test
Consider adding
  importFrom("stats", "fisher.test", "ks.test", "pchisq", "pnorm", "pt",
             "qnorm", "wilcox.test")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘rgl’ ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘canonicalizeAndMergeScene’ ‘colorScene’ ‘t2ve’ ‘vertexNormals’
  ‘vertexTriangles’
Error(s) in re-building vignettes:
  ...
--- re-building ‘miscset.Rmd’ using rmarkdown
Quitting from lines 117-122 (miscset.Rmd) 
Error: processing vignette 'miscset.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘miscset.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: isoplot
> ### Title: plot isotopologues
> ### Aliases: isoplot
> 
> ### ** Examples
> 
> data(lcms)
> explist <- prefilter(lcms, subgroup = c("B", "C", "D"), unlabel = "B")

(1) Checking input parameters...done
(2) Calculating fold change...done
(3) Performing statistical test...done
(4) Performing the first filtering...done> exp.B <- explist$B
> exp.C <- explist$C
> exp.D <- explist$D
> iso.C <- diso(iso1 = 'H2', n11 = 4, n12 = 2, exp.base = exp.B, exp.iso = exp.C)

(1) Checking input parameters...done
(2) Preparing datacube...done
(3) Performing the 2ed filtering...done> iso.D <- diso(iso1 = 'C13', n11 = 9, n12 = 6, iso2 = 'N15', n21 = 1, n22 = 0,
+ exp.base = iso.C[,1:3], exp.iso = exp.D)

(1) Checking input parameters...done
(2) Preparing datacube...done
(3) Performing the 2ed filtering...done> full_result <- Fresult(iso.C, iso.D)
> isoplot(full_result, 1)
Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto),  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: isoplot ... unitConvert -> <Anonymous> -> convertUnit -> grid.Call
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘misscompare.Rmd’ using rmarkdown
Quitting from lines 154-155 (misscompare.Rmd) 
Error: processing vignette 'misscompare.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘misscompare.Rmd’

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

Error: Vignette re-building failed.
Execution halted
missForest: no visible global function definition for ‘predict’
missForest: no visible global function definition for ‘idiv’
missForest: no visible global function definition for ‘var’
nrmse: no visible global function definition for ‘var’
Undefined global functions or variables:
  idiv predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
AndersonDarling: no visible global function definition for ‘spline’
Hawkins: no visible global function definition for ‘cov’
Hawkins: no visible global function definition for ‘pf’
Impute: no visible global function definition for ‘cov’
Mimpute: no visible global function definition for ‘rnorm’
SimNey: no visible global function definition for ‘runif’
TestMCARNormality: no visible global function definition for ‘cov’
TestMCARNormality: no visible global function definition for ‘pchisq’
TestUNey: no visible global function definition for ‘pchisq’
boxplot.testhomosc: no visible global function definition for ‘par’
boxplot.testhomosc: no visible global function definition for ‘title’
boxplot.testhomosc: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline cov par pchisq pf rnorm runif spline title
Consider adding
  importFrom("graphics", "abline", "par", "title")
  importFrom("stats", "cov", "pchisq", "pf", "rnorm", "runif", "spline")
to your NAMESPACE file.
'library' or 'require' call to ‘CompQuadForm’ which was already attached by Depends.
  Please remove these calls from your code.
linear.test: no visible global function definition for ‘lm’
linear.test: no visible global function definition for ‘pchisq’
linear.weight.test: no visible global function definition for ‘lm’
linear.weight.test: no visible global function definition for ‘dbeta’
linear.weight.test: no visible global function definition for ‘pchisq’
logit.test: no visible global function definition for ‘glm’
logit.test: no visible global function definition for ‘binomial’
logit.test: no visible binding for global variable ‘logit’
logit.test: no visible global function definition for ‘pchisq’
logit.weight.test: no visible global function definition for ‘glm’
logit.weight.test: no visible global function definition for ‘binomial’
logit.weight.test: no visible binding for global variable ‘logit’
logit.weight.test: no visible global function definition for ‘dbeta’
logit.weight.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  binomial dbeta glm lm logit pchisq
Consider adding
  importFrom("stats", "binomial", "dbeta", "glm", "lm", "pchisq")
to your NAMESPACE file.
Running examples in ‘mistr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QQplotgg
> ### Title: Implementation of Quantile-Quantile Plot with ggplot2
> ### Aliases: QQplotgg QQplotgg.default QQplotgg.dist QQnormgg
> 
> ### ** Examples
> 
> # sample vs sample
> QQplotgg(r(normdist(), 10000), r(tdist(df = 4), 10000))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mistr-extensions.Rmd’ using rmarkdown

Attaching package: 'mistr'

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

    q

Quitting from lines 180-184 (mistr-extensions.Rmd) 
Error: processing vignette 'mistr-extensions.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mistr-extensions.Rmd’

--- re-building ‘mistr-introduction.Rmd’ using rmarkdown

Attaching package: 'mistr'

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

    q

Quitting from lines 212-214 (mistr-introduction.Rmd) 
Error: processing vignette 'mistr-introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mistr-introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘mistr-extensions.Rmd’ ‘mistr-introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
MIcombine.default: no visible binding for global variable ‘vcov’
MIcombine.default: no visible binding for global variable ‘coef’
MIcombine.default: no visible global function definition for ‘var’
MIcombine.imputationResultList: no visible binding for global variable
  ‘vcov’
MIcombine.imputationResultList: no visible binding for global variable
  ‘coef’
close.DBimputationList: no visible global function definition for ‘is’
getvars: no visible global function definition for ‘is’
print.MIresult: no visible global function definition for ‘coef’
print.MIresult: no visible global function definition for ‘vcov’
summary.MIresult: no visible global function definition for ‘coef’
summary.MIresult: no visible global function definition for ‘vcov’
summary.MIresult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  coef is qt var vcov
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "coef", "qt", "var", "vcov")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘miWQS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.wqs
> ### Title: Histograms of the Weights, Beta1, and WQS using 'ggplot2'
> ### Aliases: plot.wqs
> ### Keywords: wqs
> 
> ### ** Examples
> 
> #Use simulated dataset and set seed for reproducibility.
> data(simdata87)
> set.seed(23456)
> Wa <- estimate.wqs( y = simdata87$y.scenario, X = simdata87$X.true[ , 1:9],
+                   B = 10, family = "binomial")
## No missing values in matrix detected. Regular Quantiles computed.
## No missing values in matrix detected. Regular Quantiles computed.
> plot(Wa, filename = file.path(tempdir(), "WQS_Plot"))
Saving 7 x 7 in image
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘mixR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mixfitEM
> ### Title: Plotting the Fitted Mixture Models
> ### Aliases: plot.mixfitEM
> 
> ### ** Examples
> 
> x <- rmixnormal(200, c(0.3, 0.7), c(2, 5), c(1, 0.7))
> fit <- mixfit(x, ncomp = 2)
> plot(fit)  # base R plotting system
> plot(fit, "ggplot2")  # ggplot2 plotting system
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Packages in Depends field not imported from:
  ‘MASS’ ‘RODBC’ ‘tcltk’ ‘tcltk2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.mixtNB: no visible global function definition for ‘dnbinom’
fit.mixtNB: no visible global function definition for ‘nlminb’
wald.test: no visible global function definition for ‘pnorm’
wald.test: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  dnbinom nlminb p.adjust pnorm
Consider adding
  importFrom("stats", "dnbinom", "nlminb", "p.adjust", "pnorm")
to your NAMESPACE file.
Running ‘testthat.R’ [13s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mizer)
  > 
  > test_check("mizer")
  ── 1. Error: plot (@test-plots.R#9)  ───────────────────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: plot(sim) at testthat/test-plots.R:9
  2: plot(sim)
  3: print(p1 + theme(legend.position = "none"), vp = vplayout(1, 1))
  4: print.ggplot(p1 + theme(legend.position = "none"), vp = vplayout(1, 1))
  5: grid.draw(gtable)
  6: grid.draw.gTree(gtable)
  7: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  8: drawGTree(x)
  9: preDraw(x)
  10: preDraw.gTree(x)
  11: pushvpgp(x)
  12: pushgrobvp(x$vp)
  13: pushgrobvp.viewport(x$vp)
  14: pushViewport(vp, recording = FALSE)
  15: lapply(vps, push.vp, recording)
  16: FUN(X[[i]], ...)
  17: push.vp.viewport(X[[i]], ...)
  18: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 508 SKIPPED: 2 FAILED: 1
  1. Error: plot (@test-plots.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mizer_vignette.Rnw’ using knitr
Quitting from lines 572-573 (mizer_vignette.Rnw) 
Error: processing vignette 'mizer_vignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mizer_vignette.Rnw’

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

Error: Vignette re-building failed.
Execution halted
computeContourValues: no visible global function definition for
  ‘na.omit’
deselectNonMovementSteps : coOccurProb: no visible global function
  definition for ‘dnorm’
deselectNonMovementSteps: no visible global function definition for
  ‘pnorm’
estVarMKDE: no visible global function definition for ‘na.omit’
estVarMKDE: no visible global function definition for ‘qnorm’
estVarMKDE: no visible global function definition for ‘optimize’
plotMKDE: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  dnorm na.omit optimize pnorm qnorm rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "dnorm", "na.omit", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
mkle: no visible global function definition for ‘sd’
mkle: no visible global function definition for ‘density’
mkle: no visible global function definition for ‘optimize’
mkle.ci: no visible global function definition for ‘sd’
mkle.ci: no visible binding for global variable ‘var’
mkle.ci: no visible global function definition for ‘quantile’
mkle.ci: no visible global function definition for ‘qnorm’
opt.bw: no visible global function definition for ‘sd’
opt.bw : mse: no visible global function definition for ‘var’
opt.bw: no visible global function definition for ‘optimize’
opt.bw: no visible global function definition for ‘var’
Undefined global functions or variables:
  density optimize qnorm quantile sd var
Consider adding
  importFrom("stats", "density", "optimize", "qnorm", "quantile", "sd",
             "var")
to your NAMESPACE file.
Running examples in ‘MKmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: melt.long
> ### Title: Transform data.frame to Long Form
> ### Aliases: melt.long
> ### Keywords: univar
> 
> ### ** Examples
> 
> library(ggplot2)
> ## some random data
> test <- data.frame(x = rnorm(10), y = rnorm(10), z = rnorm(10))
> test.long <- melt.long(test)
> test.long
          value variable
x1  -0.62645381        x
x2   0.18364332        x
x3  -0.83562861        x
x4   1.59528080        x
x5   0.32950777        x
x6  -0.82046838        x
x7   0.48742905        x
x8   0.73832471        x
x9   0.57578135        x
x10 -0.30538839        x
y1   1.51178117        y
y2   0.38984324        y
y3  -0.62124058        y
y4  -2.21469989        y
y5   1.12493092        y
y6  -0.04493361        y
y7  -0.01619026        y
y8   0.94383621        y
y9   0.82122120        y
y10  0.59390132        y
z1   0.91897737        z
z2   0.78213630        z
z3   0.07456498        z
z4  -1.98935170        z
z5   0.61982575        z
z6  -0.05612874        z
z7  -0.15579551        z
z8  -1.47075238        z
z9  -0.47815006        z
z10  0.41794156        z
> ggplot(test.long, aes(x = variable, y = value)) +
+   geom_boxplot(aes(fill = variable))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MKmisc.Rmd’ using rmarkdown
Quitting from lines 123-125 (MKmisc.Rmd) 
Error: processing vignette 'MKmisc.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MKmisc.Rmd’

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

Error: Vignette re-building failed.
Execution halted
mkssd: no visible global function definition for ‘txtProgressBar’
mkssd: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘Data-Administration.R’
Error(s) in re-building vignettes:
  ...
--- re-building ‘data_automation.Rmd’ using rmarkdown
--- finished re-building ‘data_automation.Rmd’

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

--- re-building ‘pitch_plotting.Rmd’ using rmarkdown
Quitting from lines 39-46 (pitch_plotting.Rmd) 
Error: processing vignette 'pitch_plotting.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pitch_plotting.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘GeneSelector’
'library' or 'require' calls in package code:
  ‘cairoDevice’ ‘gplots’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘MASS:::lda.default’ ‘MASS:::qda.default’
  ‘e1071:::naiveBayes.default’ ‘e1071:::svm.default’
  ‘randomForest:::randomForest.default’
  See the note in ?`:::` about the use of this operator.
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.
Non-standard file/directory found at top level:
  ‘CONTENTS’
dftest: no visible global function definition for ‘slot’
mctest: no visible global function definition for ‘rnorm’
mleurDiag: no visible global function definition for ‘acf’
mleurDiag: no visible global function definition for ‘pchisq’
mleurDiag: no visible global function definition for ‘par’
mleurDiag: no visible global function definition for ‘boxplot’
mleurDiag: no visible global function definition for ‘shapiroTest’
mleurDiag: no visible global function definition for ‘title’
mleurDiag: no visible global function definition for ‘abline’
mleurDiag: no visible global function definition for ‘lines’
simar1: no visible global function definition for ‘rnorm’
simar1: no visible global function definition for ‘rt’
simar1: no visible global function definition for ‘convolve’
Undefined global functions or variables:
  abline acf boxplot convolve lines par pchisq rnorm rt shapiroTest
  slot title
Consider adding
  importFrom("graphics", "abline", "boxplot", "lines", "par", "title")
  importFrom("methods", "slot")
  importFrom("stats", "acf", "convolve", "pchisq", "rnorm", "rt")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘CHANGELOG.txt’
Packages in Depends field not imported from:
  ‘methods’ ‘seqinr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
CheckStability: no visible global function definition for ‘cor’
CheckStability: no visible global function definition for ‘var’
PriorNormPCA: no visible global function definition for ‘barplot’
SortModes: no visible global function definition for ‘rnorm’
mlicaMAIN: no visible global function definition for ‘runif’
Undefined global functions or variables:
  barplot cor rnorm runif var
Consider adding
  importFrom("graphics", "barplot")
  importFrom("stats", "cor", "rnorm", "runif", "var")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘BMA’ ‘abind’ ‘maxLik’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy

Found the following assignments to the global environment:
File ‘mlPhaser/R/mlPhaser.R’:
  assign("validHaploGroups", c(get("validHaploGroups", globalenv()), 
    groupStoreList), globalenv())
  assign("validHaploGroups", list(), globalenv())
Error(s) in re-building vignettes:
  ...
--- re-building ‘mlrMBO.Rmd’ using rmarkdown
Quitting from lines 63-67 (mlrMBO.Rmd) 
Error: processing vignette 'mlrMBO.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mlrMBO.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MLZ.Rmd’ using rmarkdown
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 54-55 (MLZ.Rmd) 
Error: processing vignette 'MLZ.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MLZ.Rmd’

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

Error: Vignette re-building failed.
Execution halted
mmm2: no visible global function definition for ‘model.frame’
mmm2: no visible global function definition for ‘model.matrix’
mmm2: no visible global function definition for ‘model.response’
mmm2: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula model.frame model.matrix model.response
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
mmm: no visible global function definition for ‘model.frame’
mmm: no visible global function definition for ‘model.matrix’
mmm: no visible global function definition for ‘model.response’
mmm: no visible global function definition for ‘as.formula’
mmm: no visible global function definition for ‘gee’
Undefined global functions or variables:
  as.formula gee model.frame model.matrix model.response
Consider adding
  importFrom("stats", "as.formula", "model.frame", "model.matrix",
             "model.response")
to your NAMESPACE file.
get.score: no visible global function definition for ‘sd’
get.score: no visible global function definition for ‘coef’
get.score: no visible global function definition for ‘as’
get.score.main: no visible global function definition for ‘sd’
get.score.main: no visible global function definition for ‘coef’
get.subgroup: no visible global function definition for ‘sd’
sample.tte: no visible global function definition for ‘runif’
Undefined global functions or variables:
  as coef runif sd
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "coef", "runif", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
sadmvng: no visible global function definition for ‘cov2cor’
sadmvng: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cov2cor pnorm
Consider adding
  importFrom("stats", "cov2cor", "pnorm")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘modcmfitrOverview.Rmd’ using rmarkdown
Quitting from lines 304-389 (modcmfitrOverview.Rmd) 
Error: processing vignette 'modcmfitrOverview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘modcmfitrOverview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘model4you-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binomial_glm_plot
> ### Title: Plot for a given logistic regression model (glm with binomial
> ###   family) with one binary covariate.
> ### Aliases: binomial_glm_plot
> 
> ### ** Examples
> 
> set.seed(2017)
> 
> # number of observations
> n <- 1000
> 
> # balanced binary treatment
> # trt <- factor(rep(c("C", "A"), each = n/2),
> #               levels = c("C", "A"))
> 
> # unbalanced binary treatment
> trt <- factor(c(rep("C", n/4), rep("A", 3*n/4)),
+               levels = c("C", "A"))
> 
> # some continuous variables
> x1 <- rnorm(n)
> x2 <- rnorm(n)
> 
> # linear predictor
> lp <- -0.5 + 0.5*I(trt == "A") + 1*I(trt == "A")*I(x1 > 0)
> 
> # compute probability with inverse logit function
> invlogit <- function(x) 1/(1 + exp(-x))
> pr <- invlogit(lp)
> 
> # bernoulli response variable
> y <- rbinom(n, 1, pr)
> dat <- data.frame(y, trt, x1, x2)
> 
> # logistic regression model
> mod <- glm(y ~ trt, data = dat, family = "binomial")
> binomial_glm_plot(mod, plot_data = TRUE)
Warning: Ignoring unknown aesthetics: width
Warning: Using alpha for a discrete variable is not advised.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘modeldb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_kmeans
> ### Title: Visualize a KMeans Cluster with lots of data
> ### Aliases: plot_kmeans db_calculate_squares
> 
> ### ** Examples
> 
> plot_kmeans(mtcars, mpg, wt, group = am)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' call to ‘SparseM’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘glmnet’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘ModelGood-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Ctree
> ### Title: S3 wrapper function for party's ctree method
> ### Aliases: Ctree
> 
> ### ** Examples
> 
> library(party)
Loading required package: grid
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
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
> set.seed(7)
> x <- abs(rnorm(20))
> d <- data.frame(y=rbinom(20,1,x/max(x)),x=x,z=rnorm(20))
> ct <- Ctree(y~x+z,d)
> plot(ct$ctree)
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Running examples in ‘moderndive-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bowl
> ### Title: A sampling bowl of red and white balls
> ### Aliases: bowl
> ### Keywords: datasets
> 
> ### ** 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(ggplot2)
> 
> # Take 10 different samples of size n = 50 balls from bowl
> bowl_samples_simulated <- bowl %>%
+   rep_sample_n(50, reps = 10)
>   
> # Compute 10 different p_hats (prop red) based on 10 different samples of
> # size n = 50
> p_hats <- bowl_samples_simulated %>%
+   group_by(replicate, color) %>%
+   summarize(count = n()) %>%
+   mutate(proportion = count/50) %>%
+   filter(color == "red")
> 
> # Plot sampling distribution
> ggplot(p_hats, aes(x = proportion)) +
+   geom_histogram(binwidth = 0.05) +
+   labs(x = expression(hat(p)), y = "Number of samples", 
+   title = "Sampling distribution of p_hat based 10 samples of size n = 50")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘date’ ‘raster’ ‘rgdal’ ‘sfsmisc’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.clustOrder: no visible global function definition for ‘hclust’
.clustOrder: no visible global function definition for ‘as.dist’
consensusMEDissimilarity: no visible global function definition for
  ‘cor’
mergeCloseModules: no visible global function definition for ‘cor’
mergeCloseModules: no visible global function definition for ‘hclust’
mergeCloseModules: no visible global function definition for ‘as.dist’
moduleEigengenes: no visible global function definition for ‘cor’
moduleEigengenes: no visible global function definition for ‘cov’
moduleNumber: no visible global function definition for ‘cutree’
orderMEs: no visible global function definition for ‘cor’
orderMEs: no visible global function definition for ‘as.dist’
plotHclustColors: no visible global function definition for ‘barplot’
plotHclustColors: no visible global function definition for ‘strwidth’
plotHclustColors: no visible global function definition for ‘rect’
plotHclustColors: no visible global function definition for ‘text’
plotHclustColors: no visible global function definition for ‘lines’
Undefined global functions or variables:
  as.dist barplot cor cov cutree hclust lines rect strwidth text
Consider adding
  importFrom("graphics", "barplot", "lines", "rect", "strwidth", "text")
  importFrom("stats", "as.dist", "cor", "cov", "cutree", "hclust")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_Usage.Rmd’ using rmarkdown
--- finished re-building ‘Basic_Usage.Rmd’

--- re-building ‘Comparison_Usage.Rmd’ using rmarkdown
Quitting from lines 243-278 (Comparison_Usage.Rmd) 
Error: processing vignette 'Comparison_Usage.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Comparison_Usage.Rmd’

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

--- re-building ‘problem-definition.Rmd’ using rmarkdown
--- finished re-building ‘problem-definition.Rmd’

--- re-building ‘writing-functions-for-moeadr.Rmd’ using rmarkdown
--- finished re-building ‘writing-functions-for-moeadr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
agostino.test: no visible global function definition for
  ‘complete.cases’
agostino.test: no visible global function definition for ‘pnorm’
anscombe.test: no visible global function definition for
  ‘complete.cases’
anscombe.test: no visible global function definition for ‘pnorm’
bonett.test: no visible global function definition for ‘complete.cases’
bonett.test: no visible global function definition for ‘pnorm’
jarque.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  complete.cases pchisq pnorm
Consider adding
  importFrom("stats", "complete.cases", "pchisq", "pnorm")
to your NAMESPACE file.
Running examples in ‘momentuHMM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotSpatialCov
> ### Title: Plot observations on raster image
> ### Aliases: plotSpatialCov
> 
> ### ** Examples
> 
> stepDist <- "gamma"
> angleDist <- "vm"
> 
> # plot simulated data over forest raster automatically loaded with the packge
> spatialCov<-list(forest=forest)
> data <- simData(nbAnimals=2,nbStates=2,dist=list(step=stepDist,angle=angleDist),
+                 Par=list(step=c(100,1000,50,100),angle=c(0,0,0.1,5)),
+                 beta=matrix(c(5,-10,-25,50),nrow=2,ncol=2,byrow=TRUE),
+                 formula=~forest,spatialCovs=spatialCov,
+                 obsPerAnimal=225,states=TRUE)
=======================================================================
Simulating HMM with 2 states and 2 data streams
-----------------------------------------------------------------------

 step ~ gamma(mean=~1, sd=~1)
 angle ~ vm(mean=~1, concentration=~1)

 Transition probability matrix formula: ~forest

 Initial distribution formula: ~1
=======================================================================
DONE
> 
> plotSpatialCov(data,forest,states=data$states)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotSpatialCov ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘Momocs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PCcontrib
> ### Title: Shape variation along PC axes
> ### Aliases: PCcontrib PCcontrib.PCA
> 
> ### ** Examples
> 
> bot.p <- PCA(efourier(bot, 12))
you selected `norm=TRUE`, which is not recommended. See ?efourier
> PCcontrib(bot.p)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: PCcontrib ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Warning: no function found corresponding to methods exports from ‘mondate’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
.date.to.mondate: no visible global function definition for ‘new’
as.character.mondate: no visible global function definition for ‘slot’
Arith,array-mondate: no visible global function definition for
  ‘callGeneric’
Arith,mondate-array: no visible global function definition for
  ‘callGeneric’
Arith,mondate-mondate: no visible global function definition for
  ‘callGeneric’
Arith,mondate-numeric: no visible global function definition for
  ‘callGeneric’
Arith,numeric-mondate: no visible global function definition for
  ‘callGeneric’
Compare,mondate-ANY: no visible global function definition for
  ‘callGeneric’
Compare,mondate-ANY: no visible global function definition for
  ‘getDataPart’
Summary,mondate: no visible global function definition for
  ‘callGeneric’
[,mondate: no visible global function definition for ‘callNextMethod’
[,mondate: no visible global function definition for ‘new’
array,mondate: no visible global function definition for
  ‘callNextMethod’
as.numeric,mondate: no visible global function definition for ‘slot’
c,mondate: no visible global function definition for ‘new’
c,mondate: no visible binding for global variable ‘getDataPart’
c,mondate: no visible global function definition for ‘getDataPart’
matrix,mondate: no visible global function definition for
  ‘callNextMethod’
mondate,Date: no visible global function definition for ‘new’
mondate,POSIXt: no visible global function definition for ‘new’
mondate,missing: no visible global function definition for ‘new’
mondate,mondate: no visible global function definition for ‘new’
mondate,numeric: no visible global function definition for ‘new’
Undefined global functions or variables:
  callGeneric callNextMethod getDataPart new slot
Consider adding
  importFrom("methods", "callGeneric", "callNextMethod", "getDataPart",
             "new", "slot")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  monetdblite/src/gdk/gdk_heap.c:189:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  monetdblite/src/gdk/gdk_heap.c:260:30: warning: ‘%s’ directive writing likely 3 or more bytes into a region of size between 0 and 99 [-Wformat-overflow=]
  monetdblite/src/mal/sqlbackend/rel_bin.c:2949:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/rel_bin.c:1083:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3193:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3196:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3186:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_planner.c:82:4: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_semantic.c:54:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_updates.c:1729:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MonetDBLite.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [43s/110s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > # Sys.setenv("MONETDBLITE_INMEMORY" = "yes")
  > # test_check("MonetDBLite")
  > Sys.setenv("MONETDBLITE_INMEMORY" = "no")
  > test_check("MonetDBLite")
  Loading required package: MonetDBLite
  ── 1. Failure: db allows svyby commands (@test_05_survey.R#60)  ────────────────
  round(...) not equal to 0.022.
  1/1 mismatches
  [1] 0.019 - 0.022 == -0.003
  
  ── 2. Failure: db allows svyby commands (@test_05_survey.R#62)  ────────────────
  ...[] not equal to 10.11.
  1/1 mismatches
  [1] 10.3 - 10.1 == 0.23
  
  [1] "E"
  [1] "H"
  [1] "M"
  ── 3. Failure: db allows svyby commands (@test_05_survey.R#66)  ────────────────
  round(SE(a)[2], 2) not equal to 4708.41.
  1/1 mismatches
  [1] 5476 - 4708 == 768
  
  ── 4. Failure: db allows svyby commands (@test_05_survey.R#67)  ────────────────
  as.numeric(round(cv(a)[2], 4)) not equal to 0.2975.
  1/1 mismatches
  [1] 0.346 - 0.297 == 0.0486
  
  ── 5. Failure: db allows svyby commands (@test_05_survey.R#69)  ────────────────
  round(confint(a, df = degf(rclus1))[2, 2], 2) not equal to 30808.26.
  1/1 mismatches
  [1] 33252 - 30808 == 2443
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 315 SKIPPED: 13 FAILED: 5
  1. Failure: db allows svyby commands (@test_05_survey.R#60) 
  2. Failure: db allows svyby commands (@test_05_survey.R#62) 
  3. Failure: db allows svyby commands (@test_05_survey.R#66) 
  4. Failure: db allows svyby commands (@test_05_survey.R#67) 
  5. Failure: db allows svyby commands (@test_05_survey.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Missing or unexported objects:
  ‘dplyr::base_agg’ ‘dplyr::base_scalar’ ‘dplyr::build_sql’
  ‘dplyr::is.ident’ ‘dplyr::sql_infix’ ‘dplyr::sql_prefix’
  ‘dplyr::sql_translator’ ‘dplyr::sql_variant’ ‘dplyr::src_sql’
  ‘dplyr::tbl_sql’
Error(s) in re-building vignettes:
  ...
--- re-building ‘MonteCarlo-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

Quitting from lines 316-320 (MonteCarlo-Vignette.Rmd) 
Error: processing vignette 'MonteCarlo-Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MonteCarlo-Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
mopsocd : initialize_pop: no visible global function definition for
  ‘runif’
mopsocd : compute_velocity: no visible global function definition for
  ‘runif’
mopsocd : mutate: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
checkTH: no visible global function definition for ‘pchisq’
getOrderPval: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
ametrine : <anonymous>: no visible global function definition for
  ‘approx’
ametrine: no visible global function definition for ‘rgb’
isolum : <anonymous>: no visible global function definition for
  ‘approx’
isolum: no visible global function definition for ‘rgb’
morgenstemning : <anonymous>: no visible global function definition for
  ‘approx’
morgenstemning: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  approx rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "approx")
to your NAMESPACE file.
cor.gen: no visible global function definition for ‘rnorm’
cor.gen: no visible global function definition for ‘resid’
cor.gen: no visible global function definition for ‘lm’
cor.gen: no visible binding for global variable ‘sd’
cor.gen: no visible global function definition for ‘cor’
cor.gen: no visible global function definition for ‘write.table’
stat.gen: no visible global function definition for ‘rexp’
stat.gen: no visible global function definition for ‘rnorm’
stat.gen: no visible binding for global variable ‘sd’
stat.gen: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  cor lm resid rexp rnorm sd write.table
Consider adding
  importFrom("stats", "cor", "lm", "resid", "rexp", "rnorm", "sd")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running examples in ‘morse-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.reproData
> ### Title: Plotting method for 'reproData' objects
> ### Aliases: plot.reproData
> ### Keywords: plot
> 
> ### ** Examples
> 
> # (1) Load the data
> data(cadmium1)
> 
> # (2) Create an object of class 'reproData'
> cadmium1 <- reproData(cadmium1)
> 
> # (3) Plot the reproduction data
> plot(cadmium1)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mortAAR_vignette-1.Rmd’ using rmarkdown
Loading required package: bitops
Quitting from lines 131-132 (mortAAR_vignette-1.Rmd) 
Error: processing vignette 'mortAAR_vignette-1.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mortAAR_vignette-1.Rmd’

--- re-building ‘mortAAR_vignette_extended.Rmd’ using rmarkdown
Loading required package: bitops
Quitting from lines 146-148 (mortAAR_vignette_extended.Rmd) 
Error: processing vignette 'mortAAR_vignette_extended.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mortAAR_vignette_extended.Rmd’

SUMMARY: processing the following files failed:
  ‘mortAAR_vignette-1.Rmd’ ‘mortAAR_vignette_extended.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getCohortTable
> ### Title: Return the cohort life table as a 'mortalityTable.period' object
> ### Aliases: getCohortTable getCohortTable,mortalityTable-method
> 
> ### ** Examples
> 
> mortalityTables.load("Austria_Annuities")
Loading table dataset 'Austria_Annuities'
Loading table dataset 'Austria_Annuities_AVOe1996R'
Loading table dataset 'Austria_Annuities_AVOe2005R'
Loading table dataset 'Austria_Annuities_EROMF'
Loading table dataset 'Austria_Annuities_RR67'
> tb75 = getCohortTable(AVOe2005R.male, YOB = 1975)
> # The tb75 is a fixed table with no trend any more
> plot(AVOe2005R.male, tb75, Period = 2017)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-the-mortalityTables-package.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: scales
Quitting from lines 122-131 (using-the-mortalityTables-package.Rmd) 
Error: processing vignette 'using-the-mortalityTables-package.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-the-mortalityTables-package.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Houses_for_sale
> ### Title: Houses for sale
> ### Aliases: Houses_for_sale
> ### Keywords: datasets
> 
> ### ** Examples
> 
> mod_1 <- lm(price ~ fireplaces, data = Houses_for_sale)
> mod_2 <- lm(price ~ fireplaces + living_area, data = Houses_for_sale)
> mod_effect(mod_1, ~ fireplaces)
     slope fireplaces to_fireplaces
1 66698.82          1           1.4
> mod_effect(mod_2, ~ fireplaces)
    slope fireplaces to_fireplaces living_area
1 8962.44          1           1.4        1600
> mod_plot(mod_2, ~ living_area + fireplaces)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basics.Rmd’ using rmarkdown
Quitting from lines 66-68 (Basics.Rmd) 
Error: processing vignette 'Basics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Basics.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CIsim
> ### Title: Compute confidence intervals from (multiple) simulated data sets
> ### Aliases: CIsim
> ### Keywords: inference simulation
> 
> ### ** Examples
> 
> # 1000 95% intervals using t.test; population is N(0,1)
> CIsim(n=10, samples=1000)    
Interval coverage:
    cover
n      Low   Yes  High
  10 0.019 0.957 0.024
> # this time population is Exp(1); fewer samples, so we get a plot 
> CIsim(n=10, samples=100, rdist=rexp, estimand=1) 
Interval coverage:
    cover
n     Low  Yes High
  10 0.04 0.96 0.00
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: CIsim ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘motoRneuron.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: dygraphs
Quitting from lines 121-122 (motoRneuron.Rmd) 
Error: processing vignette 'motoRneuron.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘motoRneuron.Rmd’

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

Error: Vignette re-building failed.
Execution halted
getmouseDV: no visible global function definition for ‘tail’
interpltraj: no visible global function definition for ‘approx’
trim1: no visible global function definition for ‘tail’
Undefined global functions or variables:
  approx tail
Consider adding
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in ‘mousetrap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bezier
> ### Title: Create Bezier-curves using the Bernstein approximation.
> ### Aliases: bezier
> 
> ### ** Examples
> 
> # Generate range of Bezier-curves
> bezier_curves <- bezier(w=seq(0,10,.1))
> 
> # Plot curves
> mt_plot(bezier_curves)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘browseMovebank.Rnw’ using Sweave
--- finished re-building ‘browseMovebank.Rnw’

--- re-building ‘move.Rnw’ using Sweave
Loading required package: geosphere
Loading required package: sp
Loading required package: raster
Loading required package: rgdal
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
 Path to GDAL shared files: /usr/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: 1.3-1 
Warning in .local(x, y, time, data, proj, ...) :
  There were NA locations detected and omitted. Currently they are not stored in unusedrecords
Loading required package: ggmap
Loading required package: ggplot2
Google's Terms of Service: https://cloud.google.com/maps-platform/terms/.
Please cite ggmap if you use it! See citation("ggmap") for details.
Loading required package: mapproj
Loading required package: maps
Error: processing vignette 'move.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘move.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘corpus.useR.2008.abstracts’
Error(s) in re-building vignettes:
  ...
--- re-building ‘movMF.Rnw’ using Sweave
trying URL ‘https://datacube.wu.ac.at/src/contrib/corpus.useR.2008.abstracts_2009.08.10.tar.gz’
Content type 'application/x-gzip' length 98736 bytes (96 KB)
==================================================
downloaded 96 KB

* installing *source* package ‘corpus.useR.2008.abstracts’ ...
** using staged installation
** data
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (corpus.useR.2008.abstracts)

The downloaded source packages are in
	'/home/hornik/tmp/scratch/RtmpunnNzN/downloaded_packages'
Loading required package: NLP

Error: processing vignette 'movMF.Rnw' failed with diagnostics:
 chunk 18 
Error in unit(0.5 * showr, "strwidth", list(right)) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building 'movMF.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Non-standard file/directory found at top level:
  ‘mpa-Ex.R’
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.
GetExampleData: no visible binding for global variable ‘MPINetData’
Getenvir: no visible binding for global variable ‘MPINetData’
getPSS: no visible global function definition for ‘lines’
performpcls: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  MPINetData binomial lines
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "binomial")
to your NAMESPACE file.
Package suggested but not available for checking: ‘glmulti’
Running examples in ‘mplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: af
> ### Title: The adaptive fence procedure
> ### Aliases: af
> 
> ### ** Examples
> 
> n = 100
> set.seed(11)
> e = rnorm(n)
> x1 = rnorm(n)
> x2 = rnorm(n)
> x3 = x1^2
> x4 = x2^2
> x5 = x1*x2
> y = 1 + x1 + x2 + e
> dat = data.frame(y,x1,x2,x3,x4,x5)
> lm1 = lm(y ~ ., data = dat)
> ## Don't show: 
> af1 = af(lm1, cores = 1, B = 5, n.c = 5, seed = 1)
> summary(af1)

Call:
af(mf = lm1, B = 5, n.c = 5, cores = 1, seed = 1)

Adaptive fence model (c*=17.9):
y ~ x1 + x2

Model sizes considered: 1 to 7 (including intercept).

> plot(af1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
src/Makevars: SHLIB_OPENMP_FFLAGS is preferred to SHLIB_OPENMP_FCFLAGS in PKG_FCFLAGS
  src/Makevars: SHLIB_OPENMP_FCFLAGS is included in PKG_FCFLAGS but not SHLIB_OPENMP_CFLAGS in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_FCFLAGS is included in PKG_LIBS but linking is by C
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘KernSmooth’ ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of ‘imag’ to
  ‘imaginary’
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of ‘imag’ to
  ‘imaginary’
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
Running examples in ‘mpoly-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.mpoly
> ### Title: Convert an object to an mpoly
> ### Aliases: as.mpoly
> 
> ### ** Examples
> 
> 
> library(ggplot2); theme_set(theme_classic())

Attaching package: ‘ggplot2’

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

    vars

> library(dplyr)

Attaching package: ‘dplyr’

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

    vars

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

    filter, lag

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

    intersect, setdiff, setequal, union

> 
> n <- 101
> s <- seq(-5, 5, length.out = n)
> 
> 
> 
> # one dimensional case
> 
> df <- data.frame(x = seq(-5, 5, length.out = n)) %>% 
+   mutate(y = -x^2 + 2*x - 3 + rnorm(n, 0, 2))
> 
> (mod <- lm(y ~ x + I(x^2), data = df))

Call:
lm(formula = y ~ x + I(x^2), data = df)

Coefficients:
(Intercept)            x       I(x^2)  
     -2.709        1.983       -1.010  

> (p <- as.mpoly(mod))
1.98275 x  -  1.010312 x^2  -  2.709013> qplot(x, y, data = df) +
+   stat_function(fun = as.function(p), colour = "red", size = 1)
f(.) with . = x
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
place: no visible global function definition for ‘points’
plot,mproc: no visible binding for global variable ‘rainbow’
plot,mproc: no visible global function definition for ‘plot.default’
plot,mproc: no visible global function definition for ‘axis’
plot,mproc: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis plot.default points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "plot.default", "points")
to your NAMESPACE file.
Running examples in ‘mppR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mpp_CIM
> ### Title: MPP Composite Interval Mapping
> ### Aliases: mpp_CIM
> 
> ### ** Examples
> 
> 
> # Cross-specific effect model
> #############################
> 
> data(mppData)
> 
> SIM <- mpp_SIM(mppData = mppData, Q.eff = "cr")
> 
> cofactors <- QTL_select(Qprof = SIM, threshold = 3, window = 20)
> 
> CIM <- mpp_CIM(mppData = mppData, Q.eff = "cr", cofactors = cofactors,
+                window = 20, plot.gen.eff = TRUE)
> 
> plot(x = CIM)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mppR_vignette.rnw’ using Sweave

Error: processing vignette 'mppR_vignette.rnw' failed with diagnostics:
 chunk 15 (label = mpp_proc) 
Error in Summary.unit(structure(c(4.4, 4.4), unit = 8L, class = c("margin",  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘mppR_vignette.rnw’

SUMMARY: processing the following file failed:
  ‘mppR_vignette.rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-bayen_kuhlmann_2011.rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 220-221 (introduction-bayen_kuhlmann_2011.rmd) 
Error: processing vignette 'introduction-bayen_kuhlmann_2011.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction-bayen_kuhlmann_2011.rmd’

SUMMARY: processing the following file failed:
  ‘introduction-bayen_kuhlmann_2011.rmd’

Error: Vignette re-building failed.
Execution halted
ppersp: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette
Consider adding
  importFrom("grDevices", "colorRampPalette")
to your NAMESPACE file.
densityfn: no visible global function definition for ‘dnbinom’
densityfn: no visible global function definition for ‘dpois’
densityfn: no visible global function definition for ‘dgeom’
form.add: no visible global function definition for ‘formula’
mreg: no visible global function definition for ‘model.frame’
mreg: no visible global function definition for ‘model.response’
mreg: no visible global function definition for ‘model.matrix’
mreg: no visible global function definition for ‘model.offset’
mreg: no visible global function definition for ‘nlm’
paper: no visible global function definition for ‘model.matrix’
randfn: no visible global function definition for ‘rnbinom’
randfn: no visible global function definition for ‘rpois’
randfn: no visible global function definition for ‘rgeom’
randfn: no visible global function definition for ‘rbinom’
summary.mreg: no visible global function definition for ‘pnorm’
summary.mreg: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  dgeom dnbinom dpois formula model.frame model.matrix model.offset
  model.response nlm pnorm printCoefmat rbinom rgeom rnbinom rpois
Consider adding
  importFrom("stats", "dgeom", "dnbinom", "dpois", "formula",
             "model.frame", "model.matrix", "model.offset",
             "model.response", "nlm", "pnorm", "printCoefmat", "rbinom",
             "rgeom", "rnbinom", "rpois")
to your NAMESPACE file.
Running examples in ‘MRFcov-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotMRF_hm
> ### Title: Plot MRF interaction parameters as a heatmap
> ### Aliases: plotMRF_hm
> 
> ### ** Examples
> 
> 
> data("Bird.parasites")
> CRFmod <- MRFcov(data = Bird.parasites, n_nodes = 4, family = 'binomial')
Leave-one-out cv used for the following low-occurrence (rare) nodes:
 Microfilaria ...
Fitting MRF models in sequence using 1 core ...
> plotMRF_hm(MRF_mod = CRFmod)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bird_Parasite_CRF.Rmd’ using rmarkdown
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16

Welcome to MRFcov. If you use the package, please cite as: Clark, NJ, Wells, K and Lindberg, O. 2018. Unravelling changing interspecific interactions across environmental gradients using Markov random fields. Ecology doi: 10.1002/ecy.2221 
Quitting from lines 44-47 (Bird_Parasite_CRF.Rmd) 
Error: processing vignette 'Bird_Parasite_CRF.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Bird_Parasite_CRF.Rmd’

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bagplot
> ### Title: Draws a bagplot, a bivariate boxplot
> ### Aliases: bagplot
> ### Keywords: Graphical
> 
> ### ** Examples
> 
> data(bloodfat)
> 
> # The bagplot can be plotted for the halfspace depth,
> # the projection depth or the skewness-adjusted projection depth.
> # Note that the projection depth is not appropiate for skewed data.
> bagplot(compBagplot(bloodfat))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘MRPC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DendroModuleGraph 
> ### Title: Visualization of Nodes by Dendrogram with Modules and Inferred
> ###   Graph
> ### Aliases: 'DendroModuleGraph '
> 
> ### ** Examples
> 
> 
> # Adjacency matrix from directed example graph
> Adj_directed <- as(ExampleMRPC$complex$cont$withGV$graph,
+                    "matrix")
> 
> # Plot of the graph
> DendroModuleGraph(Adj_directed,
+                   minModuleSize = 5,
+                   GV = 14)
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
 ..cutHeight not given, setting it to 0.975  ===>  99% of the (truncated) height range in dendro.
 ..done.
$graph
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Packages in Depends field not imported from:
  ‘mvtnorm’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
MRsurvival: no visible global function definition for ‘rmvnorm’
MRsurvival: no visible global function definition for ‘optim’
MRsurvival : <anonymous>: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  optim quantile rmvnorm
Consider adding
  importFrom("stats", "optim", "quantile")
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.
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.
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘CheckingSynth.Rmd’ using rmarkdown
--- finished re-building ‘CheckingSynth.Rmd’

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

--- re-building ‘WorkingWithMSCMT.Rmd’ using rmarkdown
Quitting from lines 154-156 (WorkingWithMSCMT.Rmd) 
Error: processing vignette 'WorkingWithMSCMT.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘WorkingWithMSCMT.Rmd’

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

Error: Vignette re-building failed.
Execution halted
cv.msda: no visible global function definition for ‘predict’
formatoutput: no visible global function definition for ‘new’
msda.prep: no visible global function definition for ‘cov’
plot.msda: no visible global function definition for ‘par’
plot.msda: no visible global function definition for ‘matplot’
plot.msda: no visible global function definition for ‘rainbow’
plot.msda: no visible global function definition for ‘approx’
plot.msda: no visible global function definition for ‘axis’
predict.msda: no visible binding for global variable ‘sd’
predict.msda: no visible global function definition for ‘predict’
zeromat: no visible global function definition for ‘new’
Undefined global functions or variables:
  approx axis cov matplot new par predict rainbow sd
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "matplot", "par")
  importFrom("methods", "new")
  importFrom("stats", "approx", "cov", "predict", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘sample’
csv2list: no visible global function definition for ‘read.csv’
kgml_i: no visible global function definition for ‘xmlTreeParse’
kgml_i: no visible global function definition for ‘xmlRoot’
kgml_i: no visible global function definition for ‘xmlAttrs’
list2xml: no visible global function definition for ‘xmlNode’
list2xml: no visible global function definition for ‘append.xmlNode’
msea_ora: no visible global function definition for ‘fisher.test’
msea_ora: no visible global function definition for ‘p.adjust’
msea_sub: no visible global function definition for ‘sd’
msea_sub: no visible global function definition for ‘cor.test’
pathway_class: no visible global function definition for ‘untar’
pca_scaled: no visible binding for global variable ‘sd’
pca_scaled: no visible global function definition for ‘cor.test’
pca_scaled: no visible global function definition for ‘p.adjust’
pca_scaled: no visible binding for global variable ‘var’
read_pathway: no visible global function definition for ‘xmlTreeParse’
read_pathway: no visible global function definition for ‘xmlRoot’
read_pathway: no visible global function definition for ‘xmlToList’
read_pathway: no visible global function definition for ‘xmlAttrs’
Undefined global functions or variables:
  append.xmlNode cor.test fisher.test p.adjust read.csv sd untar var
  xmlAttrs xmlNode xmlRoot xmlToList xmlTreeParse
Consider adding
  importFrom("stats", "cor.test", "fisher.test", "p.adjust", "sd", "var")
  importFrom("utils", "read.csv", "untar")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘amap’ ‘clValid’ ‘cluster’ ‘fpc’ ‘xcms’
  Please remove these calls from your code.
'library' or 'require' call to ‘tcltk’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘mzR’ ‘xcms’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  ‘MSeasy’ ‘tcltk’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘grDevices’ ‘xcms’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘MSG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: canabalt
> ### Title: The scores of the game Canabalt from Twitter
> ### Aliases: canabalt
> 
> ### ** Examples
> 
> library(ggplot2)
> data(canabalt)
> print(qplot(device, score, data = canabalt))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
MSIseq.classify: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Running examples in ‘MSPRT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: implement.MSPRT
> ### Title: Implementing a MSPRT
> ### Aliases: implement.MSPRT
> 
> ### ** Examples
> 
> 
> # the termination thresholds are obtained from design.MSPRT()
> 
> ## one-sample tests
> 
> ### proportion test
> 
> x = c(0, 0, 0, 0, 1, 0, 1, 1, 1, 0, 1, 0, 0, 1, 0,
+       0, 1, 0, 1, 1, 1, 1, 0, 0, 0, 1, 0, 1, 0, 0)
> 
> implement.MSPRT(obs = x, test.type = "oneProp", null = 0.2,
+                 term.thresh = 22.63, N.max = 30)
[1] "-------------------------------------------------------------------------"
[1] "Implementing the MSPRT in case of a one-sample binomial proportion test:"
[1] "-------------------------------------------------------------------------"
[1] "Working with side = right (default)"
[1] "             batch.seq = 1:N.max (default)"
[1] "             type1 = 0.005 (default)"
[1] "             type2 = 0.2 (default)"
[1] "             null = 0.2 (user specified)"
[1] "Required parameters are taken care of!"
[1] "-------------------------------------------------------------------------"
[1] "The UMPBT alternative has been obtained: 0.367 & 0.4 with probabilities 0.296 & 0.704, respectively"
[1] "-------------------------------------------------------------------------"
[1] "Sequential comparison done!"
[1] "-------------------------------------------------------------------------"
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: implement.MSPRT
Execution halted
BS.var: no visible binding for global variable ‘var’
BS.var: no visible global function definition for ‘cov’
Dist.CIs: no visible global function definition for ‘qnorm’
MSM.CIs: no visible global function definition for ‘qnorm’
plot,msSurv-missing: no visible global function definition for ‘update’
summary,msSurv: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov qnorm quantile update var
Consider adding
  importFrom("stats", "cov", "qnorm", "quantile", "update", "var")
to your NAMESPACE file.
Running examples in ‘MST-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MST
> ### Title: Multivariate Survival Trees
> ### Aliases: MST splitting.stat.MST1 splitting.stat.MST2
> ###   splitting.stat.MST3 splitting.stat.MST4
> ### Keywords: Trees Survival Multivariate Correlated
> 
> ### ** Examples
> 
> set.seed(186117)
> data <- rmultime(N = 200, K = 4, beta = c(-1, 0.8, 0.8, 0, 0), cutoff = c(0.5, 0.3, 0, 0),
+     model = "marginal.multivariate.exponential", rho = 0.65)$dat
> test <- rmultime(N = 100, K = 4, beta = c(-1, 0.8, 0.8, 0, 0), cutoff = c(0.5, 0.3, 0, 0),
+     model = "marginal.multivariate.exponential", rho = 0.65)$dat
> 
> #Construct Multivariate Survival Tree:
> fit <- MST(formula = Surv(time, status) ~ x1 + x2 + x3 + x4 | id, data, test,
+     method = "marginal", minsplit = 100, minevents = 20, selection.method = "test.sample")
> 
> (tree_final <- getTree(fit, 4))

Model formula:
Surv(time, status) ~ x1 + x2 + x3 + x4 + id

Fitted party:
[1] root
|   [2] x2 > 0.3
|   |   [3] x1 > 0.5: 1.694 (n = 208)
|   |   [4] x1 <= 0.5: 0.702 (n = 292)
|   [5] x2 <= 0.3
|   |   [6] x1 > 0.5: 0.977 (n = 112)
|   |   [7] x1 <= 0.5: 0.334 (n = 188)

Number of inner nodes:    3
Number of terminal nodes: 4
> plot(tree_final)
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘create_mtc_device.Rmd’ using rmarkdown
--- finished re-building 'create_mtc_device.Rmd'

--- re-building ‘simulate_map_gcode.Rmd’ using rmarkdown
Quitting from lines 65-73 (simulate_map_gcode.Rmd) 
Error: processing vignette 'simulate_map_gcode.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building 'simulate_map_gcode.Rmd'

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

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘MASS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Designer.sobol: no visible global function definition for ‘runif’
basicMonteCarlo: no visible global function definition for ‘runif’
lhs003: no visible global function definition for ‘runif’
plmm.mtk : GenereXplmm: no visible binding for global variable ‘poly’
plmm.mtk : calc.plm: no visible global function definition for ‘lm.fit’
plmm.mtk: no visible global function definition for ‘var’
plmm.mtk: no visible global function definition for ‘lm’
plmm.mtk: no visible global function definition for ‘formula’
plmm.mtk: no visible global function definition for ‘update’
plmm.mtk: no visible global function definition for ‘stepAIC’
plot.plmm: no visible global function definition for ‘par’
plot.plmm: no visible global function definition for ‘barplot’
plot.plmm: no visible global function definition for ‘segments’
plot.plmm: no visible global function definition for ‘abline’
plot.plmm: no visible global function definition for ‘title’
plot.plmm: no visible global function definition for ‘legend’
plot.regressionSI: no visible global function definition for ‘par’
plot.regressionSI: no visible global function definition for ‘title’
plot.regressionSI: no visible global function definition for ‘abline’
plot,mtkProcess: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline barplot dev.new formula legend lm lm.fit par poly runif
  segments stepAIC title update var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "par",
             "segments", "title")
  importFrom("stats", "formula", "lm", "lm.fit", "poly", "runif",
             "update", "var")
to your NAMESPACE file.
Running examples in ‘MTLR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mtlr
> ### Title: Graphical Representation of Feature Weights
> ### Aliases: plot.mtlr
> 
> ### ** Examples
> 
> #These examples are geared towards users who have installed ggplot2 and reshape2.
> library(survival)
> mod <- mtlr(Surv(time,status)~., data = lung)
> #Basic plot with 5 most influential features
> plot(mod)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘workflow.Rmd’ using rmarkdown
Quitting from lines 115-116 (workflow.Rmd) 
Error: processing vignette 'workflow.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘workflow.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘XML’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘NightDay’ ‘RSQLite’ ‘XML’ ‘geosphere’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
drawMap: no visible global function definition for ‘plot’
drawMap: no visible global function definition for ‘box’
drawMap: no visible global function definition for ‘points’
getFlights: no visible binding for global variable ‘htmlTreeParse’
getFlights: no visible binding for global variable ‘xpathSApply’
getFlights: no visible binding for global variable ‘xmlAttrs’
getFlights: no visible binding for global variable ‘free’
movie.routes: no visible global function definition for
  ‘txtProgressBar’
movie.routes: no visible global function definition for ‘jpeg’
movie.routes: no visible global function definition for ‘plot’
movie.routes: no visible global function definition for
  ‘setTxtProgressBar’
movie.routes: no visible global function definition for ‘dev.off’
plot.routes: no visible global function definition for ‘plot’
plot.routes: no visible global function definition for ‘points’
plot.routes: no visible global function definition for ‘mtext’
plot.routes : a: no visible global function definition for ‘points’
plot.routes : a: no visible global function definition for ‘text’
plot.routes : a: no visible global function definition for
  ‘gcIntermediate’
plot.routes : a: no visible global function definition for ‘lines’
routes: no visible global function definition for ‘data’
routes: no visible global function definition for ‘distHaversine’
routes: no visible global function definition for ‘gcIntermediate’
Undefined global functions or variables:
  box data dev.off distHaversine free gcIntermediate htmlTreeParse jpeg
  lines mtext plot points setTxtProgressBar text txtProgressBar
  xmlAttrs xpathSApply
Consider adding
  importFrom("grDevices", "dev.off", "jpeg")
  importFrom("graphics", "box", "lines", "mtext", "plot", "points",
             "text")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Running examples in ‘mudata2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alta_lake
> ### Title: Alta Lake Gravity Core Data
> ### Aliases: alta_lake
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> autoplot(alta_lake, y = "depth") + scale_y_reverse()
Using x = "value"
Using first 9 facets of 14. Use max_facets = FALSE to plot all facets
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mudata.Rmd’ using rmarkdown
Warning: Removed 112 rows containing missing values (geom_path).
Quitting from lines 70-71 (mudata.Rmd) 
Error: processing vignette 'mudata.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mudata.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘DiceKriging’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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').
Running examples in ‘muHVT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HVT
> ### Title: Constructing Hierarchical Voronoi Tessellations
> ### Aliases: HVT
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(USArrests)
> hvt.results <- list()
> hvt.results <- HVT(USArrests, nclust = 6, depth = 1, quant.err = 0.2, 
+                   projection.scale = 10, normalize = TRUE)
Loading required namespace: MASS
Loading required namespace: deldir
Loading required namespace: Hmisc
Loading required namespace: splancs
Loading required namespace: conf.design

     PLEASE NOTE:  The components "delsgs" and "summary" of the
 object returned by deldir() are now DATA FRAMES rather than
 matrices (as they were prior to release 0.0-18).
 See help("deldir").
 
     PLEASE NOTE: The process that deldir() uses for determining
 duplicated points has changed from that used in version
 0.0-9 of this package (and previously). See help("deldir").


> plotHVT(hvt.results, line.width = c(0.8), color.vec = c('#141B41'))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
multeq.diff: no visible global function definition for ‘cov’
multeq.diff: no visible global function definition for ‘pt’
multeq.diff: no visible global function definition for ‘qt’
multeq.rat: no visible global function definition for ‘cov’
multeq.rat: no visible global function definition for ‘pt’
multeq.rat: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cov pt qt
Consider adding
  importFrom("stats", "cov", "pt", "qt")
to your NAMESPACE file.
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.
synthetic_multiband: no visible global function definition for ‘runif’
synthetic_multiband: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘SIR-MCMC.Rmd’ using rmarkdown
Quitting from lines 121-130 (SIR-MCMC.Rmd) 
Error: processing vignette 'SIR-MCMC.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘SIR-MCMC.Rmd’

--- re-building ‘SIRtrans.Rnw’ using knitr
--- finished re-building ‘SIRtrans.Rnw’

SUMMARY: processing the following file failed:
  ‘SIR-MCMC.Rmd’

Error: Vignette re-building failed.
Execution halted
calculate_direction: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Running examples in ‘multiDimBio-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: boxWhisker
> ### Title: A function to create a box and whisker plot by group ID
> ### Aliases: boxWhisker
> 
> ### ** Examples
> 
> data(Nuclei)
> data(Groups)
> boxWhisker(Nuclei, Groups)
Warning: Removed 98 rows containing non-finite values (stat_boxplot).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
multinb.fit: no visible global function definition for ‘nlminb’
multinbmod: no visible global function definition for ‘is.empty.model’
multinbmod: no visible global function definition for ‘model.matrix’
multinbmod: no visible binding for global variable ‘contrasts’
multinbmod: no visible global function definition for ‘model.response’
multinbmod: no visible global function definition for ‘model.offset’
Undefined global functions or variables:
  contrasts is.empty.model model.matrix model.offset model.response
  nlminb
Consider adding
  importFrom("stats", "contrasts", "is.empty.model", "model.matrix",
             "model.offset", "model.response", "nlminb")
to your NAMESPACE file.
.moments: no visible global function definition for ‘ppois’
.truncpoi: no visible global function definition for ‘ppois’
Undefined global functions or variables:
  ppois
Consider adding
  importFrom("stats", "ppois")
to your NAMESPACE file.
Package in Depends field not imported from: ‘rgenoud’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.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.
Running examples in ‘multipanelfigure-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: billing2016_suppfig4e
> ### Title: Mass spectrometry intensities by stem cell type and organelle
> ### Aliases: billing2016_suppfig4e
> 
> ### ** Examples
> 
> ggplot2::ggplot(billing2016_suppfig4e, ggplot2::aes(Experiment, Intensity)) +
+   ggplot2::geom_bar(stat = "identity") +
+   ggplot2::geom_vline(xintercept = seq(3.5, 24.5, 3), linetype = "dotted") +
+   ggplot2::facet_wrap(~ GeneName) +
+   ggplot2::xlab(NULL) +
+   ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, hjust = 1, size = 4))
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
multiPIM : expand.factors: no visible global function definition for
  ‘formula’
multiPIM : expand.factors: no visible global function definition for
  ‘model.matrix’
multiPIM : <anonymous>: no visible global function definition for ‘glm’
multiPIM : <anonymous>: no visible binding for global variable
  ‘binomial’
multiPIM : <anonymous>: no visible global function definition for
  ‘qlogis’
multiPIM : <anonymous>: no visible global function definition for
  ‘as.formula’
multiPIM : <anonymous>: no visible global function definition for ‘lm’
multiPIM: no visible global function definition for ‘glm’
multiPIM: no visible global function definition for ‘qlogis’
multiPIM: no visible binding for global variable ‘binomial’
multiPIM: no visible global function definition for ‘plogis’
multiPIM: no visible global function definition for ‘sd’
multiPIM: no visible global function definition for ‘lm’
summary.multiPIM: no visible binding for global variable ‘sd’
summary.multiPIM: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial formula glm lm model.matrix plogis pnorm qlogis
  sd
Consider adding
  importFrom("stats", "as.formula", "binomial", "formula", "glm", "lm",
             "model.matrix", "plogis", "pnorm", "qlogis", "sd")
to your NAMESPACE file.
CCM_boot : <anonymous>: no visible global function definition for ‘sd’
SSR_check_signal: no visible global function definition for ‘cor’
SSR_check_signal: no visible global function definition for ‘cor.test’
SSR_check_signal: no visible global function definition for ‘lm’
SSR_pred_boot: no visible global function definition for ‘cor’
make_ccm_data: no visible global function definition for ‘rnorm’
make_ccm_data: no visible global function definition for ‘runif’
make_ccm_data: no visible global function definition for ‘rlnorm’
Undefined global functions or variables:
  cor cor.test lm rlnorm rnorm runif sd
Consider adding
  importFrom("stats", "cor", "cor.test", "lm", "rlnorm", "rnorm",
             "runif", "sd")
to your NAMESPACE file.
PrbMlt.default: no visible binding for global variable ‘na.omit’
PrbMlt.default: no visible global function definition for ‘anova’
Undefined global functions or variables:
  anova na.omit
Consider adding
  importFrom("stats", "anova", "na.omit")
to your NAMESPACE file.
File ‘multxpert/R/zzz.R’:
  .onLoad calls:
    cat("multxpert: Implementation of commonly used p-value based and parametric\n",     "multiple testing procedures and parallel gatekeeping procedures.\n",     "For more information visit http://multxpert.com/wiki/MultXpert_package\n",     sep = "")

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

paradjp: no visible global function definition for ‘pt’
parci: no visible global function definition for ‘qt’
pdunnett: no visible global function definition for ‘GenzBretz’
pvalci: no visible global function definition for ‘qnorm’
qdunnett: no visible global function definition for ‘GenzBretz’
Undefined global functions or variables:
  GenzBretz pt qnorm qt
Consider adding
  importFrom("stats", "pt", "qnorm", "qt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘car’ ‘gplots’ ‘pdist’ ‘pls’ ‘rrcov’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘bitops’ ‘caTools’ ‘car’ ‘gplots’ ‘gtools’ ‘mvtnorm’ ‘pcaPP’ ‘pdist’
  ‘pls’ ‘robustbase’ ‘rrcov’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘munsell-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chroma_slice
> ### Title: Plot all colours with the same chroma
> ### Aliases: chroma_slice
> 
> ### ** Examples
> 
> chroma_slice(2)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_musica.Rmd’ using rmarkdown
Quitting from lines 64-67 (using_musica.Rmd) 
Error: processing vignette 'using_musica.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using_musica.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
prentice.test: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘mutSignatures-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotSignatureExposures
> ### Title: Generate Plot Signature
> ### Aliases: plotSignatureExposures
> 
> ### ** Examples
> 
> tmp <- getTestRunArgs(6)
> gp <- plotSignatureExposures(tmp)
> gp + ggtitle("de novo mutSignatures")  + scale_fill_manual(values = c("#377eb8", "#4daf4a"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
mvb.simu: no visible global function definition for ‘runif’
plot.lps: no visible global function definition for ‘matplot’
unifit: no visible global function definition for ‘model.frame’
unifit: no visible global function definition for ‘model.matrix’
unifit: no visible global function definition for ‘model.response’
unilps: no visible global function definition for ‘model.frame’
unilps: no visible global function definition for ‘model.matrix’
unilps: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  matplot model.frame model.matrix model.response runif
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "runif")
to your NAMESPACE file.
conceptIndicesSkm: no visible global function definition for
  ‘txtProgressBar’
conceptIndicesSkm: no visible global function definition for
  ‘setTxtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘txtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘setTxtProgressBar’
mvcmb: no visible global function definition for ‘runif’
mvcmb: no visible global function definition for ‘str’
mvcsph: no visible global function definition for ‘pdf’
mvcsph: no visible global function definition for ‘heatmap’
mvcsph: no visible global function definition for ‘dev.off’
mvcsph: no visible global function definition for ‘hclust’
mvcsph: no visible global function definition for ‘dist’
mvcsph: no visible global function definition for ‘str’
Undefined global functions or variables:
  dev.off dist hclust heatmap pdf runif setTxtProgressBar str
  txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "dist", "hclust", "heatmap", "runif")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file.
Running examples in ‘mvdalab-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MVComp
> ### Title: Traditional Multivariate Mean Vector Comparison
> ### Aliases: MVComp print.mvcomp
> 
> ### ** Examples
> 
> data(College)
> dat1 <- College
> #Generate a 'fake' difference of 15 units
> dat2 <- College + matrix(rnorm(nrow(dat1) * ncol(dat1), mean = 15), 
+         nrow = nrow(dat1), ncol = ncol(dat1))
> 
> Comparison <- MVComp(dat1, dat2, level = .95)
> Comparison
  lower 95 % confidence upper 95 % confidence    Significance
1             -47.95688              17.74004 Not Significant
2             -19.78226             -10.13067     Significant
3             -17.15396             -12.86984     Significant
> plot(Comparison, Diff2Plot = c(1, 2), include.zero = FALSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
mvnpermute: no visible global function definition for ‘lm’
mvnpermute: no visible global function definition for ‘coef’
mvnpermute: no visible global function definition for ‘resid’
Undefined global functions or variables:
  coef lm resid
Consider adding
  importFrom("stats", "coef", "lm", "resid")
to your NAMESPACE file.
mvorpb: no visible global function definition for ‘pnorm’
mvorpb: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
rtn: no visible global function definition for ‘runif’
rtn: no visible global function definition for ‘qnorm’
rtn: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm runif
Consider adding
  importFrom("stats", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
mvtmeta_fe: no visible global function definition for ‘combinations’
Undefined global functions or variables:
  combinations
'library' or 'require' call to ‘RColorBrewer’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘RColorBrewer’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Running examples in ‘mwaved-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiCoef
> ### Title: Wavelet coefficient estimation from a multichannel signal
> ### Aliases: multiCoef
> 
> ### ** Examples
> 
> library(mwaved)
> # Simulate the multichannel doppler signal.
> m <- 3
> n <- 2^10
> signal <- makeDoppler(n)
> # Noise levels per channel
> e <- rnorm(m*n)
> # Create Gamma blur
> shape <- seq(from = 0.5, to = 1, length = m)
> scale <- rep(0.25,m)
> G <- gammaBlur(n, shape = shape, scale = scale)
> # Convolve the signal
> X <- blurSignal(signal, G)
> # Create error with custom signal to noise ratio
> SNR <- c(10,15,20)
> sigma <- sigmaSNR(X, SNR)
> if (requireNamespace("fracdiff", quietly = TRUE)) {
+   alpha <- c(0.75, 0.8, 1)
+ } else {
+   alpha <- rep(1, m)
+ }
> E <- multiNoise(n, sigma, alpha)
> # Create noisy & blurred multichannel signal
> Y <- X + E
> plot(signal, type='l', lty='dashed', main='dashed: True signal, solid: multichannel signals')
> matlines(Y, lty = 1)
> # Estimate the wavelet coefficients
> estimatedCoefs <- multiCoef(Y, G, alpha = alpha)
> plot(estimatedCoefs)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mWaveD.Rmd’ using rmarkdown
Quitting from lines 196-215 (mWaveD.Rmd) 
Error: processing vignette 'mWaveD.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mWaveD.Rmd’

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

Error: Vignette re-building failed.
Execution halted
mxkssd: no visible global function definition for ‘txtProgressBar’
mxkssd: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
abcpred_nmer: no visible global function definition for ‘write.table’
algpred: no visible global function definition for ‘read.table’
algpred: no visible global function definition for ‘write.table’
allermatch: no visible global function definition for ‘read.table’
allermatch: no visible global function definition for ‘write.table’
bcepred_nmer: no visible global function definition for ‘write.table’
bimas_nmer: no visible global function definition for ‘write.table’
filter.firstlayer: no visible global function definition for
  ‘read.table’
filter.firstlayer: no visible global function definition for
  ‘write.table’
iedb_arb_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_arb_mhcii_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhci_nmer: no visible global function definition for
  ‘write.table’
iedb_consensus_mhcii_nmer: no visible global function definition for
  ‘write.table’
netmhcNN_nmer: no visible global function definition for ‘write.table’
netmhcWT_nmer: no visible global function definition for ‘write.table’
propred_nmer: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
update_episode: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Running examples in ‘myTAI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotContribution
> ### Title: Plot Cumuative Transcriptome Index
> ### Aliases: PlotContribution
> 
> ### ** Examples
> 
> 
>  data(PhyloExpressionSetExample)
>  data(DivergenceExpressionSetExample)
>  
>  # visualize phylostratum contribution to global TAI
>  PlotContribution(PhyloExpressionSetExample, legendName = "PS")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Advanced.Rmd’ using rmarkdown
--- finished re-building ‘Advanced.Rmd’

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

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

--- re-building ‘Intermediate.Rmd’ using rmarkdown
Quitting from lines 87-91 (Intermediate.Rmd) 
Error: processing vignette 'Intermediate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Intermediate.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 413-421 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

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

SUMMARY: processing the following files failed:
  ‘Intermediate.Rmd’ ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
abs_dif: no visible global function definition for ‘as.formula’
env_dif: no visible global function definition for ‘lm’
env_dif: no visible global function definition for ‘as.formula’
env_dif_logistic: no visible global function definition for
  ‘as.formula’
fam_env: no visible global function definition for ‘as.formula’
log_dif: no visible global function definition for ‘as.formula’
Undefined global functions or variables:
  as.formula lm
Consider adding
  importFrom("stats", "as.formula", "lm")
to your NAMESPACE file.
Running examples in ‘nandb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: matrix_raster_plot
> ### Title: Make a raster plot of a matrix.
> ### Aliases: matrix_raster_plot
> 
> ### ** Examples
> 
> img <- ijtiff::read_tif(system.file('extdata', '50.tif', package = 'nandb'))
Reading 50.tif: an 8-bit, 50x50 pixel image of unsigned
integer type with 1 channel and 50 frames . . .
 Done.
> ijtiff::display(img[, , 1, 1])
> matrix_raster_plot(img[, , 1, 1])
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘batch-mode.Rmd’ using rmarkdown
--- finished re-building ‘batch-mode.Rmd’

--- re-building ‘brightness-timeseries.Rmd’ using rmarkdown
--- finished re-building ‘brightness-timeseries.Rmd’

--- re-building ‘single-images.Rmd’ using rmarkdown
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Quitting from lines 52-70 (single-images.Rmd) 
Error: processing vignette 'single-images.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘single-images.Rmd’

SUMMARY: processing the following file failed:
  ‘single-images.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘spelling.R’ [0s/1s]
  Running ‘testthat.R’ [5s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(naniar)
  > 
  > test_check("naniar")
  ── 1. Error: (unknown) (@test-gg_miss_upset.R#3)  ──────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: gg_miss_upset(riskfactors) at testthat/test-gg_miss_upset.R:3
  2: data %>% as_shadow_upset() %>% UpSetR::upset(order.by = order.by, ...)
  3: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: eval(quote(`_fseq`(`_lhs`)), env, env)
  6: `_fseq`(`_lhs`)
  7: freduce(value, `_function_list`)
  8: withVisible(function_list[[k]](value))
  9: function_list[[k]](value)
  10: UpSetR::upset(., order.by = order.by, ...)
  ...
  36: pushvpgp(x)
  37: pushgrobvp(x$vp)
  38: pushgrobvp.viewport(x$vp)
  39: pushViewport(vp, recording = FALSE)
  40: lapply(vps, push.vp, recording)
  41: FUN(X[[i]], ...)
  42: push.vp.vpTree(X[[i]], ...)
  43: push.vp(vp$parent, recording)
  44: push.vp.viewport(vp$parent, recording)
  45: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 470 SKIPPED: 22 FAILED: 1
  1. Error: (unknown) (@test-gg_miss_upset.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘exploring-imputed-values.Rmd’ using rmarkdown
Quitting from lines 92-100 (exploring-imputed-values.Rmd) 
Error: processing vignette 'exploring-imputed-values.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘exploring-imputed-values.Rmd’

--- re-building ‘getting-started-w-naniar.Rmd’ using rmarkdown
Quitting from lines 64-67 (getting-started-w-naniar.Rmd) 
Error: processing vignette 'getting-started-w-naniar.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘getting-started-w-naniar.Rmd’

--- re-building ‘naniar-visualisation.Rmd’ using rmarkdown
Quitting from lines 29-32 (naniar-visualisation.Rmd) 
Error: processing vignette 'naniar-visualisation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘naniar-visualisation.Rmd’

--- re-building ‘replace-with-na.Rmd’ using rmarkdown
--- finished re-building ‘replace-with-na.Rmd’

--- re-building ‘special-missing-values.Rmd’ using rmarkdown
--- finished re-building ‘special-missing-values.Rmd’

SUMMARY: processing the following files failed:
  ‘exploring-imputed-values.Rmd’ ‘getting-started-w-naniar.Rmd’
  ‘naniar-visualisation.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot
> ### Title: Plot Method for the 'nblda' and 'nblda_trained' Classes
> ### Aliases: plot plot.nblda plot.nblda_trained plot,nblda-method
> ###   plot,nblda_trained-method
> 
> ### ** Examples
> 
> set.seed(2128)
> counts <- generateCountData(n = 20, p = 10, K = 2, param = 1, sdsignal = 0.5,
+                             DE = 0.8, allZero.rm = FALSE, tag.samples = TRUE)
> x <- t(counts$x + 1)
> y <- counts$y
> xte <- t(counts$xte + 1)
> ctrl <- nbldaControl(folds = 2, repeats = 2)
> 
> fit <- trainNBLDA(x = x, y = y, type = "mle", tuneLength = 10,
+                   metric = "accuracy", train.control = ctrl)
Warning in nblda(x = x, y = y, xte = NULL, rhos = best.rho, beta = tc$beta,  :
  Since no xte was provided, testing was performed on training data set.
> 
> plot(fit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
Running examples in ‘ncappc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ncappc
> ### Title: Performs NCA calculations and population PK model diagnosis.
> ### Aliases: ncappc
> 
> ### ** Examples
> 
> out <- ncappc(obsFile=system.file("extdata","pkdata.csv",package="ncappc"), 
+   onlyNCA = TRUE,
+   extrapolate = TRUE,
+   printOut = FALSE,
+   evid = FALSE,
+   psnOut=FALSE)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ncappc ... dv_vs_idv -> dv.plot -> suppressMessages -> withCallingHandlers
Execution halted
ncbit : FUN: no visible global function definition for ‘read.table’
ncbit : FUN: no visible global function definition for ‘head’
Undefined global functions or variables:
  head read.table
Consider adding
  importFrom("utils", "head", "read.table")
to your NAMESPACE file.
get.split.filename.cmip5: no visible global function definition for
  ‘tail’
nc.conform.data : <anonymous>: no visible global function definition
  for ‘na.omit’
nc.get.subset.recursive: no visible global function definition for
  ‘head’
nc.get.subset.recursive: no visible global function definition for
  ‘tail’
nc.put.subset.recursive: no visible global function definition for
  ‘head’
nc.put.subset.recursive: no visible global function definition for
  ‘tail’
Undefined global functions or variables:
  head na.omit tail
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
infoNcdfVars: no visible global function definition for ‘na.omit’
modifyNcdfDefAtts: no visible global function definition for ‘na.omit’
plotDatacube: no visible global function definition for ‘runif’
plotDatacube: no visible global function definition for
  ‘colorRampPalette’
plotDatacube: no visible global function definition for ‘dev.cur’
plotDatacube: no visible global function definition for ‘dev.new’
plotDatacube: no visible global function definition for ‘layout’
plotDatacube: no visible global function definition for ‘par’
plotDatacube: no visible global function definition for ‘points’
plotDatacube: no visible global function definition for ‘text’
plotDatacube: no visible global function definition for ‘plot.new’
plotDatacube: no visible global function definition for ‘mtext’
plotDatacube: no visible global function definition for ‘rgb’
plotDatacube: no visible global function definition for ‘legend’
transNcdfRotate: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  colorRampPalette dev.cur dev.new layout legend mtext na.omit par
  plot.new points rgb runif text
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.cur", "dev.new",
             "rgb")
  importFrom("graphics", "layout", "legend", "mtext", "par", "plot.new",
             "points", "text")
  importFrom("stats", "na.omit", "runif")
to your NAMESPACE file.
d0: no visible global function definition for ‘qnorm’
dncgamma: no visible global function definition for ‘dpois’
indncgamma: no visible global function definition for ‘pgamma’
indncgamma: no visible global function definition for ‘dpois’
inxncgamma: no visible global function definition for ‘qnorm’
inxncgamma: no visible global function definition for ‘pgamma’
inxncgamma: no visible global function definition for ‘dpois’
pncgamma: no visible global function definition for ‘pgamma’
pncgamma: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dpois pgamma qnorm
Consider adding
  importFrom("stats", "dpois", "pgamma", "qnorm")
to your NAMESPACE file.
data.reduction: no visible global function definition for ‘prcomp’
data.reduction: no visible global function definition for ‘hclust’
data.reduction: no visible global function definition for ‘as.dist’
data.reduction: no visible global function definition for ‘cor’
data.reduction: no visible global function definition for ‘dist’
heatmap1: no visible global function definition for ‘sd’
lineplot: no visible global function definition for ‘sd’
normalize: no visible global function definition for ‘sd’
profileplot3d : ColorFunction: no visible global function definition
  for ‘rgb’
profileplot3d : ColorFunction: no visible global function definition
  for ‘colorRamp’
profileplot3d: no visible global function definition for ‘sd’
profileplot3d: no visible global function definition for ‘gray’
Undefined global functions or variables:
  as.dist colorRamp cor dist gray hclust prcomp rgb sd
Consider adding
  importFrom("grDevices", "colorRamp", "gray", "rgb")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd")
to your NAMESPACE file.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NeatMap-package
> ### Title: Non-clustered Heatmaps
> ### Aliases: NeatMap-package NeatMap
> ### Keywords: package
> 
> ### ** Examples
> 
> 
> #heatmap1 using pca (the scale_x_continuous ensures that labels can be seen)
> make.heatmap1(mtcars,row.method="PCA",column.method="average.linkage",
+ row.labels=rownames(mtcars),column.labels=colnames(mtcars))+
+ scale_x_continuous(lim=c(-1,15))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘neatmaps-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: consClustResTable
> ### Title: Consensus Cluster Results in a Table
> ### Aliases: consClustResTable
> 
> ### ** Examples
> 
> # create the data frame using the network, node and edge attributes
> df <- netsDataFrame(network_attr_df,
+                     node_attr_df,
+                     edge_df)
> 
> # run the neatmap code on df
> neat_res <- neatmap(df, scale_df = "ecdf", max_k = 3, reps = 100, 
+                     xlab = "vars", ylab = "nets", xlab_cex = 1, ylab_cex = 1)
Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto),  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: neatmap ... unitConvert -> <Anonymous> -> convertUnit -> grid.Call
Execution halted
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.
The following files look like leftovers/mistakes:
  ‘Rplots.pdf’, ‘Rplots.ps’
Please remove them from your package.
nestedRanksTest.default: no visible global function definition for
  ‘setNames’
nestedRanksTest.default: no visible global function definition for
  ‘quantile’
nestedRanksTest.formula: no visible global function definition for
  ‘terms’
plot.htest_boot: no visible global function definition for ‘hist’
plot.htest_boot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline hist quantile setNames terms
Consider adding
  importFrom("graphics", "abline", "hist")
  importFrom("stats", "quantile", "setNames", "terms")
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.
netVal: no visible global function definition for ‘cutree’
netVal: no visible global function definition for ‘hclust’
netVal: no visible global function definition for ‘as.dist’
Undefined global functions or variables:
  as.dist cutree hclust
Consider adding
  importFrom("stats", "as.dist", "cutree", "hclust")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘buildcmds’
EnvInd: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Running examples in ‘netjack-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diff_test_ggPlot
> ### Title: Difference Test Plots
> ### Aliases: diff_test_ggPlot
> 
> ### ** Examples
> 
> data(GroupA)
> GroupA_Net = as_NetSample(GroupA, 1:20, node.variables = list(community = c(rep(1, 10), rep(2,10))),
+   sample.variables = list(group = c(rep(1, 10), rep(2,10))))
> Jackknife_GroupA_Net = net_apply(GroupA_Net, node_jackknife)
> GlobEff_GroupA_Net = net_stat_apply(Jackknife_GroupA_Net, global_efficiency)
> diff_test_ggPlot(GlobEff_GroupA_Net)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘developingNetjack.Rmd’ using rmarkdown
--- finished re-building ‘developingNetjack.Rmd’

--- re-building ‘netjackIntro.Rmd’ using rmarkdown
Quitting from lines 147-156 (netjackIntro.Rmd) 
Error: processing vignette 'netjackIntro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘netjackIntro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘fastshp’
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 73-74 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
network.dyadcount:
  function(x, na.omit, ...)
network.dyadcount.active:
  function(x, onset, terminus, length, at, rule, na.omit,
           active.default)

network.edgecount:
  function(x, na.omit, ...)
network.edgecount.active:
  function(x, onset, terminus, length, at, rule, na.omit,
           active.default)

network.naedgecount:
  function(x, ...)
network.naedgecount.active:
  function(x, onset, terminus, length, at, rule, active.default)

network.size:
  function(x, ...)
network.size.active:
  function(x, onset, terminus, length, at, rule, active.default)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  network.dyadcount.active network.edgecount.active
  network.naedgecount.active network.size.active
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'network.extensions':
  ‘network.dyadcount.active’ ‘network.edgecount.active’
  ‘network.naedgecount.active’ ‘network.size.active’

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 ‘VignetteNetworkExt.Rmd’ using rmarkdown
network: Classes for Relational Data
Version 1.14-377 created on 2019-03-04.
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.


Attaching package: 'NetworkExtinction'

The following object is masked _by_ '.GlobalEnv':

    net

Quitting from lines 129-133 (VignetteNetworkExt.Rmd) 
Error: processing vignette 'VignetteNetworkExt.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘VignetteNetworkExt.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.cascade
> ### Title: Plot a cascade object
> ### Aliases: plot.cascade
> 
> ### ** Examples
> 
> 
> data(cascades)
> plot(cascades, selection = names(cascades$cascade_nodes)[1:5])
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart_vignette.Rmd’ using rmarkdown
NetworkInference: Inferring latent diffusion networks.
Version 1.2.4
copyright (c) 2016, Fridolin Linder, Pennsylvania State University
                    Bruce Desmarais, Pennsylvania State University
For citation information, type citation("NetworkInference").
Type help("NetworkInference") to get started.

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

--- re-building ‘tutorial_vignette.Rmd’ using rmarkdown
NetworkInference: Inferring latent diffusion networks.
Version 1.2.4
copyright (c) 2016, Fridolin Linder, Pennsylvania State University
                    Bruce Desmarais, Pennsylvania State University
For citation information, type citation("NetworkInference").
Type help("NetworkInference") to get started.


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 188-190 (tutorial_vignette.Rmd) 
Error: processing vignette 'tutorial_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘tutorial_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘network_scaleup.Rmd’ using docco_linear
Loading required package: plyr
Loading required package: dplyr

Attaching package: 'dplyr'

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

    arrange, count, desc, failwith, id, mutate, rename, summarise,
    summarize

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: functional
Loading required package: stringr
Quitting from lines 221-222 (network_scaleup.Rmd) 
Error: processing vignette 'network_scaleup.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘network_scaleup.Rmd’

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

Error: Vignette re-building failed.
Execution halted
simulate.sisnetwork: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Running examples in ‘NeuralNetTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: garson
> ### Title: Variable importance using Garson's algorithm
> ### Aliases: garson garson.default garson.numeric garson.nnet garson.mlp
> ###   garson.nn garson.train
> 
> ### ** Examples
> 
> 
> ## using numeric input
> 
> wts_in <- c(13.12, 1.49, 0.16, -0.11, -0.19, -0.16, 0.56, -0.52, 0.81)
> struct <- c(2, 2, 1) #two inputs, two hidden, one output 
> 
> garson(wts_in, struct)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘neurobase.Rmd’ using rmarkdown
--- finished re-building ‘neurobase.Rmd’

--- re-building ‘nifti_basics.Rmd’ using rmarkdown
Quitting from lines 524-527 (nifti_basics.Rmd) 
Error: processing vignette 'nifti_basics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nifti_basics.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assess
> ### Title: Compare a given score to a parent population.
> ### Aliases: assess
> 
> ### ** Examples
> 
> require(neuropsychology)
> 
> assess(3.4, mean=2.5, sd=1.2)
[1] "The participant (score = 3.4) is positioned at 0.75 standard deviations from the mean (M = 2.5, SD = 1.2). The participant's score is greater than 77.37 % of the general population."
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
balloon: no visible global function definition for ‘convolve’
physnoise: no visible global function definition for ‘sd’
physnoise: no visible global function definition for ‘rnorm’
rrice: no visible global function definition for ‘rnorm’
simTSrestingstate: no visible global function definition for ‘runif’
simTSrestingstate: no visible global function definition for ‘fft’
spatialnoise: no visible global function definition for ‘rnorm’
spatialnoise: no visible global function definition for ‘qgamma’
spatialnoise: no visible global function definition for ‘pnorm’
specifydesign: no visible global function definition for ‘convolve’
systemnoise: no visible global function definition for ‘rnorm’
tasknoise: no visible global function definition for ‘rnorm’
tasknoise: no visible global function definition for ‘sd’
temporalnoise: no visible global function definition for ‘arima.sim’
Undefined global functions or variables:
  arima.sim convolve fft pnorm qgamma rnorm runif sd
Consider adding
  importFrom("stats", "arima.sim", "convolve", "fft", "pnorm", "qgamma",
             "rnorm", "runif", "sd")
to your NAMESPACE file.
Running examples in ‘neutralitytestr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lsq_plot
> ### Title: Plot cumulative distribution 'lsq_plot' Plots the cumulative
> ###   distribution of the data as well as the best fit linear model line.
> ### Aliases: lsq_plot
> 
> ### ** Examples
> 
> lsq_plot(neutralitytest(VAFselection, fmin = 0.1, fmax = 0.25))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(neutralitytestr)
  > 
  > test_check("neutralitytestr")
  ── 1. Error: neutralitytest returns correct object (@test_plots.R#5)  ──────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_is(plot_all(neutralitytest(VAFneutral)), "ggplot") at testthat/test_plots.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: plot_all(neutralitytest(VAFneutral))
  5: cowplot::plot_grid(p1, p2, p3, labels = c("A", "B", "C"), ncol = 3)
  6: align_plots(plotlist = plots, align = align, axis = axis)
  7: lapply(plots, function(x) {
         if (!is.null(x)) 
             plot_to_gtable(x)
         else NULL
     })
  8: FUN(X[[i]], ...)
  9: plot_to_gtable(x)
  10: ggplot2::ggplotGrob(plot)
  ...
  24: pushvpgp(x)
  25: pushgrobvp(x$vp)
  26: pushgrobvp.viewport(x$vp)
  27: pushViewport(vp, recording = FALSE)
  28: lapply(vps, push.vp, recording)
  29: FUN(X[[i]], ...)
  30: push.vp.vpTree(X[[i]], ...)
  31: push.vp(vp$parent, recording)
  32: push.vp.viewport(vp$parent, recording)
  33: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 1
  1. Error: neutralitytest returns correct object (@test_plots.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘neutraltytestr.Rmd’ using rmarkdown
Warning: Removed 2 rows containing missing values (geom_bar).
Quitting from lines 61-62 (neutraltytestr.Rmd) 
Error: processing vignette 'neutraltytestr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘neutraltytestr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘MASS’ ‘boot’ ‘lattice’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nfca : nFCAmain: no visible global function definition for ‘hist’
nfca : nFCAmain: no visible global function definition for
  ‘flush.console’
nfca : nFCAmain: no visible global function definition for ‘qnorm’
nfca : nFCAmain: no visible global function definition for ‘read.csv’
nfca : nFCAmain: no visible global function definition for ‘cor’
nfca : nFCAmain: no visible global function definition for ‘as.dist’
nfca : nFCAmain: no visible global function definition for ‘cophenetic’
nfca : nFCAmain: no visible global function definition for ‘hclust’
nfca : thresholdTEST: no visible global function definition for
  ‘read.csv’
nfca : gScript: no visible global function definition for ‘read.csv’
nfca : gScript0: no visible global function definition for ‘read.csv’
nfca : gMatrix: no visible global function definition for ‘read.csv’
nfca: no visible global function definition for ‘cor’
Undefined global functions or variables:
  as.dist cophenetic cor flush.console hclust hist qnorm read.csv
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cophenetic", "cor", "hclust", "qnorm")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Package suggested but not available for checking: ‘NFPdata’
Error(s) in re-building vignettes:
  ...
--- re-building ‘demo.Rmd’ using rmarkdown
Loading required package: maps
The 7-zip program is needed to unpack NHD downloads (http://www.7-zip.org/).
--- finished re-building ‘demo.Rmd’

--- re-building ‘flow.Rmd’ using rmarkdown
Loading required package: maps
The 7-zip program is needed to unpack NHD downloads (http://www.7-zip.org/).

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

Linking to GEOS 3.7.1, GDAL 2.4.0, PROJ 5.2.0
Quitting from lines 29-34 (flow.Rmd) 
Error: processing vignette 'flow.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘flow.Rmd’

--- re-building ‘network.Rmd’ using rmarkdown
Loading required package: maps
The 7-zip program is needed to unpack NHD downloads (http://www.7-zip.org/).

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

Linking to GEOS 3.7.1, GDAL 2.4.0, PROJ 5.2.0
Warning in st_centroid.sf(mendota_lake) :
  st_centroid assumes attributes are constant over geometries of x
Warning in st_centroid.sfc(st_geometry(x), of_largest_polygon = of_largest_polygon) :
  st_centroid does not give correct centroids for longitude/latitude data
Quitting from lines 54-59 (network.Rmd) 
Error: processing vignette 'network.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘network.Rmd’

SUMMARY: processing the following files failed:
  ‘flow.Rmd’ ‘network.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.NHEMOtree
> ### Title: Plot Method for Class NHEMOtree
> ### Aliases: plot.NHEMOtree
> ### Keywords: Plots for NHEMOtree Multi-objective optimization Evolutionary
> ###   algorithms Classification
> 
> ### ** Examples
> 
> # Simulation of data and costs
>   d         <- Sim_Data(Obs=200)
>   CostMatrix<- Sim_Costs()
> 
>   res<- NHEMOtree(type="NHEMO", formula=Y2~., data=d, CostMatrix=CostMatrix, 
+                   gens=5, popsize=5, crossover_prob=0.1, mutation_prob=0.1)
>   plot(data=d, x=res, which="P")
>   plot(data=d, x=res, which="S", col=3, type="l")
>   plot(data=d, x=res, which="V", vim=5)
>   plot(data=d, x=res, which="T")
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Running examples in ‘nhstplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotchisqtest
> ### Title: Illustrate a Chi-Squared Test graphically.
> ### Aliases: plotchisqtest
> 
> ### ** Examples
> 
> #Making a chi-squared plot with Chi-squared of 8 and df of 4
> plotchisqtest(chisq = 8, df = 4)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘nhstplot.Rmd’ using rmarkdown
Quitting from lines 44-45 (nhstplot.Rmd) 
Error: processing vignette 'nhstplot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nhstplot.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lmPlots_gg
> ### Title: Linear Model Diagnostic Plots with ggplot2
> ### Aliases: lmPlots_gg
> 
> ### ** Examples
> 
> n <- 100; x1 <- rnorm(n); y1 <- rnorm(n);
> linmod <- lm(y1 ~ x1)
> lmPlots_gg(linmod)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: lmPlots_gg ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘NIRStat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MAUCtest
> ### Title: MAUC statistics based Analysis for NIRS time series.
> ### Aliases: MAUCtest
> 
> ### ** Examples
> 
> # Data Simulation
> dat = data.frame(Y= rep(0,100),t=1:100,trans = c(rep(0,50),rep(1,50)))
> dat$Y = apply(dat,1,function(x){rnorm(1,5*rnorm(1),6*exp(rnorm(1)))})
> dat$Y = dat$Y + 15 - quantile(dat$Y,0.3) 
> dat$Y[dat$Y<=15] = 15
> 
> 
> # Estimate the MAUC statistics of the NIRS data and test on the difference. 
> MAUCtest(dat$Y,dat$t,dat$trans,TRUE,FALSE,100)
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: MAUCtest ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DataInBrief.Rmd’ using knitr
Quitting from lines 938-948 (DataInBrief.Rmd) 
Error: processing vignette 'DataInBrief.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DataInBrief.Rmd’

--- re-building ‘JEMBE.Rmd’ using knitr
Quitting from lines 468-479 (JEMBE.Rmd) 
Error: processing vignette 'JEMBE.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘JEMBE.Rmd’

SUMMARY: processing the following files failed:
  ‘DataInBrief.Rmd’ ‘JEMBE.Rmd’

Error: Vignette re-building failed.
Execution halted
nlmeODE: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
Pwr.lme: no visible global function definition for ‘anova’
Pwr.lme: no visible global function definition for ‘qf’
Pwr.lme: no visible global function definition for ‘pf’
logLik1.lme: no visible global function definition for ‘coef’
logLik1.lme: no visible global function definition for ‘model.matrix’
logLik1.lme: no visible global function definition for ‘predict’
logLik1.lme: no visible global function definition for ‘formula’
runScript: no visible binding for global variable ‘example’
sigmaTolme: no visible global function definition for ‘vcov’
simulateY.lme: no visible global function definition for ‘runif’
simulateY.lme: no visible global function definition for ‘fitted’
simulateY.lme: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  anova coef example fitted formula model.matrix pf predict qf rnorm
  runif vcov
Consider adding
  importFrom("stats", "anova", "coef", "fitted", "formula",
             "model.matrix", "pf", "predict", "qf", "rnorm", "runif",
             "vcov")
  importFrom("utils", "example")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘installing_nlmixr.Rmd’ using rmarkdown
--- finished re-building ‘installing_nlmixr.Rmd’

--- re-building ‘running_nlmixr.Rmd’ using rmarkdown
Quitting from lines 20-28 (running_nlmixr.Rmd) 
Error: processing vignette 'running_nlmixr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘running_nlmixr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package in Depends field not imported from: ‘proto’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘stats:::nlsModel’ ‘stats:::nlsModel.plinear’
  See the note in ?`:::` about the use of this operator.
nls2: no visible global function definition for ‘nls.control’
nls2: no visible global function definition for ‘as.formula’
nls2: no visible global function definition for ‘coef’
nls2: no visible global function definition for ‘runif’
nls2 : <anonymous>: no visible global function definition for
  ‘deviance’
Undefined global functions or variables:
  as.formula coef deviance nls.control runif
Consider adding
  importFrom("stats", "as.formula", "coef", "deviance", "nls.control",
             "runif")
to your NAMESPACE file.
Running examples in ‘nls.multstart-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Chlorella_TRC
> ### Title: Example metabolic thermal response curves
> ### Aliases: Chlorella_TRC
> ### Keywords: dataset
> 
> ### ** Examples
> 
> data("Chlorella_TRC")
> library(ggplot2)
> ggplot(Chlorella_TRC) +
+  geom_point(aes(temp, ln.rate, col = process)) +
+  facet_wrap(~ growth.temp + flux)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘nlstimedist-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tdCdfPlot
> ### Title: Plot the timedist PDF or CDF
> ### Aliases: tdCdfPlot tdPdfPlot
> 
> ### ** Examples
> 
> tdTilia <- tdData(tilia, x = "Day", y = "Trees")
> model <- timedist(data = tdTilia, x = "Day", y = "propMax", r = 0.1, c = 0.5,
+                   t = 120)
> tdCdfPlot(model)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘nlstimedist.Rmd’ using rmarkdown
Quitting from lines 149-150 (nlstimedist.Rmd) 
Error: processing vignette 'nlstimedist.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nlstimedist.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_nltt_values
> ### Title: Collects the nLTT values of all phylogenies in the
> ###   melted/uncast/long form
> ### Aliases: get_nltt_values
> 
> ### ** Examples
> 
>   library(ape)
>   library(ggplot2)
>   library(nLTT)
> 
>   # Create some random phylogenies
>   phylogeny1 <- rcoal(10)
>   phylogeny2 <- rcoal(20)
>   phylogeny3 <- rcoal(30)
>   phylogeny4 <- rcoal(40)
>   phylogeny5 <- rcoal(50)
>   phylogeny6 <- rcoal(60)
>   phylogeny7 <- rcoal(70)
>   phylogenies <- c(phylogeny1, phylogeny2, phylogeny3,
+     phylogeny4, phylogeny5, phylogeny6, phylogeny7
+   )
> 
>   # Obtain the nLTT values
>   dt <- 0.2
>   nltt_values <- get_nltt_values(phylogenies, dt = dt)
> 
>   # Check properties of nltt_values
>   testit::assert(names(nltt_values) == c("id", "t", "nltt"))
>   nltt_values_per_phylogeny <- (1 + (1 / dt))
>   n_phylogenies <- length(phylogenies)
>   testit::assert(nrow(nltt_values)
+     == nltt_values_per_phylogeny * n_phylogenies
+   )
> 
>   # Plot the phylognies, where the individual nLTT values are visible
>   qplot(t, nltt, data = nltt_values, geom = "point",
+     ylim = c(0,1),
+     main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)
+   ) + stat_summary(
+     fun.data = "mean_cl_boot", color = "red", geom = "smooth"
+   )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_nltt_values.Rmd’ using rmarkdown
Quitting from lines 60-65 (get_nltt_values.Rmd) 
Error: processing vignette 'get_nltt_values.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘get_nltt_values.Rmd’

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

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

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

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fwdplot
> ### Title: Forward plot(s) to monitor selected statistic(s)/method(s)
> ### Aliases: fwdplot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(smokingcessation, package = "netmeta")
> smokingcessation$id <- 1:nrow(smokingcessation)
> 
> study912 <- subset(smokingcessation, id %in% 9:12)
> p1 <- netmeta::pairwise(list(treat1, treat2, treat3),
+                         list(event1, event2, event3),
+                         list(n1, n2, n3),
+                         data = study912,
+                         sm = "OR")
> 
> # Forward search algorithm
> #
> FSresult <- NMAoutlier(p1, P = 1, small.values = "bad", n_cores = 2)
> 
> # forward plot for Cook's distance
> fwdplot(FSresult, "cook")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Examples.Rmd’ using rmarkdown
Quitting from lines 123-150 (Examples.Rmd) 
Error: processing vignette 'Examples.Rmd' failed with diagnostics:
invalid ‘type’ (list) of argument
--- failed re-building ‘Examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
nnmf_als: no visible global function definition for ‘rnorm’
nnmf_mm: no visible global function definition for ‘rnorm’
nnmf_prob: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Running examples in ‘NMF-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NMF-package
> ### Title: Algorithms and framework for Nonnegative Matrix Factorization
> ###   (NMF).
> ### Aliases: NMF NMF-package
> ### Keywords: package
> 
> ### ** 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 <- 50; counts <- c(5, 5, 8);
> V <- syntheticNMF(n, counts)
> 
> # perform a 3-rank NMF using the default algorithm
> res <- nmf(V, 3)
> 
> basismap(res)
Error in Ops.unit(m, unit(1, "grobwidth", textGrob(coln[i <- which.max(nchar(coln))],  : 
  REAL() can only be applied to a 'numeric', not a 'integer'
Calls: basismap ... aheatmap -> heatmap_motor -> draw_colnames -> Ops.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘NMF-vignette.Rnw’ using knitr
Quitting from lines 894-895 (NMF-vignette.Rnw) 
Error: processing vignette 'NMF-vignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘NMF-vignette.Rnw’

--- re-building ‘heatmaps.Rnw’ using knitr
Quitting from lines 203-206 (heatmaps.Rnw) 
Error: processing vignette 'heatmaps.Rnw' failed with diagnostics:
REAL() can only be applied to a 'numeric', not a 'integer'
--- failed re-building ‘heatmaps.Rnw’

SUMMARY: processing the following files failed:
  ‘NMF-vignette.Rnw’ ‘heatmaps.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started.Rmd’ using rmarkdown
Loading required package: testthat

Attaching package: 'dplyr'

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

    matches

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 75-89 (getting_started.Rmd) 
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘getting_started.Rmd’

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

Error: Vignette re-building failed.
Execution halted
makeRules: no visible global function definition for ‘sd’
makeRules: no visible global function definition for ‘rnorm’
nodeHarvest: no visible global function definition for ‘capture.output’
nodeHarvest: no visible global function definition for ‘lm’
nodeHarvest: no visible global function definition for ‘coef’
plot.nodeHarvest: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  capture.output coef lm rgb rnorm sd
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "coef", "lm", "rnorm", "sd")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Running examples in ‘nonet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nonet_plot
> ### Title: Plot the predictions or results of nonet_ensemble
> ### Aliases: nonet_plot
> 
> ### ** Examples
> 
> # nonet_plot functionality can be explained via below example
> # Setup
> library(caret)
Loading required package: lattice
Loading required package: ggplot2
> library(nonet)
> library(ggplot2)
> 
> # Load Data
> dataframe <- data.frame(banknote_authentication[600:900, ])
> dataframe$class <- as.factor(ifelse(dataframe$class >= 1, 'Yes', 'No'))
> 
> # Spliting into train and test
> index <- createDataPartition(dataframe$class, p=0.75, list=FALSE)
> trainSet <- dataframe[ index,]
> testSet <- dataframe[-index,]
> 
> # Feature selection 
>  control <- rfeControl(functions = rfFuncs,
+   method = "repeatedcv",
+   repeats = 2,
+   verbose = FALSE)
> 
> outcomeName <- 'class'
> predictors <- c("curtosis", "entropy")
> 
> # Model Training & predictions
> banknote_rf <- train(trainSet[,predictors],trainSet[,outcomeName],method='rf')
note: only 1 unique complexity parameters in default grid. Truncating the grid to 1 .

> predictions_rf_raw <- predict.train(object=banknote_rf,testSet[,predictors],type="raw")
> 
> # Results
> nonet_eval_rf <- confusionMatrix(predictions_rf_raw,testSet[,outcomeName])
> eval_rf_df <- data.frame(nonet_eval_rf$table)
> nonet_plot(eval_rf_df$Prediction, eval_rf_df$Reference, eval_rf_df, plot_type = "point")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘nonet_ensemble_class.Rmd’ using rmarkdown
Quitting from lines 133-135 (nonet_ensemble_class.Rmd) 
Error: processing vignette 'nonet_ensemble_class.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nonet_ensemble_class.Rmd’

--- re-building ‘nonet_ensemble_clustering.Rmd’ using rmarkdown
Quitting from lines 221-222 (nonet_ensemble_clustering.Rmd) 
Error: processing vignette 'nonet_ensemble_clustering.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nonet_ensemble_clustering.Rmd’

--- re-building ‘nonet_ensemble_reg.Rmd’ using rmarkdown
Quitting from lines 128-130 (nonet_ensemble_reg.Rmd) 
Error: processing vignette 'nonet_ensemble_reg.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nonet_ensemble_reg.Rmd’

SUMMARY: processing the following files failed:
  ‘nonet_ensemble_class.Rmd’ ‘nonet_ensemble_clustering.Rmd’
  ‘nonet_ensemble_reg.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘nonmem2R-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: basic.GOF4
> ### Title: Basic 4- and 6-panel GOF
> ### Aliases: basic.GOF4 basic.GOF6
> 
> ### ** Examples
> 
> # Get path to the example files included in nonmem2R package
> file1 <- system.file("extdata", "sdtab999", package = "nonmem2R")
> sdtab<-read.table(file=file1,skip=1,header=TRUE)
> set.script.name("MyScript.R")
> ## Example 4 panel basic GOF
> basic.GOF4(subset(sdtab,DV>0),idv2="TAPD")
Error in pSummary(..., op = "max") : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: basic.GOF4 ... gtable_cbind -> Reduce -> f -> cbind_2 -> unit.pmax -> pSummary
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GOFvignette.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: gridExtra
Quitting from lines 28-30 (GOFvignette.Rmd) 
Error: processing vignette 'GOFvignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GOFvignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘rms’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Hmisc’ ‘gdata’ ‘geometry’ ‘lpSolve’ ‘psych’ ‘pwt’ ‘rms’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
additive: no visible global function definition for ‘lp’
ar.dual.dea: no visible global function definition for ‘lp’
cost.dea: no visible global function definition for ‘lp’
ddf: no visible global function definition for ‘lp’
dea: no visible global function definition for ‘lp’
direc.dea: no visible global function definition for ‘lp’
dual.dea: no visible global function definition for ‘lp’
effdea.b.f: no visible global function definition for ‘convhulln’
effdea.b.f: no visible global function definition for ‘lp’
faremalm2: no visible binding for global variable ‘Lag’
faremalm2: no visible global function definition for ‘na.omit’
int.dea: no visible global function definition for ‘lp’
lp2: no visible global function definition for ‘lp’
revenue.dea: no visible global function definition for ‘lp’
sbm.tone: no visible global function definition for ‘lp’
sbm.vrs: no visible global function definition for ‘lp’
Undefined global functions or variables:
  Lag convhulln lp na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Running examples in ‘nord-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_color_nord
> ### Title: nord color scale for ggplot2
> ### Aliases: scale_color_nord scale_colour_nord
> 
> ### ** Examples
> 
> library(ggplot2)
> library(nord)
> 
> ggplot(diamonds) +
+  geom_point(aes(x = carat, y = price, color = cut)) +
+  scale_color_nord("lumina")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Packages in Depends field not imported from:
  ‘histogram’ ‘optimx’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dnormgam: no visible global function definition for ‘qgamma’
dnormgam: no visible global function definition for ‘fft’
dnormgam: no visible global function definition for ‘dgamma’
dnormgam: no visible global function definition for ‘approx’
normgam.fit : mkdfftNormalGammaOptim : <anonymous>: no visible global
  function definition for ‘dnorm’
normgam.fit : estimation_param_normexp_RMA : max.density: no visible
  global function definition for ‘density’
normgam.fit: no visible global function definition for ‘sd’
normgam.fit: no visible global function definition for ‘median’
normgam.fit: no visible global function definition for ‘IQR’
normgam.fit: no visible global function definition for ‘optimx’
normgam.fit: no visible global function definition for ‘coef’
normgam.signal: no visible global function definition for ‘approx’
normgam.signal: no visible global function definition for ‘hist’
Undefined global functions or variables:
  IQR approx coef density dgamma dnorm fft hist median optimx qgamma sd
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "IQR", "approx", "coef", "density", "dgamma",
             "dnorm", "fft", "median", "qgamma", "sd")
to your NAMESPACE file.
ajb.norm.test: no visible global function definition for ‘rnorm’
frosini.norm.test: no visible global function definition for ‘var’
frosini.norm.test: no visible global function definition for ‘pnorm’
frosini.norm.test: no visible global function definition for ‘rnorm’
geary.norm.test: no visible global function definition for ‘rnorm’
hegazy1.norm.test: no visible global function definition for ‘var’
hegazy1.norm.test: no visible global function definition for ‘qnorm’
hegazy1.norm.test: no visible global function definition for ‘rnorm’
hegazy2.norm.test: no visible global function definition for ‘var’
hegazy2.norm.test: no visible global function definition for ‘qnorm’
hegazy2.norm.test: no visible global function definition for ‘rnorm’
jb.norm.test: no visible global function definition for ‘rnorm’
kurtosis.norm.test: no visible global function definition for ‘rnorm’
skewness.norm.test: no visible global function definition for ‘rnorm’
spiegelhalter.norm.test: no visible global function definition for
  ‘rnorm’
wb.norm.test: no visible global function definition for ‘qnorm’
wb.norm.test: no visible global function definition for ‘var’
wb.norm.test: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "pnorm", "qnorm", "rnorm", "var")
to your NAMESPACE file.
normality.test1: no visible global function definition for ‘cov.wt’
normality.test1: no visible global function definition for ‘cor’
normality.test1: no visible global function definition for ‘pnorm’
normality.test1: no visible global function definition for ‘pchisq’
normality.test2: no visible global function definition for ‘cov.wt’
normality.test2: no visible global function definition for ‘cor’
normality.test2: no visible global function definition for ‘acf’
normality.test2: no visible global function definition for ‘pnorm’
normality.test2: no visible global function definition for ‘pchisq’
whitenoise.test: no visible global function definition for ‘acf’
whitenoise.test: no visible global function definition for ‘spec.pgram’
whitenoise.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  acf cor cov.wt pchisq pnorm spec.pgram
Consider adding
  importFrom("stats", "acf", "cor", "cov.wt", "pchisq", "pnorm",
             "spec.pgram")
to your NAMESPACE file.
CIPW: no visible global function definition for ‘data’
CIPW: no visible binding for global variable ‘AtomWeight’
CIPW: no visible binding for global variable ‘MinWeight’
CIPW: no visible binding for global variable ‘OxiWeight’
CIPW.trace: no visible global function definition for ‘data’
CIPW.trace: no visible binding for global variable ‘AtomWeight’
CIPW.trace: no visible binding for global variable ‘MinWeight’
CIPW.trace: no visible binding for global variable ‘OxiWeight’
Undefined global functions or variables:
  AtomWeight MinWeight OxiWeight data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Running examples in ‘NORRRM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TASplot
> ### Title: TASplot
> ### Aliases: TASplot
> ### Keywords: plot
> 
> ### ** Examples
> 
> data(Andes)
> TASplot(Andes, color="blue")
Warning: Removed 1 rows containing missing values (geom_point).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
BoundingRA: no visible global function definition for ‘rnorm’
check_y_estimator: no visible global function definition for ‘rnorm’
genNORTARA: no visible global function definition for ‘rnorm’
genNORTARA: no visible global function definition for ‘pnorm’
valid_input_cormat: no visible global function definition for ‘rnorm’
valid_input_cormat: no visible global function definition for ‘pnorm’
valid_input_cormat: no visible global function definition for ‘cor’
y_control_estimator: no visible global function definition for ‘pnorm’
y_control_estimator: no visible global function definition for ‘cor’
y_control_estimator : <anonymous>: no visible global function
  definition for ‘cor’
y_control_estimator: no visible global function definition for ‘cov’
y_control_estimator: no visible global function definition for ‘var’
y_crude_estimator: no visible global function definition for ‘pnorm’
y_crude_estimator: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor cov pnorm rnorm var
Consider adding
  importFrom("stats", "cor", "cov", "pnorm", "rnorm", "var")
to your NAMESPACE file.
.newReportId : <anonymous>: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘nparACT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nparACT-package
> ### Title: Non-Parametric Measures of Actigraphy Data
> ### Aliases: nparACT-package nparACT
> ### Keywords: package
> 
> ### ** Examples
> 
> # example function nparACT_base
> data(sleepstudy)
> r <- nparACT_base("sleepstudy", SR = 4/60) 
Warning: Removed 24 rows containing missing values (geom_bar).
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: nparACT_base ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘NPflow-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DPMGibbsN
> ### Title: Slice Sampling of the Dirichlet Process Mixture Model with a
> ###   prior on alpha
> ### Aliases: DPMGibbsN
> 
> ### ** Examples
> 
> rm(list=ls())
> #Number of data
> n <- 500
> #n <- 2000
> set.seed(1234)
> #set.seed(123)
> #set.seed(4321)
> 
> # Sample data
> m <- matrix(nrow=2, ncol=4, c(-1, 1, 1.5, 2, 2, -2, -1.5, -2))
> p <- c(0.2, 0.1, 0.4, 0.3) # frequence des clusters
> 
> sdev <- array(dim=c(2,2,4))
> sdev[, ,1] <- matrix(nrow=2, ncol=2, c(0.3, 0, 0, 0.3))
> sdev[, ,2] <- matrix(nrow=2, ncol=2, c(0.1, 0, 0, 0.3))
> sdev[, ,3] <- matrix(nrow=2, ncol=2, c(0.3, 0.15, 0.15, 0.3))
> sdev[, ,4] <- .3*diag(2)
> c <- rep(0,n)
> z <- matrix(0, nrow=2, ncol=n)
> for(k in 1:n){
+  c[k] = which(rmultinom(n=1, size=1, prob=p)!=0)
+  z[,k] <- m[, c[k]] + sdev[, , c[k]]%*%matrix(rnorm(2, mean = 0, sd = 1), nrow=2, ncol=1)
+  #cat(k, "/", n, " observations simulated\n", sep="")
+ }
> 
>  d<-2
>  # Set parameters of G0
>  hyperG0 <- list()
>  hyperG0[["mu"]] <- rep(0,d)
>  hyperG0[["kappa"]] <- 0.001
>  hyperG0[["nu"]] <- d+2
>  hyperG0[["lambda"]] <- diag(d)/10
> 
>  # hyperprior on the Scale parameter of DPM
>  a <- 0.0001
>  b <- 0.0001
> 
>  # Number of iterations
>  N <- 30
> 
>  # do some plots
>  doPlot <- TRUE
>  nbclust_init <- 30
> 
> 
> 
>  ## Data
>  ########
>  library(ggplot2)
>  p <- (ggplot(data.frame("X"=z[1,], "Y"=z[2,]), aes(x=X, y=Y))
+        + geom_point()
+        + ggtitle("Toy example Data"))
>  p
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Packages in Depends field not imported from:
  ‘smcure’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Non-standard file/directory found at top level:
  ‘tmp.R’
nppbib: no visible global function definition for ‘read.table’
nppbib: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq read.table
Consider adding
  importFrom("stats", "pchisq")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in ‘npregfast-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.frfast
> ### Title: Visualization of 'frfast' objects with ggplot2 graphics
> ### Aliases: autoplot.frfast
> 
> ### ** Examples
> 
> 
> library(npregfast)
> library(ggplot2)
> 
> 
> data(barnacle)
> 
> # Nonparametric regression without interactions
> fit <- frfast(DW ~ RC, data = barnacle, nboot = 50) 
> autoplot(fit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘nprobust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nprobust.plot
> ### Title: Graphical Presentation of Results from 'nprobust' Package.
> ### Aliases: nprobust.plot
> 
> ### ** Examples
> 
> x   <- runif(500) 
> y   <- sin(4*x) + rnorm(500)
> est <- lprobust(y,x)
> nprobust.plot(est)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
File ‘NPsimex/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("NPsimex 0.2-1 loaded")

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

lambda.select: no visible global function definition for ‘bw.nrd0’
lambda.select: no visible global function definition for ‘bw.nrd’
lambda.select: no visible global function definition for ‘bw.ucv’
lambda.select: no visible global function definition for ‘bw.bcv’
lambda.select: no visible global function definition for ‘bw.SJ’
plot.NPsimex: no visible global function definition for ‘plot.default’
simex.H.density : simex1.est: no visible global function definition for
  ‘lm’
simex.density : simex1.est: no visible global function definition for
  ‘lm’
span.H.select: no visible global function definition for ‘density’
span.H.select : conden : <anonymous>: no visible global function
  definition for ‘dnorm’
span.select: no visible global function definition for ‘density’
span.select : conden : <anonymous>: no visible global function
  definition for ‘dnorm’
Undefined global functions or variables:
  bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv density dnorm lm plot.default
Consider adding
  importFrom("graphics", "plot.default")
  importFrom("stats", "bw.SJ", "bw.bcv", "bw.nrd", "bw.nrd0", "bw.ucv",
             "density", "dnorm", "lm")
to your NAMESPACE file.
nps.test: no visible global function definition for ‘qnorm’
nps.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘parallel’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
npst: no visible global function definition for ‘mclapply’
Undefined global functions or variables:
  mclapply
Package in Depends field not imported from: ‘mco’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boundedPolyMutation: no visible global function definition for ‘runif’
boundedSBXover: no visible global function definition for ‘runif’
nsga2R : <anonymous>: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
.mcmc.bar: no visible global function definition for ‘rnorm’
.mcmc.bar: no visible global function definition for ‘runif’
.mcmc.comb: no visible global function definition for ‘rnorm’
.mcmc.comb: no visible global function definition for ‘runif’
.mcmc.rd: no visible global function definition for ‘rnorm’
.mcmc.rd: no visible global function definition for ‘runif’
.mcmc.trans: no visible global function definition for ‘rnorm’
.mcmc.trans: no visible global function definition for ‘runif’
.simulate.bar: no visible global function definition for ‘rlnorm’
.simulate.bar: no visible global function definition for ‘rbeta’
.simulate.bar: no visible global function definition for ‘rbinom’
.simulate.comb: no visible global function definition for ‘rlnorm’
.simulate.comb: no visible global function definition for ‘rbeta’
.simulate.comb: no visible global function definition for ‘rbinom’
.simulate.rd: no visible global function definition for ‘rlnorm’
.simulate.rd: no visible global function definition for ‘rbinom’
.simulate.trans: no visible global function definition for ‘rlnorm’
.simulate.trans: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbeta rbinom rlnorm rnorm runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rlnorm", "rnorm", "runif")
to your NAMESPACE file.
Running examples in ‘nullabor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lineup
> ### Title: The line-up protocol.
> ### Aliases: lineup
> 
> ### ** Examples
> 
> library(ggplot2)
> ggplot(lineup(null_permute('mpg'), mtcars), aes(mpg, wt)) +
+   geom_point() +
+   facet_wrap(~ .sample)
decrypt("DCZ3 cImI EL UQREmEQL GG")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘distances.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 114-116 (distances.Rmd) 
Error: processing vignette 'distances.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘distances.Rmd’

--- re-building ‘nullabor-examples.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

Warning: Removed 20 rows containing missing values (geom_rect).
Quitting from lines 78-95 (nullabor-examples.Rmd) 
Error: processing vignette 'nullabor-examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nullabor-examples.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 48-49 (nullabor.Rmd) 
Error: processing vignette 'nullabor.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘nullabor.Rmd’

SUMMARY: processing the following files failed:
  ‘distances.Rmd’ ‘nullabor-examples.Rmd’ ‘nullabor.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘NutrienTrackeR.Rmd’ using rmarkdown
Quitting from lines 146-147 (NutrienTrackeR.Rmd) 
Error: processing vignette 'NutrienTrackeR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘NutrienTrackeR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘nutshell.audioscrobbler’ ‘nutshell.bbdb’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

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

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of ‘env’ to ‘envir’
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of ‘env’ to ‘envir’
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘nws/R/workerLoop.R’:
  assign("SleighName", displayName, globalenv())
  assign("SleighNws", nws, globalenv())
  assign("SleighUserNws", userNws, globalenv())
  assign("SleighRank", rank, globalenv())
  assign("SleighWorkerCount", workerCount, globalenv())
Running examples in ‘nzelect-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: parties_v
> ### Title: New Zealand political party colours
> ### Aliases: parties_v
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # Example use of parties_v in a colour scale for ggplot2
> if(require(ggplot2) & require(scales) & require(dplyr) & require(forcats)){
+ polls %>%
+     filter(MidDate > as.Date("2014-11-20") & !is.na(VotingIntention)) %>%
+     filter(Party %in% c("National", "Labour", "Green", "NZ First")) %>%
+     mutate(Party = fct_reorder(Party, VotingIntention, .desc = TRUE),
+            Party = fct_drop(Party)) %>%
+     ggplot(aes(x = MidDate, y = VotingIntention, colour = Party, linetype = Pollster)) +
+     geom_line(alpha = 0.5) +
+     geom_point(aes(shape = Pollster)) +
+     geom_smooth(aes(group = Party), se = FALSE, colour = "grey15", span = .4) +
+     scale_colour_manual(values = parties_v) +
+     scale_y_continuous("Voting intention", label = percent) +
+     scale_x_date("") +
+     facet_wrap(~Party, scales = "free_y") 
+     }
Loading required package: ggplot2
Loading required package: scales
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: forcats
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘README.Rmd’ using rmarkdown
Quitting from lines 64-82 (README.Rmd) 
Error: processing vignette 'README.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘README.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filterDepth
> ### Title: Filter price level volume.
> ### Aliases: filterDepth
> 
> ### ** Examples
> 
> 
> # obtain price level volume for a 15 minute window.
> filtered <- with(lob.data, filterDepth(depth,
+     from=as.POSIXct("2015-05-01 02:45:00.000", tz="UTC"),
+     to=as.POSIXct("2015-05-01 03:00:00.000", tz="UTC")))
> 
> # top 5 most active price levels during this 15 minute window.
> head(sort(tapply(filtered$volume, filtered$price, length),
+     decreasing=TRUE), 5)
212.35 254.57 233.78 233.77 235.58 
    96     74     64     59     58 
> 
> # extract available volume for price level 233.78, then plot it.
> level.233.78 <- filtered[filtered$price == 233.78, c("timestamp", "volume")]
> plotTimeSeries(level.233.78$timestamp, level.233.78$volume*10^-8)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘guide.Rmd’ using rmarkdown
Quitting from lines 375-382 (guide.Rmd) 
Error: processing vignette 'guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘guide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘objectSignals’
A package should be listed in only one of these fields.
Color: no visible global function definition for ‘new’
NegativeInteger: no visible global function definition for ‘new’
NonnegativeInteger: no visible global function definition for ‘new’
NonpositiveInteger: no visible global function definition for ‘new’
PositiveInteger: no visible global function definition for ‘new’
setMultipleEnum: no visible global function definition for ‘setClass’
setMultipleEnum: no visible global function definition for ‘prototype’
setNumericWithRange: no visible global function definition for
  ‘setClass’
setNumericWithRange: no visible global function definition for
  ‘prototype’
setPropertySet: no visible binding for global variable ‘extends’
setPropertySet: no visible global function definition for ‘setRefClass’
setSingleEnum: no visible global function definition for ‘setClass’
setSingleEnum: no visible global function definition for ‘prototype’
as.list,PropertySet: no visible global function definition for ‘as’
initialize,SingleEnum: no visible global function definition for
  ‘callNextMethod’
initialize,SingleEnum: no visible global function definition for ‘head’
Undefined global functions or variables:
  as callNextMethod extends head new prototype setClass setRefClass
Consider adding
  importFrom("methods", "as", "callNextMethod", "extends", "new",
             "prototype", "setClass", "setRefClass")
  importFrom("utils", "head")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’
A package should be listed in only one of these fields.
Signal.gen: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
obliclus: no visible global function definition for ‘rnorm’
obliclus: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  kmeans rnorm
Consider adding
  importFrom("stats", "kmeans", "rnorm")
to your NAMESPACE file.
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.
Packages in Depends field not imported from:
  ‘ROCR’ ‘e1071’ ‘mda’ ‘pls’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
log_wrapper: no visible global function definition for ‘glm’
log_wrapper: no visible global function definition for ‘binomial’
log_wrapper: no visible global function definition for ‘coef’
log_wrapper: no visible global function definition for ‘anova’
obliqueRF.default: no visible binding for global variable ‘predict’
obliqueRF.default: no visible global function definition for
  ‘prediction’
obliqueRF.default: no visible global function definition for
  ‘performance’
pls_wrapper: no visible global function definition for ‘kernelpls.fit’
pls_wrapper: no visible global function definition for ‘coef’
ridge_slow_wrapper: no visible global function definition for
  ‘gen.ridge’
ridge_slow_wrapper: no visible global function definition for ‘predict’
ridge_svd_wrapper: no visible global function definition for
  ‘gen.ridge’
rnd_wrapper: no visible global function definition for ‘rnorm’
svm_wrapper: no visible global function definition for ‘svm’
svm_wrapper: no visible global function definition for ‘predict’
Undefined global functions or variables:
  anova binomial coef gen.ridge glm kernelpls.fit performance predict
  prediction rnorm svm
Consider adding
  importFrom("stats", "anova", "binomial", "coef", "glm", "predict",
             "rnorm")
to your NAMESPACE file.
IBMD: no visible global function definition for ‘runif’
IBMD: no visible global function definition for ‘quantile’
RAI: no visible global function definition for ‘runif’
RAI: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile runif
Consider adding
  importFrom("stats", "quantile", "runif")
to your NAMESPACE file.
obsSensCCC: no visible global function definition for ‘coef’
obsSensCCC: no visible global function definition for ‘confint’
obsSensCCN: no visible global function definition for ‘coef’
obsSensCCN: no visible global function definition for ‘confint’
obsSensCNN: no visible global function definition for ‘coef’
obsSensCNN: no visible global function definition for ‘confint’
obsSensCNN: no visible global function definition for ‘sd’
obsSensCNN: no visible global function definition for ‘model.matrix’
obsSensNNN: no visible global function definition for ‘coef’
obsSensNNN: no visible global function definition for ‘confint’
obsSensNNN: no visible global function definition for ‘sd’
obsSensNNN: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  coef confint model.matrix sd
Consider adding
  importFrom("stats", "coef", "confint", "model.matrix", "sd")
to your NAMESPACE file.
Found the following significant warnings:
  connection.cpp:67:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
  odbc_connection.cpp:37:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
  odbc_connection.cpp:75:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/odbc.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘DBI’ ‘RJDBC’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘oddsratio-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: insert_or
> ### Title: Insert odds ratios of GAM(M)s into smoothing function
> ### Aliases: insert_or
> 
> ### ** Examples
> 
> # load data (Source: ?mgcv::gam) and fit model
> library(mgcv)
Loading required package: nlme
This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
> fit_gam <- gam(y ~ s(x0) + s(I(x1^2)) + s(x2) +
+                offset(x3) + x4, data = data_gam) # fit model
> 
> # create input objects (plot + odds ratios)
> library(oddsratio)
> plot_object <- plot_gam(fit_gam, pred = "x2", title = "Predictor 'x2'")
> or_object1 <- or_gam(data = data_gam, model = fit_gam,
+                      pred = "x2", values = c(0.099, 0.198))
> 
> # insert first odds ratios to plot
> plot_object <- insert_or(plot_object, or_object1, or_yloc = 3,
+                          values_xloc = 0.04, line_size = 0.5,
+                          line_type = "dotdash", text_size = 6,
+                          values_yloc = 0.5, arrow_col = "red")
> 
> # calculate second odds ratio
> or_object2 <- or_gam(data = data_gam, model = fit_gam, pred = "x2",
+                      values = c(0.4, 0.6))
> 
> # add or_object2 into plot
> insert_or(plot_object, or_object2, or_yloc = 2.1, values_yloc = 2,
+           line_col = "green4", text_col = "black",
+           rect_col = "green4", rect_alpha = 0.2,
+           line_alpha = 1, line_type = "dashed",
+           arrow_xloc_r = 0.01, arrow_xloc_l = -0.01,
+           arrow_length = 0.01, rect = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘function_tutorial.Rmd’ using rmarkdown
Quitting from lines 88-89 (function_tutorial.Rmd) 
Error: processing vignette 'function_tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘function_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘OECD.Rmd’ using rmarkdown
Quitting from lines 123-131 (OECD.Rmd) 
Error: processing vignette 'OECD.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘OECD.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: body_add_gg
> ### Title: add ggplot
> ### Aliases: body_add_gg
> 
> ### ** Examples
> 
> if( require("ggplot2") ){
+   doc <- read_docx()
+ 
+   gg_plot <- ggplot(data = iris ) +
+     geom_point(mapping = aes(Sepal.Length, Petal.Length))
+ 
+   if( capabilities(what = "png") )
+     doc <- body_add_gg(doc, value = gg_plot, style = "centered" )
+ 
+   print(doc, target = tempfile(fileext = ".docx") )
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: body_add_gg ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [11s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > suppressPackageStartupMessages({
  +   library(testthat)
  +   library(officer)
  +   library(magrittr)
  +   library(xml2)
  + })
  > 
  > test_check("officer")
  ── 1. Error: ggplot add (@test-docx-add.R#146)  ────────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: read_docx() %>% body_add_gg(value = gg_plot, style = "centered") at testthat/test-docx-add.R:146
  2: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  3: eval(quote(`_fseq`(`_lhs`)), env, env)
  4: eval(quote(`_fseq`(`_lhs`)), env, env)
  5: `_fseq`(`_lhs`)
  6: freduce(value, `_function_list`)
  7: withVisible(function_list[[k]](value))
  8: function_list[[k]](value)
  9: body_add_gg(., value = gg_plot, style = "centered")
  10: print(value)
  ...
  16: preDraw(x)
  17: preDraw.gTree(x)
  18: pushvpgp(x)
  19: pushgrobvp(x$vp)
  20: pushgrobvp.viewport(x$vp)
  21: pushViewport(vp, recording = FALSE)
  22: lapply(vps, push.vp, recording)
  23: FUN(X[[i]], ...)
  24: push.vp.viewport(X[[i]], ...)
  25: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 460 SKIPPED: 1 FAILED: 1
  1. Error: ggplot add (@test-docx-add.R#146) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘officer_reader.Rmd’ using rmarkdown
--- finished re-building ‘officer_reader.Rmd’

--- re-building ‘powerpoint.Rmd’ using rmarkdown
Note: zip::zip() is deprecated, please use zip::zipr() instead
Loading required package: ggplot2
Quitting from lines 235-287 (powerpoint.Rmd) 
Error: processing vignette 'powerpoint.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘powerpoint.Rmd’

--- re-building ‘word.Rmd’ using rmarkdown
Quitting from lines 146-163 (word.Rmd) 
Error: processing vignette 'word.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘word.Rmd’

SUMMARY: processing the following files failed:
  ‘powerpoint.Rmd’ ‘word.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following hidden files and directories:
  .Rapp.history
  data/.Rapp.history
  data/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RCurl’ ‘maps’
A package should be listed in only one of these fields.
mapvar: no visible global function definition for ‘data’
mapvar: no visible binding for global variable ‘state.fips’
mapvar: no visible global function definition for ‘rgb’
mapvar: no visible global function definition for ‘rect’
mapvar: no visible global function definition for ‘text’
rowScrape: no visible global function definition for ‘tail’
rowScrape: no visible global function definition for ‘head’
scrapeTable: no visible binding for global variable ‘tail’
Undefined global functions or variables:
  data head rect rgb state.fips tail text
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "rect", "text")
  importFrom("utils", "data", "head", "tail")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘OIdata/R/mapvar.R’:
  data(state.fips)
See section ‘Good practice’ in ‘?data’.
avgokmts: no visible global function definition for ‘aggregate’
downloadstn: no visible global function definition for ‘read.csv’
nearstn: no visible binding for global variable ‘okstations’
nearstn: no visible binding for global variable ‘Commissioned’
nearstn: no visible binding for global variable ‘Decommissioned’
okcurobs: no visible global function definition for ‘read.csv’
okmts: no visible binding for global variable ‘okstations’
okmts: no visible binding for global variable ‘TIME’
retrievemts: no visible global function definition for ‘read.csv’
totalprecip: no visible binding for global variable ‘TIME’
totalprecip: no visible global function definition for ‘aggregate’
vincenty: no visible global function definition for ‘runif’
Undefined global functions or variables:
  Commissioned Decommissioned TIME aggregate okstations read.csv runif
Consider adding
  importFrom("stats", "aggregate", "runif")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
OLScurve: no visible global function definition for ‘as.formula’
OLScurve: no visible global function definition for ‘na.omit’
OLScurve: no visible global function definition for ‘lm’
OLScurve: no visible global function definition for ‘predict’
OLScurve: no visible global function definition for ‘residuals’
OLScurve: no visible global function definition for ‘model.frame’
OLScurve: no visible global function definition for ‘model.matrix’
plot.OLScurve : plotOLScurve: no visible global function definition for
  ‘reshape’
print.OLScurve: no visible global function definition for ‘na.omit’
print.OLScurve: no visible global function definition for ‘model.frame’
print.OLScurve: no visible global function definition for
  ‘model.matrix’
print.OLScurve: no visible global function definition for ‘cov’
print.OLScurve: no visible global function definition for ‘cor’
print.OLScurve: no visible global function definition for ‘sd’
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for ‘devAskNewPage’
subjplot.OLScurve : plotOLScurve: no visible global function definition
  for ‘reshape’
subjplot.OLScurve : plotOLScurve : mypanel: no visible global function
  definition for ‘gray’
subjplot.OLScurve: no visible global function definition for
  ‘devAskNewPage’
Undefined global functions or variables:
  as.formula cor cov devAskNewPage gray lm model.frame model.matrix
  na.omit predict reshape residuals sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "gray")
  importFrom("stats", "as.formula", "cor", "cov", "lm", "model.frame",
             "model.matrix", "na.omit", "predict", "reshape",
             "residuals", "sd")
to your NAMESPACE file.
Running examples in ‘olsrr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ols_plot_added_variable
> ### Title: Added variable plots
> ### Aliases: ols_plot_added_variable ols_avplots
> 
> ### ** Examples
> 
> model <- lm(mpg ~ disp + hp + wt, data = mtcars)
> ols_plot_added_variable(model)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
fhcor: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor
Consider adding
  importFrom("stats", "cor")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘OmicsPLS_vignette.Rmd’ using rmarkdown
Quitting from lines 87-89 (OmicsPLS_vignette.Rmd) 
Error: processing vignette 'OmicsPLS_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘OmicsPLS_vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PCA_plot
> ### Title: Create a PCA plot
> ### Aliases: PCA_plot
> 
> ### ** Examples
> 
> PCA_plot(count_data = c57_nos2KO_mouse_countDF, metadata = c57_nos2KO_mouse_metadata,
+ variable = "Treatment", color = "Treatment", response_variable = "Metabolite")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Omu_vignette.Rmd’ using rmarkdown
Warning: Column `KEGG` joining factors with different levels, coercing to character vector
Warning: Column `KEGG` joining factors with different levels, coercing to character vector
Warning: Column `Metabolite` joining factors with different levels, coercing to character vector
Warning: Column `Rxn` joining factor and character vector, coercing into character vector
Warning: Column `Org` joining character vector and factor, coercing into character vector
Quitting from lines 264-267 (Omu_vignette.Rmd) 
Error: processing vignette 'Omu_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Omu_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Omu_vignette.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.
generate.data: no visible global function definition for ‘rbinom’
least.common.ancestor: no visible global function definition for
  ‘na.omit’
oncotree.fit : estimate.error.rates: no visible global function
  definition for ‘optim’
plot.boottree: no visible global function definition for ‘par’
plot.boottree: no visible global function definition for
  ‘dev.interactive’
plot.boottree: no visible global function definition for ‘mtext’
plot.oncotree: no visible global function definition for ‘par’
plot.oncotree: no visible global function definition for ‘xinch’
plot.oncotree: no visible global function definition for ‘yinch’
plot.oncotree: no visible global function definition for ‘lines’
plot.oncotree: no visible global function definition for ‘rect’
plot.oncotree: no visible global function definition for ‘strwidth’
plot.oncotree: no visible global function definition for ‘strheight’
plot.oncotree: no visible global function definition for ‘text’
Undefined global functions or variables:
  dev.interactive lines mtext na.omit optim par rbinom rect strheight
  strwidth text xinch yinch
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "lines", "mtext", "par", "rect", "strheight",
             "strwidth", "text", "xinch", "yinch")
  importFrom("stats", "na.omit", "optim", "rbinom")
to your NAMESPACE file.
Running examples in ‘onewaytests-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gplot
> ### Title: Box-and-Whisker Plots and Error Bars
> ### Aliases: gplot
> ### Keywords: functions
> 
> ### ** Examples
> 
> 
> library(onewaytests)
> 
> gplot(Sepal.Length ~ Species, data = iris, type = "boxplot")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
ci.prop: no visible global function definition for ‘qf’
ci.prop: no visible global function definition for ‘qnorm’
ePCP: no visible global function definition for ‘qnorm’
sevennum: no visible global function definition for ‘na.omit’
sevennum: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  na.omit qf qnorm quantile
Consider adding
  importFrom("stats", "na.omit", "qf", "qnorm", "quantile")
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: calendarPlot
> ### Title: Plot time series values in convential calendar format
> ### Aliases: calendarPlot
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> 
> # load example data from package
> data(mydata)
> 
> # basic plot
> calendarPlot(mydata, pollutant = "o3", year = 2003)
Error in unit(0.5 * showr, "strwidth", list(right)) : 
  no string supplied for 'strwidth/height' unit
Calls: calendarPlot ... strip -> do.call -> strip.default -> paste.and.draw -> unit
Execution halted
Package suggested but not available for checking: ‘openNLPmodels.en’
Error(s) in re-building vignettes:
  ...
--- re-building ‘osem-history.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

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

    date


Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Quitting from lines 57-66 (osem-history.Rmd) 
Error: processing vignette 'osem-history.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘osem-history.Rmd’

--- re-building ‘osem-intro.Rmd’ using rmarkdown
Loading required package: maps
Loading required package: maptools
Loading required package: sp
Checking rgeos availability: TRUE
Loading required package: rgeos
rgeos version: 0.4-2, (SVN revision 581)
 GEOS runtime version: 3.7.1-CAPI-1.11.1 
 Linking to sp version: 1.3-1 
 Polygon checking: TRUE 

--- finished re-building ‘osem-intro.Rmd’

--- re-building ‘osem-serialization.Rmd’ using rmarkdown
--- finished re-building ‘osem-serialization.Rmd’

SUMMARY: processing the following file failed:
  ‘osem-history.Rmd’

Error: Vignette re-building failed.
Execution halted
Df2SpLinesDf: no visible global function definition for ‘slot’
PlotTraj: no visible global function definition for ‘par’
PlotTraj: no visible global function definition for ‘grid’
PlotTraj: no visible global function definition for ‘box’
PlotTrajFreq: no visible global function definition for ‘par’
PlotTrajFreq: no visible global function definition for ‘grid’
PlotTrajFreq: no visible global function definition for
  ‘colorRampPalette’
PlotTrajFreq: no visible global function definition for ‘legend’
PlotTrajFreq: no visible binding for global variable ‘title’
PlotTrajFreq: no visible global function definition for ‘dev.off’
ReadFiles: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  box colorRampPalette dev.off grid legend par read.table slot title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.off")
  importFrom("graphics", "box", "grid", "legend", "par", "title")
  importFrom("methods", "slot")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
nlsolve: no visible global function definition for ‘optim’
nlsolve: no visible global function definition for ‘runif’
optAUC: no visible global function definition for ‘var’
Undefined global functions or variables:
  optim runif var
Consider adding
  importFrom("stats", "optim", "runif", "var")
to your NAMESPACE file.
avg2Lower: no visible global function definition for ‘optimize’
classificationError.data.frame: no visible binding for global variable
  ‘na.omit’
classificationError.data.frame: no visible global function definition
  for ‘terms’
classificationError.data.frame: no visible binding for global variable
  ‘predict’
classpredict.lda: no visible global function definition for ‘predict’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
simData: no visible global function definition for ‘var’
tnormAvg: no visible global function definition for ‘dnorm’
tnormAvg: no visible global function definition for ‘pnorm’
yapprox: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
calculate.empirical.AUC: no visible global function definition for
  ‘qnorm’
ci.AgrestiCoull: no visible global function definition for ‘qnorm’
ci.GartNam: no visible global function definition for ‘qnorm’
ci.NotTransformed: no visible global function definition for ‘qnorm’
ci.RubinSchenker: no visible global function definition for ‘qnorm’
ci.RubinSchenker: no visible global function definition for ‘plogis’
ci.RubinSchenker: no visible global function definition for ‘qlogis’
ci.exact: no visible global function definition for ‘qf’
ci.quadratic: no visible global function definition for ‘qnorm’
ci.transformed: no visible global function definition for ‘qnorm’
ci.wald: no visible global function definition for ‘qnorm’
function.MinPvalue: no visible global function definition for
  ‘chisq.test’
function.MinPvalue : PADJMS: no visible global function definition for
  ‘qnorm’
function.MinPvalue : PADJMS: no visible global function definition for
  ‘dnorm’
optimal.cutpoints.default: no visible global function definition for
  ‘na.omit’
optimal.cutpoints.formula: no visible global function definition for
  ‘terms’
plot.optimal.cutpoints: no visible global function definition for ‘par’
plot.optimal.cutpoints: no visible global function definition for
  ‘plot’
plot.optimal.cutpoints: no visible global function definition for
  ‘abline’
plot.optimal.cutpoints: no visible global function definition for
  ‘lines’
plot.optimal.cutpoints: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  abline chisq.test dnorm lines na.omit par plogis plot points qf
  qlogis qnorm terms
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot", "points")
  importFrom("stats", "chisq.test", "dnorm", "na.omit", "plogis", "qf",
             "qlogis", "qnorm", "terms")
to your NAMESPACE file.
print.optimbase: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 141-144 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: giniChart
> ### Title: Produce a ROC curve with gini coefficient title
> ### Aliases: giniChart
> ### Keywords: AUROC gini roc
> 
> ### ** Examples
> 
>   sampledata<- data.frame(val= rnorm(100) , outcome=rbinom(100,1,.8))
>   giniChart(sampledata$val,sampledata$outcome)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘index.Rmd’ using rmarkdown
--- finished re-building ‘index.Rmd’

--- re-building ‘presentation.Rmd’ using rmarkdown
Quitting from lines 39-49 (presentation.Rmd) 
Error: processing vignette 'presentation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘presentation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
calc.stress: no visible global function definition for ‘sd’
opscale: no visible global function definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ocs-vignette.Rmd’ using rmarkdown
--- finished re-building ‘ocs-vignette.Rmd’

--- re-building ‘ped-vignette.Rmd’ using rmarkdown
Warning in kinship2::pedigree(id = Pedig$Indiv, dadid = Pedig$Sire, momid = Pedig$Dam,  :
  More than 25% of the gender values are 'unknown'
Quitting from lines 119-122 (ped-vignette.Rmd) 
Error: processing vignette 'ped-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ped-vignette.Rmd’

--- re-building ‘seg-vignette.Rmd’ using rmarkdown
--- finished re-building ‘seg-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
getMinimumArborescence: no visible global function definition for
  ‘capture.output’
getMinimumCutTree: no visible global function definition for
  ‘capture.output’
getMinimumCutTree: no visible global function definition for ‘par’
getMinimumSpanningTree: no visible global function definition for
  ‘capture.output’
getShortestPathTree: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output par
Consider adding
  importFrom("graphics", "par")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Running examples in ‘optweight-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.optweight
> ### Title: Plot Dual Variables for Assessing Balance Constraints
> ### Aliases: plot.optweight plot.optweight.svy
> 
> ### ** Examples
> 
> library("cobalt")
> data("lalonde", package = "cobalt")
> 
> #Balancing covariates between treatment groups (binary)
> ow1 <- optweight(treat ~ age + educ + married +
+                 nodegree + re74, data = lalonde,
+                 tols = c(.1, .1, .1, .1, .1),
+                 estimand = "ATT")
> 
> summary(ow1) # Note the coefficient of variation
Summary of weights:

- Weight ranges:
        Min                                  Max
treated   1                   ||          1.0000
control   0 |---------------------------| 1.5946

- Units with 5 greatest weights by group:
                                           
              2      3      4      5      6
 treated      1      1      1      1      1
            604    599    589    572    569
 control 1.5946 1.5946 1.5946 1.5946 1.5946

        Coef of Var Mean Abs Dev
treated      0.0000       0.0000
control      0.5319       0.4619
overall      0.4446       0.3227

- Effective Sample Sizes:
           Control Treated
Unweighted 429.000     185
Weighted   334.408     185
>              # and effective sample size (ESS)
> 
> plot(ow1) # age has a low value, married is high
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Found the following significant warnings:
  opus_miner.cpp:90:15: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/opusminer.Rcheck/00install.out’ for details.
Agrestiind.CI: no visible global function definition for ‘qnorm’
BPexact.CI: no visible global function definition for ‘uniroot’
BPmidp.CI: no visible global function definition for ‘uniroot’
Cornfieldexact.CI: no visible global function definition for ‘uniroot’
Cornfieldmidp.CI: no visible global function definition for ‘uniroot’
Gart.CI: no visible global function definition for ‘qnorm’
Invsinh.CI: no visible global function definition for ‘qnorm’
Woolf.CI: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm uniroot
Consider adding
  importFrom("stats", "qnorm", "uniroot")
to your NAMESPACE file.
BTLboost: no visible global function definition for ‘as.formula’
design: no visible global function definition for ‘as.formula’
wide2long: no visible global function definition for ‘reshape’
Undefined global functions or variables:
  as.formula reshape
Consider adding
  importFrom("stats", "as.formula", "reshape")
to your NAMESPACE file.
'library' or 'require' call to ‘psych’ which was already attached by Depends.
  Please remove these calls from your code.
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of ‘nr’ to ‘nrow’
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of ‘nc’ to ‘ncol’
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘grid’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘orderedLasso-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: orderedLasso.path
> ### Title: Fit a path of ordered lasso models
> ### Aliases: orderedLasso.path
> 
> ### ** Examples
> 
> set.seed(3)
> n = 50
> b = c(4,3,1,0)
> p = length(b)
> x = matrix(rnorm(n*p),nrow = n)
> sigma = 5
> y = x %*% b + sigma * rnorm(n, 0, 1)
> path1 = orderedLasso.path(x,y, intercept =  FALSE, 
+         method = "Solve.QP", strongly.ordered = TRUE)
> plot(path1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ordinalClust.Rmd’ using rmarkdown

Attaching package: 'ordinalClust'

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

    plot

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 14 rows containing missing values (geom_bar).
Quitting from lines 63-82 (ordinalClust.Rmd) 
Error: processing vignette 'ordinalClust.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ordinalClust.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
boat3d: no visible global function definition for ‘rgl.cur’
boat3d: no visible global function definition for ‘open3d’
boat3d: no visible global function definition for ‘clear3d’
boat3d: no visible global function definition for ‘bg3d’
boat3d: no visible global function definition for ‘rgl.set’
boat3d: no visible global function definition for ‘triangles3d’
boat3d: no visible global function definition for ‘quads3d’
boat3d: no visible global function definition for ‘decorate3d’
boat3d: no visible global function definition for ‘scatterplot3d’
orientlm: no visible global function definition for ‘model.matrix’
orientlm: no visible global function definition for ‘lm’
Undefined global functions or variables:
  bg3d clear3d decorate3d lm model.matrix open3d quads3d rgl.cur
  rgl.set scatterplot3d triangles3d
Consider adding
  importFrom("stats", "lm", "model.matrix")
to your NAMESPACE file.
Running ‘testthat.R’ [20s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(origami)
  origami: Generalized Cross-Validation Framework
  Version: 1.0.0
  > library(data.table)
  > test_check("origami")
  ── 1. Failure: CV MSE matches previous value (@test-overall.R#36)  ─────────────
  `cv_MSE` not equal to 13.32.
  1/1 mismatches
  [1] 14.1 - 13.3 == 0.791
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 0 FAILED: 1
  1. Failure: CV MSE matches previous value (@test-overall.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
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’
  Found ‘_gfortran_st_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.
mdr.c: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
dicomTable: no visible global function definition for ‘txtProgressBar’
dicomTable: no visible global function definition for
  ‘setTxtProgressBar’
readDICOM: no visible global function definition for ‘txtProgressBar’
readDICOM: no visible global function definition for
  ‘setTxtProgressBar’
writeHeader: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  setTxtProgressBar txtProgressBar write.table
Consider adding
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘genefilter’ ‘gtools’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of ‘ties’ to ‘ties.method’
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
plot.SplineBasis: no visible global function definition for ‘matplot’
plot,SplineBasis-matrix: no visible global function definition for
  ‘matplot’
plot,SplineBasis-missing: no visible global function definition for
  ‘matplot’
Undefined global functions or variables:
  matplot
Consider adding
  importFrom("graphics", "matplot")
to your NAMESPACE file.
'library' or 'require' call to ‘polynom’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘polynom’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
chebyshev.c.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.s.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.t.polynomials: no visible global function definition for
  ‘polynomial’
chebyshev.u.polynomials: no visible global function definition for
  ‘polynomial’
gegenbauer.polynomials: no visible global function definition for
  ‘polynomial’
ghermite.h.polynomials: no visible global function definition for
  ‘polynomial’
glaguerre.polynomials: no visible global function definition for
  ‘polynomial’
hermite.h.polynomials: no visible global function definition for
  ‘polynomial’
hermite.he.polynomials: no visible global function definition for
  ‘polynomial’
jacobi.g.polynomials: no visible global function definition for
  ‘polynomial’
jacobi.p.polynomials: no visible global function definition for
  ‘polynomial’
legendre.polynomials: no visible global function definition for
  ‘polynomial’
monic.polynomials: no visible global function definition for
  ‘polynomial’
orthogonal.polynomials: no visible global function definition for
  ‘polynomial’
orthonormal.polynomials: no visible global function definition for
  ‘polynomial’
polynomial.derivatives: no visible global function definition for
  ‘deriv’
polynomial.integrals: no visible global function definition for
  ‘integral’
polynomial.values: no visible global function definition for ‘predict’
schebyshev.t.polynomials: no visible global function definition for
  ‘polynomial’
schebyshev.u.polynomials: no visible global function definition for
  ‘polynomial’
slegendre.polynomials: no visible global function definition for
  ‘polynomial’
Undefined global functions or variables:
  deriv integral polynomial predict
Consider adding
  importFrom("stats", "deriv", "predict")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘igraph’ ‘sp’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
Running examples in ‘osmplotr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_axes
> ### Title: add_axes
> ### Aliases: add_axes
> 
> ### ** Examples
> 
> bbox <- get_bbox (c (-0.13, 51.5, -0.11, 51.52))
> map <- osm_basemap (bbox = bbox, bg = "gray20")
> map <- add_osm_objects (map, london$dat_BNR, col = "gray40") 
> map <- add_axes (map)
> print (map)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-maps.Rmd’ using rmarkdown
Loading osmplotr
Data (c) OpenStreetMap contributors, ODbL 1.0. http://www.openstreetmap.org/copyright
Quitting from lines 66-68 (basic-maps.Rmd) 
Error: processing vignette 'basic-maps.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘basic-maps.Rmd’

--- re-building ‘data-maps.Rmd’ using rmarkdown
Loading osmplotr
Data (c) OpenStreetMap contributors, ODbL 1.0. http://www.openstreetmap.org/copyright
Quitting from lines 78-95 (data-maps.Rmd) 
Error: processing vignette 'data-maps.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘data-maps.Rmd’

--- re-building ‘maps-with-ocean.Rmd’ using rmarkdown
--- finished re-building ‘maps-with-ocean.Rmd’

SUMMARY: processing the following files failed:
  ‘basic-maps.Rmd’ ‘data-maps.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotBarplot
> ### Title: Creates a bar plot for a discrete (or binary) variable
> ### Aliases: PlotBarplot
> 
> ### ** Examples
> 
> data(bankData)
> bankData = PrepData(bankData, dateNm = "date", dateGp = "months", 
+                     dateGpBp = "quarters", weightNm = NULL)
The following variables will be plotted:
Numerical: age balance duration campaign pdays previous
Categorical: job marital education default housing loan contact poutcome y

> PlotBarplot(bankData, "job")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘outbreaker2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: custom_likelihoods
> ### Title: Customise likelihood functions for outbreaker
> ### Aliases: custom_likelihoods print.custom_likelihoods
> 
> ### ** Examples
> 
> 
> ## specify a null model by disabling all likelihood components
> f_null <- function(data, param) {
+   return(0.0)
+ }
> 
> null_model <- custom_likelihoods(genetic = f_null,
+                                 timing_sampling = f_null,
+                                 timing_infections = f_null,
+                                 reporting = f_null,
+                                 contact = f_null)
> 
> null_config <- list(find_import = FALSE,
+                     n_iter = 200,
+                     sample_every = 1)
> 
> ## load data
> x <- fake_outbreak
> data <- outbreaker_data(dates = x$sample, dna = x$dna, w_dens = x$w)
> 
> res_null <- outbreaker(data = data,
+                        config = null_config,
+                        likelihoods = null_model)
> 
> ## visualise ancestries to see if all transmission trees have been explored
> plot(res_null, type = "alpha")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
--- finished re-building ‘Rcpp_API.Rmd’

--- re-building ‘customisation.Rmd’ using rmarkdown
Quitting from lines 136-143 (customisation.Rmd) 
Error: processing vignette 'customisation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘customisation.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 143-146 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nipah_malaysia
> ### Title: Nipah in Malaysia and Sinagapore, 1997-1999
> ### Aliases: nipah_malaysia
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ## show first few weeks of Dengue incidence
> head(nipah_malaysia)
        date perak negeri_sembilan selangor singapore
1 1997-01-04     0               0        0         0
2 1997-01-11     1               0        0         0
3 1997-01-18     0               0        0         0
4 1997-01-25     1               0        0         0
5 1997-02-01     1               0        0         0
6 1997-02-08     0               0        0         0
> 
> ## convert data to incidence object and plot epicurve using the incidence package
> library(incidence)
> cases <- subset(nipah_malaysia, select = c("perak", "negeri_sembilan", "selangor",
+  "singapore"))
> i <- as.incidence(cases, dates = nipah_malaysia$date, interval = 7L)
> plot(i)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-to-outcomerate.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 162-176 (intro-to-outcomerate.Rmd) 
Error: processing vignette 'intro-to-outcomerate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro-to-outcomerate.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: UnivariateOutlierDetection
> ### Title: Univariate Outlier Detection(Intersection of all the methods)
> ### Aliases: UnivariateOutlierDetection
> 
> ### ** Examples
> 
> #Create dataset
> X=iris[,1:4]
> #Outlier detection
> depthout(X,cutoff=0.05)
$`Outlier Observations`
    Sepal.Length Sepal.Width Petal.Length Petal.Width
14           4.3         3.0          1.1         0.1
23           4.6         3.6          1.0         0.2
38           4.9         3.6          1.4         0.1
42           4.5         2.3          1.3         0.3
110          7.2         3.6          6.1         2.5
118          7.7         3.8          6.7         2.2
119          7.7         2.6          6.9         2.3
132          7.9         3.8          6.4         2.0

$`Location of Outlier`
[1]  14  23  38  42 110 118 119 132

$`Outlier Probability`
[1] 0.71 0.82 0.54 0.92 1.00 1.00 1.00 0.98

> UnivariateOutlierDetection(iris[,1],cutoff=.95,Method="euclidean",rnames=FALSE)
$`Outlier Observations`
[1] 7.6 7.7 7.7 7.7 7.4 7.9 7.7

$`Location of Outlier`
[1] 106 118 119 123 131 132 136

$`Scatter plot`
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
odm: no visible binding for global variable ‘sd’
odm : <anonymous>: no visible global function definition for ‘sd’
odm : <anonymous>: no visible global function definition for ‘quantile’
odm: no visible global function definition for ‘prcomp’
quant.const: no visible global function definition for ‘quantile’
quant.const.D: no visible global function definition for ‘reshape’
quant.const.D: no visible global function definition for ‘quantile’
quant.linear.D: no visible global function definition for ‘reshape’
quant.nonlin : FrankModel: no visible global function definition for
  ‘qt’
quant.nonlin : FrankModel: no visible global function definition for
  ‘pt’
quant.nonlin: no visible global function definition for ‘predict’
quant.nonlin.D: no visible global function definition for ‘reshape’
quant.nonlin.D: no visible global function definition for ‘predict’
quant.nonpar.D: no visible global function definition for ‘reshape’
rgrubbs.test: no visible global function definition for ‘sd’
plot,OutlierDM-missing: no visible binding for global variable ‘pch’
summary,OutlierDM: no visible global function definition for ‘head’
Undefined global functions or variables:
  head pch prcomp predict pt qt quantile reshape sd
Consider adding
  importFrom("stats", "prcomp", "predict", "pt", "qt", "quantile",
             "reshape", "sd")
  importFrom("utils", "head")
to your NAMESPACE file.
Running examples in ‘OutliersO3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: O3plotColours
> ### Title: Set colours for O3 plots
> ### Aliases: O3plotColours
> 
> ### ** Examples
> 
> c1 <- O3prep(stackloss, k1=2, method=c("HDo", "BAC"), tolHDo=0.025, tolBAC=0.01)
> c2 <- O3plotM(c1)
> c2$gO3
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DrawingO3plots.Rmd’ using rmarkdown
Quitting from lines 25-32 (DrawingO3plots.Rmd) 
Error: processing vignette 'DrawingO3plots.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DrawingO3plots.Rmd’

--- re-building ‘MultTolLevels.Rmd’ using rmarkdown
Quitting from lines 24-35 (MultTolLevels.Rmd) 
Error: processing vignette 'MultTolLevels.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MultTolLevels.Rmd’

--- re-building ‘PCPsO3.Rmd’ using rmarkdown
Quitting from lines 30-53 (PCPsO3.Rmd) 
Error: processing vignette 'PCPsO3.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PCPsO3.Rmd’

--- re-building ‘xtraO3methods.Rmd’ using rmarkdown
--- finished re-building ‘xtraO3methods.Rmd’

SUMMARY: processing the following files failed:
  ‘DrawingO3plots.Rmd’ ‘MultTolLevels.Rmd’ ‘PCPsO3.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: final.plot
> ### Title: Final plot
> ### Aliases: final.plot
> ### Keywords: utility
> 
> ### ** Examples
> 
> set.seed(20150605)
> x <- list(X1=rnorm(100),X2=rt(50,8),X3=rchisq(80,2))
> out <- overlap(x)
> final.plot(x,out$OV)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
ms.exec: no visible global function definition for ‘tail’
p2c2m.readstarb: no visible global function definition for ‘head’
p2c2m.readstarb: no visible binding for global variable ‘head’
rmOutlrs: no visible global function definition for ‘boxplot.stats’
rmext: no visible global function definition for ‘tail’
rowMedians: no visible binding for global variable ‘median’
stats.acrGenes: no visible binding for global variable ‘sd’
stats.perGene: no visible binding for global variable ‘sd’
statshelpers.cv: no visible binding for global variable ‘sd’
statshelpers.qntls: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  boxplot.stats head median quantile sd tail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "median", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘P2C2M_Vignette.Rnw’ using Sweave
Loading required package: P2C2M
Loading required package: ggplot2
Loading required package: grid
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: Removed 575 rows containing non-finite values
(stat_density).
Warning: Removed 2 rows containing missing values (geom_vline).
Error: processing vignette 'P2C2M_Vignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘P2C2M_Vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘P2C2M_Vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
loadCSVtoP2distance: no visible global function definition for
  ‘read.table’
p2distance : calcularDistancia: no visible binding for global variable
  ‘sd’
p2distance : ordenarVariables: no visible global function definition
  for ‘cor’
p2distance : calculoFactoresPonderacion: no visible global function
  definition for ‘lm’
p2distance: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor lm read.table sd
Consider adding
  importFrom("stats", "cor", "lm", "sd")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
p3state: no visible global function definition for ‘survfit’
p3state: no visible global function definition for ‘terms’
p3state: no visible global function definition for ‘as.formula’
p3state: no visible global function definition for ‘coxph’
p3state: no visible binding for global variable ‘na.exclude’
plot.p3state: no visible global function definition for ‘matplot’
plot.p3state: no visible global function definition for ‘devAskNewPage’
plot.p3state: no visible global function definition for ‘persp’
plot.p3state: no visible global function definition for ‘colours’
plot.p3state: no visible global function definition for
  ‘filled.contour’
Undefined global functions or variables:
  as.formula colours coxph devAskNewPage filled.contour matplot
  na.exclude persp survfit terms
Consider adding
  importFrom("grDevices", "colours", "devAskNewPage")
  importFrom("graphics", "filled.contour", "matplot", "persp")
  importFrom("stats", "as.formula", "na.exclude", "terms")
to your NAMESPACE file.
pacbpred : thetaFunc: no visible global function definition for ‘lsfit’
pacbpred : thetaFunc: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘var’
pacbpred: no visible global function definition for ‘runif’
pacbpred: no visible global function definition for ‘rnorm’
pacbpred: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  lsfit rbinom rnorm runif var
Consider adding
  importFrom("stats", "lsfit", "rbinom", "rnorm", "runif", "var")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘graph_packing.Rmd’ using rmarkdown
--- finished re-building ‘graph_packing.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 98-112 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro.Rmd’

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
Quitting from lines 70-80 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘progressive_packing.Rmd’

SUMMARY: processing the following files failed:
  ‘intro.Rmd’ ‘progressive_packing.Rmd’

Error: Vignette re-building failed.
Execution halted
Non-standard files/directories found at top level:
  ‘DESCRIPTION_EX’ ‘divers’ ‘main.R’ ‘testsDev’
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  ‘EXP’ to ‘EXPR’
[,ClassW: warning in return(x@u1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@u2): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in return(x@w1): partial argument match of ‘EXP’ to
  ‘EXPR’
[,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of ‘EXP’ to ‘EXPR’
[<-,ClassW: warning in x@u1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, u2 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@u2 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }, w1 = {: partial argument match of ‘EXP’ to
  ‘EXPR’
[<-,ClassW: warning in x@w1 <- value: partial argument match of ‘EXP’
  to ‘EXPR’
[<-,ClassW: warning in }): partial argument match of ‘EXP’ to ‘EXPR’
Running examples in ‘padr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: center_interval
> ### Title: Shift to the middle of each interval
> ### Aliases: center_interval
> 
> ### ** 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(ggplot2)
> plot_set <- emergency %>%
+   thicken("hour", "h") %>%
+   count(h) %>%
+   head(24)
> 
> ggplot(plot_set, aes(h, n)) + geom_col()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(padr)
  > 
  > test_check("padr")
  ── 1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  ── 2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y1 %>% median not equal to 14.77.
  1/1 mismatches
  [1] 14.8 - 14.8 == 0.04
  
  ── 3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#
  fill_by_function(x_df, y1, y2)$y2 %>% median not equal to 22.765.
  1/1 mismatches
  [1] 25.3 - 22.8 == 2.5
  
  ── 4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R
  `fill_by_prevalent(x_df, y1)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 584 SKIPPED: 1 FAILED: 4
  1. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#36) 
  2. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#37) 
  3. Failure: fill_by_function gives expected outcomes (@test_fill_functions.R#38) 
  4. Failure: fill_by_prevalent gives expected outcomes (@test_fill_functions.R#48) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘padr.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

pad applied on the interval: day
Quitting from lines 27-36 (padr.Rmd) 
Error: processing vignette 'padr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘padr.Rmd’

--- re-building ‘padr_custom.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

pad applied on the interval: 3 hour
Quitting from lines 19-41 (padr_custom.Rmd) 
Error: processing vignette 'padr_custom.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘padr_custom.Rmd’

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

SUMMARY: processing the following files failed:
  ‘padr.Rmd’ ‘padr_custom.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.
Running examples in ‘pagenum-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pagenum
> ### Title: Put Page Numbers on Graphics
> ### Aliases: pagenum setPagenum getPagenum setPagenum getPagenum
> 
> ### ** Examples
> 
> # base graphics
> setPagenum(1)
> plot(Sepal.Length~Sepal.Width, data=iris, col=Species, pch=19)
> pagenum()
> 
> # lattice, date
> setPagenum(getPagenum()+1) # Manual increment
> require(lattice)
Loading required package: lattice
> xyplot(Sepal.Length~Sepal.Width, data=iris, groups=Species)
> pagenum(date=TRUE)
> 
> # ggplot2, top-right
> require(ggplot2)
Loading required package: ggplot2
> ggplot(iris, aes(x=Sepal.Width, y=Sepal.Length,
+   color=Species)) + geom_point() + theme_classic()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pagenum_examples.Rmd’ using rmarkdown
Quitting from lines 74-79 (pagenum_examples.Rmd) 
Error: processing vignette 'pagenum_examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pagenum_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
CalGIF: no visible binding for global variable ‘PAGIData’
CalGIF2: no visible binding for global variable ‘PAGIData’
PAGI.Main: no visible binding for global variable ‘PAGIData’
PAGI.Main: no visible global function definition for ‘p.adjust’
PAGI.Main: no visible global function definition for ‘pt’
getclass.labels: no visible binding for global variable ‘ExampleData’
getdataset: no visible binding for global variable ‘ExampleData’
Undefined global functions or variables:
  ExampleData PAGIData p.adjust pt
Consider adding
  importFrom("stats", "p.adjust", "pt")
to your NAMESPACE file.
paired.Loc: no visible global function definition for ‘qt’
paired.Loc: no visible global function definition for ‘median’
paired.Loc: no visible global function definition for ‘qsignrank’
paired.Loc: no visible global function definition for ‘qnorm’
paired.Scale: no visible global function definition for ‘var’
paired.Scale: no visible global function definition for ‘cor’
paired.Scale: no visible global function definition for ‘qt’
paired.Scale: no visible global function definition for ‘median’
paired.Scale: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  cor median qnorm qsignrank qt var
Consider adding
  importFrom("stats", "cor", "median", "qnorm", "qsignrank", "qt", "var")
to your NAMESPACE file.
Running examples in ‘PairedData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Anorexia
> ### Title: Anorexia data from Pruzek & Helmreich (2009)
> ### Aliases: Anorexia
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Anorexia)
> 
> # Visualization of the cluster
> with(Anorexia,plot(paired(Prior,Post),type="profile"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
pairsD3: no visible global function definition for ‘gray.colors’
Undefined global functions or variables:
  gray.colors
Consider adding
  importFrom("grDevices", "gray.colors")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘CorShrink’
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘lattice’ ‘vegan’
  Please remove these calls from your code.
Running examples in ‘paletteer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot2-scales-continuous
> ### Title: Continuous scales to use for ggplot2
> ### Aliases: ggplot2-scales-continuous scale_colour_paletteer_c
> ###   scale_color_paletteer_c scale_fill_paletteer_c
> 
> ### ** Examples
> 
> 
> if (require('ggplot2')) {
+ 
+   ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, colour = Petal.Length)) +
+     geom_point() +
+     scale_colour_paletteer_c(package = "scico", palette = "tokyo")
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘palettetown-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_colour_poke
> ### Title: Add a pokemon palette to a ggplot2 colour or fill scale.
> ### Aliases: scale_color_poke scale_colour_poke scale_fill_poke
> 
> ### ** Examples
> 
> library(ggplot2)
> qplot(Sepal.Length, Sepal.Width, colour = Species, data=iris) +
+  scale_colour_poke(pokemon = 'Metapod')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bivariate_choropleths.Rmd’ using rmarkdown
--- finished re-building ‘bivariate_choropleths.Rmd’

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

--- re-building ‘pals_examples.Rmd’ using rmarkdown
Quitting from lines 314-320 (pals_examples.Rmd) 
Error: processing vignette 'pals_examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pals_examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
EAMM: no visible global function definition for ‘anova’
PAMM: no visible global function definition for ‘anova’
SSF: no visible global function definition for ‘anova’
Undefined global functions or variables:
  anova
Consider adding
  importFrom("stats", "anova")
to your NAMESPACE file.
Running examples in ‘pammtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_hazard
> ### Title: (Cumulative) (Step-) Hazard Plots.
> ### Aliases: geom_hazard GeomHazard geom_stephazard GeomStepHazard
> ###   geom_surv GeomSurv
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> library(pammtools)
> ped <- tumor[10:50,] %>% as_ped(Surv(days, status)~1)
> pam <- mgcv::gam(ped_status ~ s(tend), data=ped, family = poisson(), offset = offset)
> ndf <- make_newdata(ped, tend = unique(tend)) %>% add_hazard(pam)
> # piece-wise constant hazards
> ggplot(ndf, aes(x = tend, y = hazard)) +
+  geom_vline(xintercept = c(0, ndf$tend[c(1, (nrow(ndf)-2):nrow(ndf))]), lty = 3) +
+  geom_hline(yintercept = c(ndf$hazard[1:3], ndf$hazard[nrow(ndf)]), lty = 3) +
+  geom_stephazard() +
+  geom_step(col=2) +
+  geom_step(col=2, lty = 2, direction="vh")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
Paneldata.formula: no visible global function definition for
  ‘model.frame’
Paneldata.formula: no visible global function definition for
  ‘model.matrix’
Paneldata.formula: no visible global function definition for
  ‘model.response’
summary.Paneldata: no visible global function definition for ‘coef’
summary.Paneldata: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.frame model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.frame", "model.matrix",
             "model.response", "pt")
to your NAMESPACE file.
Running examples in ‘panelvar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stability
> ### Title: Stability of PVAR(p) model
> ### Aliases: stability stability.pvargmm stability.pvarfeols
> 
> ### ** Examples
> 
> data("ex1_dahlberg_data")
> stability_info <- stability(ex1_dahlberg_data)
> print(stability_info)
Eigenvalue stability condition:

             Eigenvalue    Modulus
1 0.5370657+0.00000000i 0.53706574
2 0.0633651+0.06442426i 0.09036383
3 0.0633651-0.06442426i 0.09036383

All the eigenvalues lie inside the unit circle.
PVAR satisfies stability condition.
> plot(stability_info)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘panelView-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: panelView
> ### Title: Panel Data Visualizations
> ### Aliases: panelView
> 
> ### ** Examples
> 
> library(panelView)
> data(panelView)
> panelView(turnout ~ policy_edr + policy_mail_in + policy_motor, 
+           data = turnout, index = c("abb","year"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: panelView
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘parallelDist.Rnw’ using Sweave
Loading required package: ggplot2

Error: processing vignette 'parallelDist.Rnw' failed with diagnostics:
 chunk 2 (label = performanceDtw) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

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

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

Error: Vignette re-building failed.
Execution halted
Warning: no function found corresponding to methods exports from ‘parallelize.dynamic’ for: ‘initialize’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to ‘package’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘methods’ ‘parallel’ ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
parallelExport: no visible global function definition for ‘setNames’
parallelGetOptions: no visible global function definition for
  ‘setNames’
parallelStop: no visible global function definition for
  ‘getFromNamespace’
stopWithJobErrorMessages: no visible global function definition for
  ‘head’
Undefined global functions or variables:
  getFromNamespace head setNames
Consider adding
  importFrom("stats", "setNames")
  importFrom("utils", "getFromNamespace", "head")
to your NAMESPACE file.
consensusMCcov: no visible global function definition for ‘var’
consensusMCcov: no visible global function definition for ‘cov’
consensusMCindep: no visible global function definition for ‘var’
semiparamDPE: no visible binding for global variable ‘var’
semiparamDPE: no visible global function definition for ‘cov’
semiparamDPE: no visible global function definition for ‘runif’
Undefined global functions or variables:
  cov runif var
Consider adding
  importFrom("stats", "cov", "runif", "var")
to your NAMESPACE file.
parallelSVM.default: no visible binding for global variable ‘na.omit’
parallelSVM.formula: no visible binding for global variable ‘na.omit’
predict.parallelSVM: no visible binding for global variable ‘predict’
Undefined global functions or variables:
  na.omit predict
Consider adding
  importFrom("stats", "na.omit", "predict")
to your NAMESPACE file.
Running examples in ‘ParallelTree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Parallel_Tree
> ### Title: Parallel_Tree
> ### Aliases: Parallel_Tree
> 
> ### ** Examples
> 
> #the msleep data can be found in the ggplot2 package
> #This plots the sleep totals for a number of different mammals, as well as the grand,
> # order and genus mean levels of sleep.
> Means_sleep<-Group_function(msleep,"sleep_total",c("order","genus"))
Warning in mean.default(data[, name_x[j]]) :
  argument is not numeric or logical: returning NA
> Parallel_Tree(Means_sleep)
Warning: Removed 83 rows containing missing values (geom_path).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Simulating-Power.Rmd’ using rmarkdown
This is lavaan 0.6-3
lavaan is BETA software! Please report any bugs.

Attaching package: 'dplyr'

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

    collapse

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 116-126 (Simulating-Power.Rmd) 
Error: processing vignette 'Simulating-Power.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Simulating-Power.Rmd’

SUMMARY: processing the following file failed:
  ‘Simulating-Power.Rmd’

Error: Vignette re-building failed.
Execution halted
.formula.make: no visible global function definition for ‘formula’
regress: no visible global function definition for ‘lm’
regress: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  formula lm model.matrix
Consider adding
  importFrom("stats", "formula", "lm", "model.matrix")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘pa.Rnw’ using Sweave
Loading required package: grid

Error: processing vignette 'pa.Rnw' failed with diagnostics:
 chunk 6 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘pa.Rnw’

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

Error: Vignette re-building failed.
Execution halted
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.
ParentOffspring: no visible global function definition for ‘axis’
ParentOffspring: no visible global function definition for ‘abline’
ParentOffspring: no visible global function definition for ‘title’
ParentOffspring: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "title")
to your NAMESPACE file.
par.nmds : nmdscalc: no visible global function definition for ‘runif’
par.nmds : nmdscalc: no visible global function definition for ‘dist’
par.nmds: no visible binding for global variable ‘j’
par.nmds: no visible global function definition for ‘cor’
par.nmds: no visible global function definition for ‘dist’
par.spp.est: no visible binding for global variable ‘i’
par.spp.est: no visible global function definition for ‘sd’
Undefined global functions or variables:
  cor dist i j runif sd
Consider adding
  importFrom("stats", "cor", "dist", "runif", "sd")
to your NAMESPACE file.
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.
Running examples in ‘parmsurvfit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_cumhaz
> ### Title: Plotting parametric cumulative hazard curves
> ### Aliases: plot_cumhaz
> 
> ### ** Examples
> 
> data("rearrest")
> plot_cumhaz(rearrest, "lnorm", time = "months")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_cumhaz ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘parmsurvfit_vig.Rmd’ using rmarkdown
Quitting from lines 55-60 (parmsurvfit_vig.Rmd) 
Error: processing vignette 'parmsurvfit_vig.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘parmsurvfit_vig.Rmd’

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

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 97-113 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: partialAR-package
> ### Title: Partial autoregression
> ### Aliases: partialAR-package partialAR
> ### Keywords: package
> 
> ### ** Examples
> 
> 
>     set.seed(1)
>     x <- rpar(1000, 0.8, 1, 0.5)  # Generate a random PAR sequence
>     fit.par(x)                  # Estimate its parameters
Fitted model:
  X[t] = M[t] + R[t]
  M[t] = 0.7314 M[t-1] + eps_M,t,  eps_M,t ~ N(0, 1.0211^2)
        (0.0571)                                 (0.0585)
  R[t] = R[t-1] + eps_R,t,         eps_R,t ~ N(0, 0.6206^2)
                                                 (0.0896)
  M_0 = 0.0000, R_0 = -0.0310
           (NA)      (1.1558)
Proportion of variance attributable to mean reversion (pvmr) = 0.7577
Negative log likelihood = 1596.99
>     plot(fit.par(x))            # Plot the estimate
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Package in Depends field not imported from: ‘nnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitOR: no visible global function definition for ‘multinom’
fitOR: no visible global function definition for ‘formula’
fitOR: no visible global function definition for ‘coef’
fitOR: no visible global function definition for ‘optim’
reportOR: no visible global function definition for ‘qnorm’
reportOR: no visible global function definition for ‘pchisq’
reportOR: no visible global function definition for ‘coef’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
Undefined global functions or variables:
  coef formula multinom optim pchisq qnorm rnorm runif
Consider adding
  importFrom("stats", "coef", "formula", "optim", "pchisq", "qnorm",
             "rnorm", "runif")
to your NAMESPACE file.
partitionMap: no visible global function definition for ‘predict’
partitionMap: no visible global function definition for ‘rnorm’
partitionMap: no visible binding for global variable ‘sd’
partitionMap: no visible global function definition for ‘sd’
partitionMap: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  predict quantile rnorm sd
Consider adding
  importFrom("stats", "predict", "quantile", "rnorm", "sd")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘partsm’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘constparty.Rnw’ using Sweave
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: RWeka
Loading required namespace: XML
Loading required package: XML
--- finished re-building ‘constparty.Rnw’

--- re-building ‘ctree.Rnw’ using Sweave
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: coin
Loading required package: survival
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: Formula

Error: processing vignette 'ctree.Rnw' failed with diagnostics:
 chunk 11 (label = party-plot) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building ‘ctree.Rnw’

--- re-building ‘mob.Rnw’ using Sweave
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm

Error: processing vignette 'mob.Rnw' failed with diagnostics:
 chunk 8 (label = PimaIndiansDiabetes-plot) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building 'mob.Rnw'

--- re-building ‘partykit.Rnw’ using Sweave
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm

Error: processing vignette 'partykit.Rnw' failed with diagnostics:
 chunk 3 (label = weather-plot0) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building ‘partykit.Rnw’

SUMMARY: processing the following files failed:
  ‘ctree.Rnw’ ‘mob.Rnw’ ‘partykit.Rnw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Conditional Inference Trees
> ### Title: Conditional Inference Trees
> ### Aliases: ctree conditionalTree
> ### Keywords: tree
> 
> ### ** Examples
> 
> 
>     set.seed(290875)
> 
>     ### regression
>     airq <- subset(airquality, !is.na(Ozone))
>     airct <- ctree(Ozone ~ ., data = airq, 
+                    controls = ctree_control(maxsurrogate = 3))
>     airct

	 Conditional inference tree with 5 terminal nodes

Response:  Ozone 
Inputs:  Solar.R, Wind, Temp, Month, Day 
Number of observations:  116 

1) Temp <= 82; criterion = 1, statistic = 56.086
  2) Wind <= 6.9; criterion = 0.998, statistic = 12.969
    3)*  weights = 10 
  2) Wind > 6.9
    4) Temp <= 77; criterion = 0.997, statistic = 11.599
      5)*  weights = 48 
    4) Temp > 77
      6)*  weights = 21 
1) Temp > 82
  7) Wind <= 10.3; criterion = 0.997, statistic = 11.712
    8)*  weights = 30 
  7) Wind > 10.3
    9)*  weights = 7 
>     plot(airct)
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MOB.Rnw’ using Sweave
Loading required package: party
Loading required package: grid
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
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

Error: processing vignette 'MOB.Rnw' failed with diagnostics:
 chunk 10 (label = BostonHousing-plot) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building 'MOB.Rnw'

--- re-building ‘party.Rnw’ using Sweave
Loading required package: party
Loading required package: grid
Loading required package: mvtnorm
Loading required package: modeltools
Loading required package: stats4
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: coin
Loading required package: survival

Error: processing vignette 'party.Rnw' failed with diagnostics:
 chunk 12 (label = party-plot) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building ‘party.Rnw’

SUMMARY: processing the following files failed:
  ‘MOB.Rnw’ ‘party.Rnw’

Error: Vignette re-building failed.
Execution halted
parviol: no visible global function definition for ‘plot.new’
parviol: no visible global function definition for ‘plot.window’
parviol: no visible global function definition for ‘title’
parviol: no visible global function definition for ‘lines’
parviol: no visible global function definition for ‘text’
parviol: no visible global function definition for ‘rgb’
selecto: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot.new plot.window rgb text title
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "lines", "plot.new", "plot.window", "text",
             "title")
to your NAMESPACE file.
Running examples in ‘PASenseWear-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Heatmap
> ### Title: Heatmap
> ### Aliases: Heatmap
> 
> ### ** Examples
> 
> #Continuous METs
> Heatmap(sampledata);
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘passport-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: country_format
> ### Title: Construct formatter function to format country codes as country
> ###   names
> ### Aliases: country_format
> 
> ### ** Examples
> 
> if (require(ggplot2, quietly = TRUE)) {
+     ggplot(data.frame(country = c("KOR", "MMR", "TWN", "COG"),
+                       y = 1:4),
+            aes(x = country, y = y)) +
+         geom_col() +
+         scale_x_discrete(labels = country_format(from = "iso3c"))
+ }
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘passport.Rmd’ using rmarkdown
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.4.0  
✔ readr   1.3.1       ✔ forcats 0.4.0  
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Parsed with column specification:
cols(
  Athlete = col_character(),
  Country = col_character(),
  NOC = col_character(),
  Gender = col_character(),
  Sport = col_character(),
  Discipline = col_character(),
  Event = col_character(),
  Event_gender = col_character(),
  Olympic_Record = col_character(),
  Olympic_Record_Type = col_character()
)
Quitting from lines 121-146 (passport.Rmd) 
Error: processing vignette 'passport.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘passport.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘ape’ ‘caper’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
conch: no visible global function definition for ‘read.tree’
conch: no visible global function definition for ‘reorder’
conch: no visible global function definition for ‘read.nexus’
conch: no visible global function definition for ‘.compressTipLabel’
conch: no visible global function definition for ‘drop.tip’
conch: no visible global function definition for ‘extract.clade’
conch: no visible global function definition for ‘which.edge’
conch: no visible global function definition for ‘write.tree’
pastis_main: no visible global function definition for ‘combn’
read_input: no visible global function definition for ‘read.tree’
read_input: no visible global function definition for ‘reorder’
read_input: no visible global function definition for ‘read.csv’
read_input: no visible global function definition for ‘read.dna’
Undefined global functions or variables:
  .compressTipLabel combn drop.tip extract.clade read.csv read.dna
  read.nexus read.tree reorder which.edge write.tree
Consider adding
  importFrom("stats", "reorder")
  importFrom("utils", "combn", "read.csv")
to your NAMESPACE file.
Running examples in ‘PASWR2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AGGRESSION
> ### Title: TV and Behavior
> ### Aliases: AGGRESSION
> ### Keywords: datasets
> 
> ### ** Examples
> 
> AL <- reshape(AGGRESSION, varying = c("violence", "noviolence"), 
+ v.names = "aggression", direction = "long")
> ggplot(data = AL, aes(x = factor(time), y = aggression, fill = factor(time))) + 
+ geom_boxplot() + labs(x = "") + scale_x_discrete(breaks = c(1, 2), 
+ labels = c("Violence", "No Violence")) + guides(fill = FALSE) + scale_fill_brewer()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘e1071’
  Please remove these calls from your code.
SweaveAll: no visible global function definition for ‘file_test’
texi2dvi: no visible global function definition for ‘file_test’
Undefined global functions or variables:
  file_test
Consider adding
  importFrom("utils", "file_test")
to your NAMESPACE file.
Package in Depends field not imported from: ‘datautils’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
animatePatches: no visible global function definition for
  ‘getTimestamp’
animatePatches: no visible global function definition for ‘getElapsed’
colorPlot: no visible global function definition for ‘layout’
colorPlot: no visible global function definition for ‘par’
colorPlot: no visible global function definition for ‘image’
colorPlot: no visible global function definition for ‘axis’
drawPatches: no visible global function definition for ‘rgb’
getInterRGB: no visible global function definition for ‘col2rgb’
getInterRGB: no visible global function definition for ‘rgb’
plotGmmOverlay: no visible global function definition for ‘rgb’
plotGreyPatches : squarepatch: no visible global function definition
  for ‘rgb’
plotGreyPatches : trianglepatch: no visible global function definition
  for ‘rgb’
Undefined global functions or variables:
  axis col2rgb getElapsed getTimestamp image layout par rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
  importFrom("graphics", "axis", "image", "layout", "par")
to your NAMESPACE file.
Package in Depends field not imported from: ‘shape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
arrow: no visible global function definition for ‘arrows’
draw: no visible global function definition for ‘rect’
draw: no visible global function definition for ‘text’
draw: no visible global function definition for ‘plotellipse’
wall: no visible global function definition for ‘plot.new’
wall: no visible global function definition for ‘plot.window’
Undefined global functions or variables:
  arrows plot.new plot.window plotellipse rect text
Consider adding
  importFrom("graphics", "arrows", "plot.new", "plot.window", "rect",
             "text")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘pathfindr_manual_exec.Rmd’ using rmarkdown
--- finished re-building ‘pathfindr_manual_exec.Rmd’

--- re-building ‘pathfindr_vignette.Rmd’ using rmarkdown
Quitting from lines 168-185 (pathfindr_vignette.Rmd) 
Error: processing vignette 'pathfindr_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pathfindr_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘plspm’ ‘tester’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘patternplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: imagebar
> ### Title: Plot a bar chart with bars filled with png and jpeg images.
> ### Aliases: imagebar
> 
> ### ** Examples
> 
> library(patternplot)
> library(jpeg)
> 
> #http://all-free-download.com/free-vector/modern-seamless-pattern.html
> childcare<-readJPEG(system.file("img", "childcare.jpg", package="patternplot"))
> food<-readJPEG(system.file("img", "food.jpg", package="patternplot"))
> housing <-readJPEG(system.file("img", "housing.jpg", package="patternplot"))
> 
> #Example 1
> data <- read.csv(system.file("extdata", "monthlyexp.csv", package="patternplot"))
> data<-data[which(data$Location=='City 1'),]
> x<-factor(data$Type, c('Housing', 'Food',  'Childcare'))
> y<-data$Amount
> pattern.type<-list(housing, food, childcare)
> imagebar(data,x, y,group=NULL,pattern.type=pattern.type,
+          frame.color=c('darkred', 'darkgreen', 'orange'),
+          ylab='Monthly Expenses, Dollars')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘patternplot-intro.Rmd’ using docco_linear
Quitting from lines 28-47 (patternplot-intro.Rmd) 
Error: processing vignette 'patternplot-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘patternplot-intro.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ba_plot
> ### Title: Create a Bland-Altman plot
> ### Aliases: ba_plot
> 
> ### ** Examples
> 
> data(ex_data, package = "PAutilities")
> 
> # Reduce the number of data points (for illustration purposes) by isolating
> # the 150 largest cases
> 
> illustration_threshold <-
+     quantile(ex_data$Axis1, probs = 1 - (150 / nrow(ex_data)))
> ex_data <- ex_data[ex_data$Axis1 > illustration_threshold, ]
> 
> # Generate the plot
> my_ba <- ba_plot(
+     ex_data,
+     "(Axis1 + Axis3) / 2",
+     "Axis1 - Axis3",
+     "mean(Axis1, Axis3)",
+     "Axis1 - Axis3"
+ )
> 
> my_ba
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
add_noise: no visible global function definition for ‘rnorm’
estimate_risk_dream6 : <anonymous>: no visible global function
  definition for ‘var’
generate_sample: no visible global function definition for ‘rnorm’
generate_sample: no visible global function definition for ‘runif’
sample_function: no visible global function definition for ‘runif’
sample_function : <anonymous>: no visible global function definition
  for ‘var’
sample_function_multi_mod_weight: no visible global function definition
  for ‘runif’
sample_function_multi_mod_weight : <anonymous>: no visible global
  function definition for ‘var’
sample_function_single_mod: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  rnorm runif var
Consider adding
  importFrom("stats", "rnorm", "runif", "var")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘pauwels2014.Rnw’ using Sweave
Loading required package: deSolve
Loading required package: ggplot2
Error: processing vignette 'pauwels2014.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pauwels2014.Rnw’

SUMMARY: processing the following file failed:
  ‘pauwels2014.Rnw’

Error: Vignette re-building failed.
Execution halted
Warning: no function found corresponding to methods exports from ‘PAWL’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘foreach’ ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘foreach’ ‘ggplot2’ ‘methods’ ‘mvtnorm’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘PBImisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flu
> ### Title: Numbers of flu occurences in the 10 years period in the Poland.
> ### Aliases: flu
> ### Keywords: flu
> 
> ### ** Examples
> 
> data(flu)
> library(ggplot2)
> subflu = flu[flu$region=="Mazowieckie", ]
> # linear scale
> qplot(date, inception.rate,data=subflu, geom="line")+scale_y_sqrt() +theme_bw()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
dotplot.pbo: no visible global function definition for ‘reorder’
pbo: no visible global function definition for ‘%dopar%’
pbo: no visible global function definition for ‘foreach’
pbo: no visible global function definition for ‘lm’
xyplot.pbo: no visible global function definition for ‘ecdf’
xyplot.pbo: no visible global function definition for ‘doubleYScale’
xyplot.pbo: no visible global function definition for ‘reorder’
Undefined global functions or variables:
  %dopar% doubleYScale ecdf foreach lm reorder
Consider adding
  importFrom("stats", "ecdf", "lm", "reorder")
to your NAMESPACE file.
a_get_native: no visible global function definition for ‘par’
a_get_relative: no visible global function definition for ‘par’
brackets: no visible global function definition for ‘par’
brackets: no visible global function definition for ‘dist’
brackets: no visible global function definition for ‘lines’
Undefined global functions or variables:
  dist lines par
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "dist")
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘pcadapt.Rmd’ using rmarkdown
Quitting from lines 67-68 (pcadapt.Rmd) 
Error: processing vignette 'pcadapt.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pcadapt.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CEPlot
> ### Title: Cumulative eigenvalue plot
> ### Aliases: CEPlot
> 
> ### ** Examples
> 
> #load iris data
> data(iris)
> 
> #Define grouping variable, grouping the observations by whether their species is
> #Setosa or not
> iris$group <- "setosa"
> iris$group[iris$Species != "setosa"] <- "non-setosa"
> iris$Species <- NULL
> 
> ## Not run: 
> ##D #make a PCADSC object, splitting the data by "group"
> ##D irisPCADSC <- PCADSC(iris, "group")
> ##D 
> ##D #make a partial PCADSC object from iris and fill out CEInfo in the next call
> ##D irisPCADSC2 <- PCADSC(iris, "group", doCE = FALSE)
> ##D irisPCADSC2 <- doCE(irisPCADSC2)
> ##D 
> ##D #make a CE plot
> ##D CEPlot(irisPCADSC)
> ##D CEPlot(irisPCADSC2)
> ## End(Not run)
> 
> #Only do CE information and use less resamplings for a faster runtime
> irisPCADSC_fast <- PCADSC(iris, "group", doAngle = FALSE, doChroma = FALSE,
+   B = 1000)
> CEPlot(irisPCADSC_fast)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
src/Makevars.win: incorrect macro SHLIB_OPENMP_CFLAGS included in PKG_CXXFLAGS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Running examples in ‘pcalg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: backdoor
> ### Title: Find Set Satisfying the Generalized Backdoor Criterion (GBC)
> ### Aliases: backdoor
> ### Keywords: multivariate models graphs
> 
> ### ** Examples
> 
> #####################################################################
> ##DAG
> #####################################################################
> ## Simulate the true DAG
> set.seed(123)
> p <- 7
> myDAG <- randomDAG(p, prob = 0.2) ## true DAG
> 
> ## Extract the adjacency matrix of the true DAG
> true.amat <- (amat <- as(myDAG, "matrix")) != 0 # TRUE/FALSE <==> 1/0
> print.table(1*true.amat, zero.=".") # "visualization"
  1 2 3 4 5 6 7
1 . . . 1 . . .
2 . . . 1 . . 1
3 . . . . . . 1
4 . . . . 1 . .
5 . . . . . . 1
6 . . . . . . .
7 . . . . . . .
> 
> ## Compute set satisfying the GBC:
> backdoor(true.amat, 5, 7, type="dag")
[1] 4
> ## Don't show: 
> stopifnot(backdoor(true.amat, 5, 7, type="dag") == 3)
Error: backdoor(true.amat, 5, 7, type = "dag") == 3 is not TRUE
Execution halted
PCDReg.wf: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
defineTasks: no visible global function definition for ‘par’
defineTasks: no visible global function definition for ‘abline’
plotCorCoeff: no visible global function definition for ‘hist’
plotCorCoeff: no visible global function definition for ‘plot.new’
plotCorCoeff: no visible global function definition for ‘plot.window’
plotCorCoeff: no visible global function definition for ‘rect’
plotCorCoeff: no visible global function definition for ‘axis’
plotCorCoeff: no visible global function definition for ‘title’
plotCorCoeff: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline axis hist legend par plot.new plot.window rect title
Consider adding
  importFrom("graphics", "abline", "axis", "hist", "legend", "par",
             "plot.new", "plot.window", "rect", "title")
to your NAMESPACE file.
Running examples in ‘PCMBase-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PCMTrajectory
> ### Title: Generate a trajectory for the mean in one regime of a PCM
> ### Aliases: PCMTrajectory
> 
> ### ** Examples
> 
> set.seed(1, kind = "Mersenne-Twister", normal.kind = "Inversion")
> 
> # a Brownian motion model with one regime
> modelOU <- PCM(model = PCMDefaultModelTypes()['F'], k = 2)
> 
> # assign the model parameters at random: this will use uniform distribution
> # with boundaries specified by PCMParamLowerLimit and PCMParamUpperLimit
> # We do this in two steps:
> # 1. First we generate a random vector. Note the length of the vector equals
> # PCMParamCount(modelBM).
> 
> randomParams <- PCMParamRandomVecParams(
+   modelOU, PCMNumTraits(modelOU), PCMNumRegimes(modelOU))
> # 2. Then we load this random vector into the model.
> PCMParamLoadOrStore(
+   modelOU,
+   randomParams,
+   0, PCMNumTraits(modelBM), PCMNumRegimes(modelBM), load = TRUE)
[1] 11
> 
> # let's plot the trajectory of the model starting from X0 = c(0,0)
> PCMTrajectory(
+   model = modelOU,
+   X0 = c(0, 0),
+   doPlot2D = TRUE)
Warning: Removed 98 rows containing non-finite values (stat_ellipse).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘pcr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pcr_analyze
> ### Title: Apply qPCR analysis methods
> ### Aliases: pcr_analyze
> 
> ### ** Examples
> 
> # applying the delta delta ct method
> ## locate and read raw ct data
> fl <- system.file('extdata', 'ct1.csv', package = 'pcr')
> ct1 <- readr::read_csv(fl)
Parsed with column specification:
cols(
  c_myc = col_double(),
  GAPDH = col_double()
)
> 
> # add grouping variable
> group_var <- rep(c('brain', 'kidney'), each = 6)
> 
> # calculate all values and errors in one step
> pcr_analyze(ct1,
+             group_var = group_var,
+             reference_gene = 'GAPDH',
+             reference_group = 'brain',
+             method = 'delta_delta_ct')
Joining, by = c("group", "gene")
Joining, by = c("group", "gene", "calibrated")
Joining, by = c("group", "gene")
# A tibble: 2 x 8
  group  gene  normalized calibrated relative_expression  error lower upper
  <chr>  <chr>      <dbl>      <dbl>               <dbl>  <dbl> <dbl> <dbl>
1 brain  c_myc       6.86       0                   1    0.174  0.886  1.13
2 kidney c_myc       4.36      -2.50                5.64 0.0954 5.28   6.02
> 
> # return a plot
> pcr_analyze(ct1,
+             group_var = group_var,
+             reference_gene = 'GAPDH',
+             reference_group = 'brain',
+             method = 'delta_delta_ct',
+             plot = TRUE)
Joining, by = c("group", "gene")
Joining, by = c("group", "gene", "calibrated")
Joining, by = c("group", "gene")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘qpcr_analysis.Rmd’ using rmarkdown
Parsed with column specification:
cols(
  c_myc = col_double(),
  GAPDH = col_double()
)
Joining, by = c("group", "gene")
Joining, by = c("group", "gene", "calibrated")
Joining, by = c("group", "gene")
Parsed with column specification:
cols(
  c_myc = col_double(),
  GAPDH = col_double()
)

Attaching package: 'cowplot'

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

    ggsave

Parsed with column specification:
cols(
  c_myc = col_double(),
  GAPDH = col_double()
)
Joining, by = c("group", "gene")
Joining, by = "gene"
Quitting from lines 412-421 (qpcr_analysis.Rmd) 
Error: processing vignette 'qpcr_analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘qpcr_analysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
PdofCSGt.bootstrap5: no visible global function definition for ‘rnorm’
PdofCSGt.bootstrap5: no visible global function definition for ‘rt’
PdofCSt.T1or2: no visible global function definition for ‘combn’
PofCSGt: no visible global function definition for ‘combn’
PofCSLt.bootstrap5: no visible global function definition for ‘rnorm’
PofCSLt.bootstrap5: no visible global function definition for ‘rt’
PofCSt: no visible global function definition for ‘pnorm’
tindep: no visible binding for global variable ‘var’
tindep: no visible global function definition for ‘pt’
Undefined global functions or variables:
  combn pnorm pt rnorm rt var
Consider adding
  importFrom("stats", "pnorm", "pt", "rnorm", "rt", "var")
  importFrom("utils", "combn")
to your NAMESPACE file.
pdist: no visible global function definition for ‘dist’
pdist: no visible global function definition for ‘new’
Undefined global functions or variables:
  dist new
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dist")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error(s) in re-building vignettes:
  ...
--- re-building ‘PDQutils.Rnw’ using knitr
Quitting from lines 734-750 (PDQutils.Rnw) 
Error: processing vignette 'PDQutils.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PDQutils.Rnw’

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

Error: Vignette re-building failed.
Execution halted
band.chol.cv: no visible global function definition for ‘cov’
pdsoft.cv: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘depth_ranktests.Rmd’ using rmarkdown
--- finished re-building ‘depth_ranktests.Rmd’

--- re-building ‘wavelet_est_clust.Rmd’ using rmarkdown
Quitting from lines 257-258 (wavelet_est_clust.Rmd) 
Error: processing vignette 'wavelet_est_clust.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘wavelet_est_clust.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binSum
> ### Title: binSum
> ### Aliases: binSum
> 
> ### ** Examples
> 
> ## bins of size 3bp.
> ## -1-   -3-   -5-
> ##    -2-   -4-
> ## 123456789012345 base index.
> ## --2---
> ##       --1-
> ##           --0-------
> ## Coverage profile.
> profile <- data.frame(chromStart=as.integer(c(0, 6, 10)),
+                       chromEnd=as.integer(c(6, 10, 10000)),
+                       count=as.integer(c(2, 1, 0)))
> library(PeakSegJoint)
> bins <- binSum(profile,
+                bin.chromStart=0L,
+                bin.size=3L,
+                n.bins=2000L)
> library(ggplot2)
> bases <- data.frame(position=1:15, base="N")
> ggplot()+
+   ylab("")+
+   geom_text(aes(position, 0, label=base),
+             data=bases)+
+   geom_step(aes(chromStart+0.5, count, color=what),
+             data=data.frame(profile, what="profile"),
+             size=2)+
+   geom_step(aes(chromStart+0.5, count, color=what),
+             data=data.frame(bins, what="bin total"))+
+   geom_step(aes(chromStart+0.5, mean, color=what),
+             data=data.frame(bins, what="bin mean"))+
+   coord_cartesian(xlim=c(0, max(bases$position)))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
The following files should probably not be installed:
  ‘addendum.tex’, ‘slplot.tex’, ‘table1.tex’, ‘table3.tex’

Consider the use of a .Rinstignore file: see ‘Writing R Extensions’,
or move the vignette sources from ‘inst/doc’ to ‘vignettes’.
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.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’ ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AssoTestProc: no visible global function definition for ‘rbinom’
AssoTestProc: no visible global function definition for ‘princomp’
AssoTestProc: no visible global function definition for ‘loadings’
AssoTestProc: no visible global function definition for ‘lm’
CNVtypeAnay: no visible global function definition for ‘cov’
ClusProc: no visible global function definition for ‘princomp’
ClusProc: no visible global function definition for ‘prcomp’
ClusProc0: no visible global function definition for ‘kmeans’
ClusProc0: no visible global function definition for ‘cov’
Inde: no visible global function definition for ‘lm’
Inde: no visible global function definition for ‘var’
STE: no visible global function definition for ‘pchisq’
STIM: no visible global function definition for ‘cor’
STIM: no visible global function definition for ‘pchisq’
plot.clust: no visible global function definition for ‘princomp’
plot.clust: no visible global function definition for ‘loadings’
plot.clust: no visible global function definition for ‘qplot’
plot.clust: no visible global function definition for ‘geom_histogram’
plot.clust: no visible global function definition for ‘aes_string’
plot.clust: no visible global function definition for ‘barplot’
plot.clust: no visible global function definition for ‘title’
plot.clust: no visible global function definition for ‘mtext’
plot.clust: no visible global function definition for ‘text’
Undefined global functions or variables:
  aes_string barplot cor cov geom_histogram kmeans lm loadings mtext
  pchisq prcomp princomp qplot rbinom text title var
Consider adding
  importFrom("graphics", "barplot", "mtext", "text", "title")
  importFrom("stats", "cor", "cov", "kmeans", "lm", "loadings", "pchisq",
             "prcomp", "princomp", "rbinom", "var")
to your NAMESPACE file.
Running examples in ‘PedCNV-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.clust
> ### Title: Plots clustering result
> ### Aliases: plot.clust
> 
> ### ** Examples
> 
> # Fit the data under the given clustering numbers
> clus.fit <- ClusProc(signal=signal,N=2:6,varSelection='PC.9')
The first 5 principal components are used.
The logliklihood for signal model is -1663.629 when clustering number is 2.
The logliklihood for signal model is -1477.954 when clustering number is 3.
The logliklihood for signal model is -1394.682 when clustering number is 4.
The logliklihood for signal model is -1342.043 when clustering number is 5.
The logliklihood for signal model is -1282.491 when clustering number is 6.
> plot(clus.fit,type='histo')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Package in Depends field not imported from: ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
blup: no visible global function definition for ‘model.matrix’
blup: no visible global function definition for ‘model.frame’
blup: no visible global function definition for ‘read.table’
calcG: no visible global function definition for ‘as’
gblup: no visible global function definition for ‘model.matrix’
gblup: no visible global function definition for ‘model.frame’
Undefined global functions or variables:
  as model.frame model.matrix read.table
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "model.frame", "model.matrix")
  importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
PEMM_fun : find.lambda: no visible global function definition for
  ‘optimize’
PEMM_fun: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optimize
Consider adding
  importFrom("stats", "cov", "optimize")
to your NAMESPACE file.
Running examples in ‘penaltyLearning-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ROChange
> ### Title: ROC curve for changepoints
> ### Aliases: ROChange
> 
> ### ** Examples
> 
> 
> library(penaltyLearning)
> data(neuroblastomaProcessed, envir=environment())
> ## Get incorrect labels data for one profile.
> pid <- 11
> pro.errors <- neuroblastomaProcessed$errors[profile.id==pid,]
> ## Get the feature that corresponds to the BIC penalty = log(n),
> ## meaning log(penalty) = log(log(n)).
> chr.vec <- paste(c(1:4, 11, 17))
> pid.names <- paste0(pid, ".", chr.vec)
> BIC.feature <- neuroblastomaProcessed$feature.mat[pid.names, "log2.n"]
> pred <- data.table(pred.log.lambda=BIC.feature, chromosome=chr.vec)
> result <- ROChange(pro.errors, pred, "chromosome")
> library(ggplot2)
> ## Plot the ROC curves.
> ggplot()+
+   geom_path(aes(FPR, TPR), data=result$roc)+
+   geom_point(aes(FPR, TPR, color=threshold), data=result$thresholds, shape=1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
create.data: no visible global function definition for ‘rexp’
create.data: no visible global function definition for ‘runif’
create.data: no visible global function definition for ‘rbinom’
opt.splitval: no visible global function definition for ‘na.omit’
opt2D : opt.both: no visible global function definition for ‘optim’
Undefined global functions or variables:
  na.omit optim rbinom rexp runif
Consider adding
  importFrom("stats", "na.omit", "optim", "rbinom", "rexp", "runif")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘CoxBoost’ ‘codetools’ ‘locfit’ ‘penalized’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
complexity.LASSO: no visible global function definition for ‘profL1’
complexity.ipec.CoxBoost: no visible global function definition for
  ‘CoxBoost’
complexity.ipec.CoxBoost: no visible global function definition for
  ‘locfit’
complexity.mincv.CoxBoost: no visible global function definition for
  ‘cv.CoxBoost’
complexity.ripec.CoxBoost: no visible global function definition for
  ‘CoxBoost’
complexity.ripec.CoxBoost: no visible global function definition for
  ‘locfit’
extract: no visible global function definition for ‘findGlobals’
fit.CoxBoost: no visible global function definition for ‘CoxBoost’
fit.LASSO: no visible global function definition for ‘penalized’
Undefined global functions or variables:
  CoxBoost cv.CoxBoost findGlobals locfit penalized profL1
Running examples in ‘peptider-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: detect
> ### Title: Detection probability in a single library of size N
> ### Aliases: detect
> 
> ### ** Examples
> 
> summary(detect())
    Min.  1st Qu.   Median     Mean  3rd Qu.     Max. 
0.003628 0.061622 0.242643 0.360004 0.602151 0.999647 
> 
> require(ggplot2)
Loading required package: ggplot2
> lib <- libscheme("NNK", 7)
> qplot(detect(lib, size=10^8), weight=di, geom="histogram", data=lib$data)
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘perc_calculator_example.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 198-205 (perc_calculator_example.Rmd) 
Error: processing vignette 'perc_calculator_example.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘perc_calculator_example.Rmd’

--- re-building ‘perc_warning_example.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 ‘perc_warning_example.Rmd’

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

Error: Vignette re-building failed.
Execution halted
performance.curves.plot: no visible global function definition for
  ‘postscript’
performance.curves.plot: no visible global function definition for
  ‘axis’
performance.curves.plot: no visible global function definition for
  ‘lines’
performance.curves.plot: no visible global function definition for
  ‘legend’
performance.curves.plot: no visible global function definition for
  ‘grid’
performance.curves.plot: no visible global function definition for
  ‘dev.off’
precision.recall.curves.plot: no visible global function definition for
  ‘postscript’
precision.recall.curves.plot: no visible global function definition for
  ‘axis’
precision.recall.curves.plot: no visible global function definition for
  ‘lines’
precision.recall.curves.plot: no visible global function definition for
  ‘legend’
precision.recall.curves.plot: no visible global function definition for
  ‘grid’
precision.recall.curves.plot: no visible global function definition for
  ‘dev.off’
Undefined global functions or variables:
  axis dev.off grid legend lines postscript
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "axis", "grid", "legend", "lines")
to your NAMESPACE file.
Package suggested but not available for checking: ‘dendextendRcpp’
permalgorithm: no visible global function definition for ‘is’
Undefined global functions or variables:
  is
Consider adding
  importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
ksample.pclt: no visible global function definition for ‘pchisq’
pCI: no visible global function definition for ‘qbeta’
permKS.formula: no visible global function definition for ‘terms’
permTREND.default: no visible global function definition for ‘cor’
permTREND.formula: no visible global function definition for ‘terms’
permTS.formula: no visible global function definition for ‘terms’
trend.pclt: no visible global function definition for ‘pnorm’
twosample.pclt: no visible global function definition for ‘pnorm’
twosample.pclt: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cor pchisq pnorm qbeta terms
Consider adding
  importFrom("stats", "cor", "pchisq", "pnorm", "qbeta", "terms")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘permutes.Rmd’ using rmarkdown
Quitting from lines 125-126 (permutes.Rmd) 
Error: processing vignette 'permutes.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘permutes.Rmd’

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

Error: Vignette re-building failed.
Execution halted
hasMethod: no visible global function definition for ‘getS3method’
Undefined global functions or variables:
  getS3method
Consider adding
  importFrom("utils", "getS3method")
to your NAMESPACE file.
Running examples in ‘personalized-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: check.overlap
> ### Title: Check propensity score overlap
> ### Aliases: check.overlap
> 
> ### ** Examples
> 
> library(personalized)
> 
> set.seed(123)
> n.obs  <- 250
> n.vars <- 15
> x <- matrix(rnorm(n.obs * n.vars, sd = 3), n.obs, n.vars)
> 
> 
> # simulate non-randomized treatment
> xbetat   <- 0.25 + 0.5 * x[,11] - 0.5 * x[,12]
> trt.prob <- exp(xbetat) / (1 + exp(xbetat))
> trt01    <- rbinom(n.obs, 1, prob = trt.prob)
> 
> # create function for fitting propensity score model
> prop.func <- function(x, trt)
+ {
+     # fit propensity score model
+     propens.model <- cv.glmnet(y = trt,
+                                x = x, family = "binomial")
+     pi.x <- predict(propens.model, s = "lambda.min",
+                     newx = x, type = "response")[,1]
+     pi.x
+ }
> 
> check.overlap(x = x,
+               trt = trt01,
+               propensity.func = prop.func)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘usage_of_the_personalized_package.Rmd’ using rmarkdown
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16

Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-28. For overview type 'help("mgcv-package")'.
Loading required package: gbm
Loaded gbm 2.1.5
Loading required package: ggplot2
Loading required package: plotly

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 176-177 (usage_of_the_personalized_package.Rmd) 
Error: processing vignette 'usage_of_the_personalized_package.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘usage_of_the_personalized_package.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: perspectev.test
> ### Title: Test for irreducibility of relationship between upper level
> ###   traits and survivorship
> ### Aliases: perspectev.test
> 
> ### ** Examples
> 
> 	data(testData)
> 
>   	data = perspectev.read(testData,extinctionAge=5,occurrenceAge="Age",
+   	upper="Genus",lower="Species",traits=c("Lat","Long"),traitfun=mcpRange,projection=FALSE)
[1] "Assigning survivorship = 1 to taxa with ages < extinctionAge (backward time)"
  traitdata_index traitdata_value
1               1             Lat
2               2            Long
> 
>   	#4 iterations chosen out of convenience - use more!
> 	mcpTest  = perspectev.test(data,4,1,traitfun=mcpRange)
> 	mcpSim  = perspectev.simulate(data,4,1,traitfun=mcpRange)
[1] "Intercept and slope parameters not specified. Assigning model fit through logistic regression."
[1] "Level parameter not specified (can be 'lower' or 'upper'). Performing upper level simulation."
[1] "Binary/continuous survivorship not specified, setting binary = TRUE"
[1] "Upper Level Selection Intercept -2.2264213772787"
[1] "Upper Level Selection Slope -0.273533830039319"
> 	perspectev.plot(mcpTest,list(mcpSim),c("S1"),"Test")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘artificial_intelligence_evolution.Rmd’ using rmarkdown
Quitting from lines 38-48 (artificial_intelligence_evolution.Rmd) 
Error: processing vignette 'artificial_intelligence_evolution.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘artificial_intelligence_evolution.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
pGLS: no visible global function definition for ‘model.response’
pGLS: no visible global function definition for ‘model.matrix’
pGLS: no visible global function definition for ‘pt’
Undefined global functions or variables:
  model.matrix model.response pt
Consider adding
  importFrom("stats", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
Found the following significant warnings:
  fdouble_metaphone.c:268:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PGRdup.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
ERROR: Duplicated records found in prim.key field
ERROR: NULL records found in prim.key field
OK: No duplicated records found in prim.key field
OK: No NULL records found in prim.key field
Fuzzy matching
Phonetic matching
Semantic matching
Fuzzy matching
Phonetic matching
Semantic matching
Quitting from lines 1112-1120 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
PharmPow_crossover: no visible global function definition for
  ‘read.table’
PharmPow_crossover: no visible global function definition for
  ‘write.csv’
PharmPow_crossover: no visible global function definition for ‘pdf’
PharmPow_crossover: no visible global function definition for ‘dev.off’
PharmPow_parallel: no visible global function definition for
  ‘read.table’
PharmPow_parallel: no visible global function definition for
  ‘write.csv’
PharmPow_parallel: no visible global function definition for ‘pdf’
PharmPow_parallel: no visible global function definition for ‘dev.off’
fig_PharmPow_crossover: no visible global function definition for
  ‘read.csv’
fig_PharmPow_parallel: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  dev.off pdf read.csv read.table write.csv
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "read.csv", "read.table", "write.csv")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘ggplot2’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.phtMCMC: no visible global function definition for ‘ggplot’
plot.phtMCMC: no visible global function definition for ‘melt’
plot.phtMCMC: no visible global function definition for ‘geom_line’
plot.phtMCMC: no visible global function definition for ‘aes_string’
plot.phtMCMC: no visible global function definition for ‘geom_smooth’
plot.phtMCMC: no visible global function definition for ‘facet_wrap’
plot.phtMCMC: no visible global function definition for ‘ggtitle’
plot.phtMCMC: no visible global function definition for ‘xlab’
plot.phtMCMC: no visible global function definition for ‘ylab’
plot.phtMCMC: no visible global function definition for ‘geom_density’
Undefined global functions or variables:
  aes_string facet_wrap geom_density geom_line geom_smooth ggplot
  ggtitle melt xlab ylab
File ‘PhaseType/libs/PhaseType.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘LJMA_arms.o’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: opt_FUN
> ### Title: Unified optimization function
> ### Aliases: opt_FUN opt_ucminf opt_nlminb opt_nlm opt_optim
> 
> ### ** Examples
> 
> library(phenofit)
> library(ggplot2)
> library(magrittr)
> library(purrr)

Attaching package: ‘purrr’

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

    set_names

> 
> # simulate vegetation time-series
> fFUN = doubleLog.Beck
> par = c(
+   mn  = 0.1,
+   mx  = 0.7,
+   sos = 50,
+   rsp = 0.1,
+   eos = 250,
+   rau = 0.1)
> t    <- seq(1, 365, 8)
> tout <- seq(1, 365, 1)
> y <- fFUN(par, t)
> 
> # initial parameter
> par0 <- c(
+   mn  = 0.15,
+   mx  = 0.65,
+   sos = 100,
+   rsp = 0.12,
+   eos = 200,
+   rau = 0.12)
> 
> objective <- f_goal # goal function
> optFUNs   <- c("opt_ucminf", "opt_nlminb", "opt_nlm", "opt_optim") %>% set_names(., .)
> 
> opts <- lapply(optFUNs, function(optFUN){
+     optFUN <- get(optFUN)
+     opt <- optFUN(par0, objective, y = y, t = t, fun = fFUN)
+     opt$ysim <- fFUN(opt$par, t)
+     opt
+ })
> 
> # visualization
> df   <- map(opts, "ysim") %>% as.data.frame() %>% cbind(t, y, .)
> pdat <- reshape2::melt(df, c("t", "y"), variable.name = "optFUN")
> 
> ggplot(pdat) + 
+     geom_point(data = data.frame(t, y), aes(t, y), size = 2) + 
+     geom_line(aes(t, value, color = optFUN), size = 0.9)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
pheno.ddm: no visible global function definition for ‘new’
pheno.flm.fit: no visible binding for global variable ‘na.exclude’
pheno.flm.fit: no visible global function definition for ‘terms’
pheno.flm.fit: no visible global function definition for ‘residuals’
pheno.flm.fit: no visible global function definition for ‘qt’
pheno.lad.fit: no visible binding for global variable ‘na.exclude’
pheno.mlm.fit: no visible binding for global variable ‘na.exclude’
pheno.mlm.fit: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  na.exclude new qt residuals terms
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "na.exclude", "qt", "residuals", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error(s) in re-building vignettes:
  ...
--- re-building ‘PhenotypeSimulator.Rmd’ using rmarkdown
--- finished re-building ‘PhenotypeSimulator.Rmd’

--- re-building ‘Sample-scripts-external-genotype-simulation.Rmd’ using rmarkdown
--- finished re-building ‘Sample-scripts-external-genotype-simulation.Rmd’

--- re-building ‘Simulation-and-LinearModel.Rmd’ using rmarkdown
Quitting from lines 196-258 (Simulation-and-LinearModel.Rmd) 
Error: processing vignette 'Simulation-and-LinearModel.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Simulation-and-LinearModel.Rmd’

SUMMARY: processing the following file failed:
  ‘Simulation-and-LinearModel.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Quitting from lines 198-199 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘user-guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Loading required package: tibble
For news and documentation about the R for Photobiology packages, please, visit http://www.r4photobiology.info/
For news about 'photobiologyInOut', please, see https://www.r4photobiology.info/
For on-line documentation see https://docs.r4photobiology.info/photobiologyInOut/

Attaching package: 'lubridate'

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

    date

Loading required package: lattice
Loading required package: grid
Package hyperSpec, version 0.99-20180627

To get started, try
   vignette ("hyperspec")
   package?hyperSpec 
   vignette (package = "hyperSpec")

If you use this package please cite it appropriately.
   citation("hyperSpec")
will give you the correct reference.

The project homepage is http://hyperspec.r-forge.r-project.org


This is colorSpec.  Version: 0.8-3.  Author: Glenn Davis [aut, cre].  Built: R 3.7.0; ; 2019-03-29
 14:02:32 UTC; unix

Attaching package: 'colorSpec'

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

    bind

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

    normalize

Read 3 items
Read 16 items
Quitting from lines 131-132 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘user-guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Loading required package: tibble
For news and documentation about the R for Photobiology packages, please, visit http://www.r4photobiology.info/
For news about 'photobiologyLamps', please, see http://www.r4photobiology.info/
For on-line documentation see http://docs.r4photobiology.info/photobiologyLamps/
Quitting from lines 167-168 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘user-guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Quitting from lines 209-210 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘user-guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dataplotsPlants.Rnw’ using knitr
Quitting from lines 79-81 (dataplotsPlants.Rnw) 
Error: processing vignette 'dataplotsPlants.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dataplotsPlants.Rnw’

--- re-building ‘userguideplants.Rnw’ using knitr
Warning in Red("Smith") :
  The definition of 'Smith' defaults to 'Smith10', to restore old behaviour use 'Smith20'.
Warning in Far_red("Smith") :
  The definition of 'Smith' defaults to 'Smith10', to restore old behaviour use 'Smith20'.
Quitting from lines 102-106 (userguideplants.Rnw) 
Error: processing vignette 'userguideplants.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘userguideplants.Rnw’

SUMMARY: processing the following files failed:
  ‘dataplotsPlants.Rnw’ ‘userguideplants.Rnw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: photobiologySensors-package
> ### Title: photobiologySensors: Spectral Response Data for Light Sensors
> ### Aliases: photobiologySensors photobiologySensors-package
> 
> ### ** Examples
> 
> library(photobiology)
> library(photobiologyWavebands)
> library(ggspectra)
Loading required package: ggplot2
> 
> names(sensors.mspct)
 [1] "Berger_UV_Biometer" "BF5"                "flat_e"            
 [4] "flat_q"             "CUV_5"              "PQS1"              
 [7] "UVS_A"              "UVS_B"              "UVS_E"             
[10] "LI_190"             "LI_200"             "LI_210"            
[13] "TOCON_blue4"        "SG01D_A"            "SG01D_B"           
[16] "SG01D_C"            "SG01L"              "SKE510"            
[19] "SKL310"             "SKP210"             "SKP215"            
[22] "SKR110_FR"          "SKR110_R"           "SKS1110"           
[25] "SKU421"             "SKU421a"            "SKU430a"           
[28] "SKU440a"            "SL_501_high_UVA"    "SL_501_low_UVA"    
[31] "SL_501_typical"     "SM60"               "E1c"               
[34] "BW_20"             
> 
> licor_sensors
[1] "LI_190" "LI_200" "LI_210"
> par_sensors
[1] "SKP215" "SKE510" "SKP210" "PQS1"   "LI_190" "BF5"   
> intersect(par_sensors, licor_sensors)
[1] "LI_190"
> 
> photon_as_default()
> 
> response(sensors.mspct$LI_190, w.band = PAR(), quantity = "contribution.pc")
 Total PAR 
  99.18297 
attr(,"time.unit")
[1] "second"
attr(,"radiation.unit")
[1] "photon response contribution.pc"
> 
> plot(sensors.mspct$LI_190, w.band = PAR(), label.qty = "contribution.pc")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Loading required package: tibble
For news and documentation about the R for Photobiology packages, please, visit http://www.r4photobiology.info/
For news about 'photobiologySensors', please, see http://www.r4photobiology.info/
For on-line documentation see http://docs.r4photobiology.info/photobiologySensors/
Quitting from lines 150-151 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘user-guide.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘user-guide.Rmd’ using rmarkdown
Loading required package: tibble
For news and documentation about the R for Photobiology packages, please, visit http://www.r4photobiology.info/

Attaching package: 'lubridate'

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

    date

Quitting from lines 86-87 (user-guide.Rmd) 
Error: processing vignette 'user-guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user-guide.Rmd’

SUMMARY: processing the following file failed:
  ‘user-guide.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Phxnlme-package
> ### Title: Package 'Phxnlme'
> ### Aliases: Phxnlme-package
> ### Keywords: package
> 
> ### ** Examples
> 
> data(ex1phxd)
> phxd=ex1phxd
> phxplot(phxd=phxd,plot.type="residual.scatter",outpdf=FALSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: phxplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Package suggested but not available for checking: ‘OutbreakTools’
Running examples in ‘phylopath-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DAG
> ### Title: Directed acyclic graphs (DAGs)
> ### Aliases: DAG
> 
> ### ** Examples
> 
>   # Use formula notation to create DAGs:
>   plot(DAG(A~B, B~C))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘binary_models.Rmd’ using rmarkdown
Quitting from lines 51-70 (binary_models.Rmd) 
Error: processing vignette 'binary_models.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘binary_models.Rmd’

--- re-building ‘intro_to_phylopath.Rmd’ using rmarkdown
Quitting from lines 114-115 (intro_to_phylopath.Rmd) 
Error: processing vignette 'intro_to_phylopath.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro_to_phylopath.Rmd’

SUMMARY: processing the following files failed:
  ‘binary_models.Rmd’ ‘intro_to_phylopath.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_permutations
> ### Title: Plots the permutation distribution
> ### Aliases: plot_permutations
> 
> ### ** Examples
> 
> library(phyloseq)
> data(enterotype)
> gt = graph_perm_test(enterotype, sampletype = "SeqTech")
> plot_permutations(gt)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gt_vignette.Rmd’ using rmarkdown
Quitting from lines 175-176 (gt_vignette.Rmd) 
Error: processing vignette 'gt_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gt_vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_phylota_pa
> ### Title: Plot presence/absence matrix
> ### Aliases: plot_phylota_pa
> 
> ### ** Examples
> 
> library(phylotaR)
> data(cycads)
> # drop all but first ten
> cycads <- drop_clstrs(cycads, cycads@cids[1:10])
> # plot all
> p <- plot_phylota_pa(phylota = cycads, cids = cycads@cids, txids = cycads@txids)
> print(p)  # lots of information, difficult to interpret
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Everest.Rmd’ using rmarkdown
--- finished re-building ‘Everest.Rmd’

--- re-building ‘IdealWeightComparison.Rmd’ using rmarkdown
Quitting from lines 16-43 (IdealWeightComparison.Rmd) 
Error: processing vignette 'IdealWeightComparison.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘IdealWeightComparison.Rmd’

--- re-building ‘NeonatalVentilation.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

Loading required namespace: reshape2
--- finished re-building ‘NeonatalVentilation.Rmd’

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

Error: Vignette re-building failed.
Execution halted
incident: no visible global function definition for ‘splinefun’
incident: no visible global function definition for ‘integrate’
phytoprod: no visible global function definition for ‘approx’
phytoprod: no visible global function definition for ‘splinefun’
phytoprod: no visible global function definition for ‘integrate’
reflectance: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx integrate splinefun
Consider adding
  importFrom("stats", "approx", "integrate", "splinefun")
to your NAMESPACE file.
Running examples in ‘pid-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: contourPlot
> ### Title: 2-dimensional contour plot of a factorial design model
> ### Aliases: contourPlot
> 
> ### ** Examples
> 
> 
> # 2-factor example
> # ----------------
> T <- c(-1, +1, -1, +1)  # centered and scaled temperature
> S <- c(-1, -1, +1, +1)  # centered and scaled speed variable
> y <- c(69, 60, 64, 53)  # conversion, is our response variable, y
> doe.model <- lm(y ~ T + S + T * S)  # model with main effects, and interaction
> contourPlot(doe.model)  
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: contourPlot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘pifpaf-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: counterfactual.plot
> ### Title: Plot exposure's distribution under counterfactual scenario
> ### Aliases: counterfactual.plot
> 
> ### ** Examples
> 
> 
> #Example 1: Bivariate exposure
> #--------------------------------------------------------
> set.seed(2783569)
> X   <- data.frame(Exposure = 
+            sample(c("Exposed","Unexposed"), 100, replace = TRUE, 
+            prob = c(0.3, 0.7)))
> cft <- function(X){
+ 
+      #Find which indivuals are exposed
+      exposed    <- which(X[,"Exposure"] == "Exposed")
+      
+      #Change 1/3 of exposed to unexposed
+      reduced               <- sample(exposed, length(exposed)/3)
+      X[reduced,"Exposure"] <- "Unexposed"
+      
+      return(X)
+ }  
> counterfactual.plot(X, cft)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction_to_pifpaf_package.Rmd’ using rmarkdown
Loading required package: pifpaf
Loading required package: ggplot2
Quitting from lines 133-134 (Introduction_to_pifpaf_package.Rmd) 
Error: processing vignette 'Introduction_to_pifpaf_package.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction_to_pifpaf_package.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File which contains pragma(s) suppressing diagnostics:
  ‘src/pijavski.cpp’
Running examples in ‘pimeta-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.cima
> ### Title: Plot Results
> ### Aliases: plot.cima
> 
> ### ** Examples
> 
> data(sbp, package = "pimeta")
> ciex <- pimeta::cima(sbp$y, sbp$sigmak, method = "DL")
> cairo_pdf("forestplot.pdf", width = 6, height = 3, family = "Arial")
> plot(ciex, digits = 2, base_size = 10, studylabel = sbp$label)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot -> plot.cima
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pimeta.Rmd’ using rmarkdown
Quitting from lines 16-29 (pimeta.Rmd) 
Error: processing vignette 'pimeta.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pimeta.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot.qpin
> ### Title: PIN Visualization
> ### Aliases: ggplot.qpin
> 
> ### ** Examples
> 
> # Loading one year of simulated daily buys and sells
> 
> data('BSfrequent2015')
> 
> # Quarterly estimates for model parameters and the probability of informed trading
> # Rownames of 'BSfrequent2015' equal the business days in 2015.
> 
> qpin_list <- qpin(numbuys = BSfrequent2015[,"Buys"], numsells = BSfrequent2015[,"Sells"],
+                   dates = as.Date(rownames(BSfrequent2015), format = "%Y-%m-%d"))
> 
> # Visualization of quarterly estimates
> library(ggplot2)
> ggplot(qpin_list[["res"]])
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pinbasicVignette.Rmd’ using rmarkdown
pin_ll(param = NULL, numbuys = NULL, numsells = NULL,
    factorization = "Lin_Ke")
initial_vals(numbuys = NULL, numsells = NULL, method = "HAC", length = 5,
    num_clust = 5, details = FALSE)
Quitting from lines 91-93 (./Examples/Examples.Rmd) 
Quitting from lines 70-71 (./Examples/Examples.Rmd) 
Error: processing vignette 'pinbasicVignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pinbasicVignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
plot.pred.int: no visible global function definition for ‘plot.default’
plot.pred.int: no visible global function definition for ‘axis’
plot.pred.int: no visible global function definition for ‘box’
plot.pred.int : cidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : negcidist: no visible global function definition for
  ‘ecdf’
plot.pred.int : pi.col.fun: no visible global function definition for
  ‘gray’
plot.pred.int: no visible global function definition for ‘segments’
plot.pred.int: no visible global function definition for ‘points’
plot.pred.int: no visible global function definition for ‘abline’
pred.int: no visible binding for global variable ‘sd’
prop.test.mult: no visible global function definition for ‘qnorm’
sim.basic: no visible global function definition for ‘rbinom’
sim.basic: no visible global function definition for ‘rnorm’
t.test.mult: no visible global function definition for ‘qt’
Undefined global functions or variables:
  abline axis box ecdf gray plot.default points qnorm qt rbinom rnorm
  sd segments
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "box", "plot.default",
             "points", "segments")
  importFrom("stats", "ecdf", "qnorm", "qt", "rbinom", "rnorm", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ggsubplot’
Running examples in ‘pitchRx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: strikeFX
> ### Title: Visualize PITCHf/x strikezones
> ### Aliases: strikeFX
> 
> ### ** Examples
> 
> data(pitches)
> 
> strikeFX(pitches)
Warning: Removed 56 rows containing missing values (geom_point).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_pkggraph.Rmd’ using rmarkdown
Quitting from lines 34-58 (vignette_pkggraph.Rmd) 
Error: processing vignette 'vignette_pkggraph.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette_pkggraph.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RGtk2’ ‘gWidgetsRGtk2’
A package should be listed in only one of these fields.
Package in Depends field not imported from: ‘cairoDevice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error(s) in re-building vignettes:
  ...
--- re-building ‘AUC-Calculation-with-PKNCA.Rmd’ using rmarkdown
Quitting from lines 22-43 (AUC-Calculation-with-PKNCA.Rmd) 
Error: processing vignette 'AUC-Calculation-with-PKNCA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘AUC-Calculation-with-PKNCA.Rmd’

--- re-building ‘Data-Cleaning-in-PKNCA.Rmd’ using rmarkdown
--- finished re-building ‘Data-Cleaning-in-PKNCA.Rmd’

--- re-building ‘Introduction-and-Usage.Rmd’ using rmarkdown
--- finished re-building ‘Introduction-and-Usage.Rmd’

--- re-building ‘Methods-for-Dose-Aware-Interpolation-and-Extrapolation.Rmd’ using rmarkdown
--- finished re-building ‘Methods-for-Dose-Aware-Interpolation-and-Extrapolation.Rmd’

--- re-building ‘Options-for-Controlling-PKNCA.Rmd’ using rmarkdown
--- finished re-building ‘Options-for-Controlling-PKNCA.Rmd’

--- re-building ‘PKNCA-validation.Rmd’ using rmarkdown
--- finished re-building ‘PKNCA-validation.Rmd’

--- re-building ‘Selection-of-Calculation-Intervals.Rmd’ using rmarkdown
Quitting from lines 28-55 (Selection-of-Calculation-Intervals.Rmd) 
Error: processing vignette 'Selection-of-Calculation-Intervals.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Selection-of-Calculation-Intervals.Rmd’

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

--- re-building ‘Writing-Parameter-Functions.Rmd’ using rmarkdown
--- finished re-building ‘Writing-Parameter-Functions.Rmd’

SUMMARY: processing the following files failed:
  ‘AUC-Calculation-with-PKNCA.Rmd’
  ‘Selection-of-Calculation-Intervals.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: color_pallete
> ### Title: design-quality color palletes to use in ggplot2
> ### Aliases: color_pallete
> 
> ### ** Examples
> 
> library(PKPDmisc)
> library(ggplot2)
> 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

> ggplot(sd_oral_richpk %>% filter(ID < 10), 
+ aes(x = Time,
+ y= Conc, 
+ group = ID, 
+ color = Gender)) + 
+   geom_line(size = 1.5) + scale_color_manual(values =color_pallete(1)) +
+   base_theme()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘multiplot.Rmd’ using rmarkdown
Quitting from lines 28-31 (multiplot.Rmd) 
Error: processing vignette 'multiplot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘multiplot.Rmd’

--- re-building ‘noncompartmental-analysis.Rmd’ using rmarkdown
--- finished re-building ‘noncompartmental-analysis.Rmd’

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

Error: Vignette re-building failed.
Execution halted
PKmod: no visible global function definition for ‘deriv’
Undefined global functions or variables:
  deriv
Consider adding
  importFrom("stats", "deriv")
to your NAMESPACE file.
PKadjust: no visible binding for global variable ‘jpeg’
PKadjust: no visible binding for global variable ‘bmp’
PKadjust: no visible binding for global variable ‘png’
PKadjust: no visible binding for global variable ‘tiff’
PKadjust: no visible binding for global variable ‘dev.new’
PKadjust: no visible global function definition for ‘dev.off’
PKfigure: no visible global function definition for ‘dev.cur’
PKfigure: no visible global function definition for ‘dev.off’
PKoutput: no visible global function definition for ‘heatmap’
PKoutput: no visible global function definition for
  ‘packageDescription’
PKshow: no visible global function definition for ‘browseURL’
addList1: no visible global function definition for ‘formula’
addList1.old: no visible global function definition for ‘formula’
addList2: no visible global function definition for ‘formula’
generate.plot: no visible global function definition for ‘dev.off’
writeHTML: no visible global function definition for
  ‘packageDescription’
writeLst: no visible global function definition for
  ‘packageDescription’
writeLst.tab: no visible global function definition for
  ‘packageDescription’
writeTable: no visible global function definition for
  ‘packageDescription’
writeTable: no visible global function definition for ‘quantile’
initialize,nonmem: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  bmp browseURL dev.cur dev.new dev.off formula heatmap jpeg
  packageDescription png quantile read.table tiff
Consider adding
  importFrom("grDevices", "bmp", "dev.cur", "dev.new", "dev.off", "jpeg",
             "png", "tiff")
  importFrom("stats", "formula", "heatmap", "quantile")
  importFrom("utils", "browseURL", "packageDescription", "read.table")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Overview.Rmd’ using rmarkdown

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Network of items is not strongly connected
Removed rankings with less than 2 items
Quitting from lines 806-807 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
no string supplied for 'strwidth/height' unit
--- failed re-building ‘Overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘decay_rates.Rmd’ using knitr
--- finished re-building ‘decay_rates.Rmd’

--- re-building ‘fresnel.Rmd’ using knitr
--- finished re-building ‘fresnel.Rmd’

--- re-building ‘gaussian.rmd’ using knitr
Loading required package: dielectric
Quitting from lines 137-177 (gaussian.rmd) 
Error: processing vignette 'gaussian.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘gaussian.rmd’

SUMMARY: processing the following file failed:
  ‘gaussian.rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DetectPlasmaMutation
> ### Title: function DetectPlasmaMutation
> ### Aliases: DetectPlasmaMutation
> 
> ### ** Examples
> 
>      patient.dir=system.file("extdata","4test_only/case/",package="PlasmaMutationDetector")
>      if (substr(patient.dir,nchar(patient.dir),nchar(patient.dir))!='/')
+        patient.dir = paste0(patient.dir,'/') # TO RUN UNDER WINDOWS
>      DetectPlasmaMutation(patient.dir,output.dir=paste0(tempdir(),'/'))
[1] "Looking for bam and bai in /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/PlasmaMutationDetector/extdata/4test_only/case/rBAM/ ..."
[1] "Detecting mutations from /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/PlasmaMutationDetector/extdata/4test_only/case/BER/case1.chr7_MAF.txt"
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: DetectPlasmaMutation ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘Plasmidprofiler-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: main
> ### Title: Main: Run everything
> ### Aliases: main
> 
> ### ** Examples
> 
> main(blastdata,
+ srst2data,
+ coverage.filter=NA,
+ sureness.filter=0.75,
+ length.filter=10000,
+ main.title="Example Results")
Selecting by pident
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: main ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘platetools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: b_grid
> ### Title: Plots multiple b-scored normalised platemaps
> ### Aliases: b_grid
> 
> ### ** Examples
> 
> df01 <- data.frame(well = num_to_well(1:96),
+   vals = rnorm(96),
+   plate = 1)
> 
> df02 <- data.frame(well = num_to_well(1:96),
+   vals = rnorm(96),
+   plate = 2)
> 
> df <- rbind(df01, df02)
> 
> b_grid(data = df$vals,
+     well = df$well,
+     plate_id = df$plate,
+     plate = 96)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
bwfw.hmm: no visible global function definition for ‘dnorm’
bwfw1.hmm: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘Formula’ ‘sm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
nrmlepln: no visible global function definition for ‘pchisq’
nrmlerasch: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Running examples in ‘plot3logit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: field3logit
> ### Title: Computation of the vector field
> ### Aliases: field3logit plot3logit print.field3logit plot.field3logit
> ###   as.data.frame.field3logit fortify.field3logit
> 
> ### ** Examples
> 
> data(cross_1year)
> 
> # Model fit
> mod0 <- nnet::multinom(employment_sit ~ finalgrade + irregularity + hsscore,
+   cross_1year)
# weights:  21 (12 variable)
initial  value 3605.645531 
iter  10 value 2187.709284
iter  20 value 2157.087955
final  value 2157.087854 
converged
> mod0
Call:
nnet::multinom(formula = employment_sit ~ finalgrade + irregularity + 
    hsscore, data = cross_1year)

Coefficients:
           (Intercept) finalgradeLow finalgradeHigh irregularityLow
Unemployed  -0.4481761    0.05551765    -0.07810893     -0.01874354
Trainee     -1.3751140    0.14456683    -0.26849829      0.05764144
           irregularityLong      hsscore
Unemployed       0.15691595 -0.016619227
Trainee         -0.03477569 -0.009964381

Residual Deviance: 4314.176 
AIC: 4338.176 
> 
> # Assessing the effect of "finalgradeHigh" (explicit notation)
> field0 <- field3logit(mod0, c(0, 0, 1, 0, 0, 0))
> gg3logit(field0) + stat_3logit()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘plotGMM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_mix_comps
> ### Title: Plot a Mixture Component
> ### Aliases: plot_mix_comps
> 
> ### ** Examples
> 
> set.seed(1)
> mixmdl <- mixtools::normalmixEM(faithful$waiting, k = 2)
number of iterations= 29 
> x <- mixmdl$x
> x <- data.frame(x)
> ggplot2::ggplot(data.frame(x)) +
+   ggplot2::geom_histogram(ggplot2::aes(x, ..density..)) +
+   ggplot2::stat_function(geom = "line", fun = plot_mix_comps,
+                 args = list(mixmdl$mu[1], mixmdl$sigma[1], lam = mixmdl$lambda[1]),
+                 colour = "red") +
+   ggplot2::stat_function(geom = "line", fun = plot_mix_comps,
+                 args = list(mixmdl$mu[2], mixmdl$sigma[2], lam = mixmdl$lambda[2]),
+                colour = "blue")
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘plotluck-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotluck
> ### Title: "I'm feeling lucky" for ggplot
> ### Aliases: plotluck
> ### Keywords: aplot, dplot hplot,
> 
> ### ** Examples
> 
> # Single-variable density
> data(diamonds, package='ggplot2')
> plotluck(diamonds, price~1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(plotluck)
  > 
  > test_check("plotluck")
  *** 1D density plot ***
  ── 1. Error: (unknown) (@test_plotluck.R#57)  ──────────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: test_that_ref("1d_density", "1D density plot", {
         eq_ref(plotluck(iris, Petal.Length ~ 1))
     }) at testthat/test_plotluck.R:57
  2: eq_ref(plotluck(iris, Petal.Length ~ 1)) at testthat/test_plotluck.R:58
  3: print(x) at testthat/test_plotluck.R:39
  4: print.ggplot(x)
  5: grid.draw(gtable)
  6: grid.draw.gTree(gtable)
  7: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  8: drawGTree(x)
  9: preDraw(x)
  10: preDraw.gTree(x)
  11: pushvpgp(x)
  12: pushgrobvp(x$vp)
  13: pushgrobvp.viewport(x$vp)
  14: pushViewport(vp, recording = FALSE)
  15: lapply(vps, push.vp, recording)
  16: FUN(X[[i]], ...)
  17: push.vp.viewport(X[[i]], ...)
  18: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_plotluck.R#57) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plotluck.Rmd’ using rmarkdown
Quitting from lines 36-39 (plotluck.Rmd) 
Error: processing vignette 'plotluck.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plotluck.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: highlight
> ### Title: Query graphical elements in multiple linked views
> ### Aliases: highlight
> 
> ### ** Examples
> 
> 
> # These examples are designed to show you how to highlight/brush a *single*
> # view. For examples of multiple linked views, see `demo(package = "plotly")` 
> 
> library(crosstalk)
> d <- highlight_key(txhousing, ~city)
> p <- ggplot(d, aes(date, median, group = city)) + geom_line()
> gg <- ggplotly(p, tooltip = "city") 
Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto),  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ggplotly ... unitConvert -> <Anonymous> -> convertUnit -> grid.Call
Execution halted
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.
Running examples in ‘plotMElm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_me
> ### Title: Plot marginal effects from two-way interactions in linear
> ###   regressions
> ### Aliases: plot_me
> 
> ### ** Examples
> 
> ## Continuous Term1 and Term2
> # Estimate model
> states <- as.data.frame(state.x77)
> m1 <- lm(Murder ~ Income * Population, data = states)
> 
> # Plot marginal effect of Income across the observed range of Population
> # on the Murder rate
> plot_me(m1, 'Income', 'Population', ci = 95)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘PlotPrjNetworks-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GanttChart
> ### Title: GanttChart
> ### Aliases: GanttChart
> 
> ### ** Examples
> 
> project1=data.frame(
+     task=c("Market Research","Concept Development","Viability Test",
+ "Preliminary Design","Process Design","Prototyping","Market Testing","Final Design",
+ "Launching"),
+     start=c("2015-07-05","2015-07-05","2015-08-05","2015-10-05","2015-10-05","2016-02-18",
+ "2016-03-18","2016-05-18","2016-07-18"),
+     end=c("2015-08-05","2015-08-05","2015-10-05","2016-01-05","2016-02-18","2016-03-18",
+ "2016-05-18","2016-07-18","2016-09-18"))
> project2=data.frame(
+     from=c(1,2,3,4,5,6,7,8),
+     to=c(2,3,4,5,6,7,8,9),
+     type=c("SS","FS","FS","SS","FS","FS","FS","FS"),
+     delay=c(7,7,7,8,10,10,10,10))
> GanttChart(project1,project2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
generateEnvelope: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in ‘plotrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multhist
> ### Title: Plot a multiple histogram, as a barplot
> ### Aliases: multhist
> ### Keywords: hplot
> 
> ### ** Examples
> 
>  l <- list(runif(10)*10,1:10,c(1,1,1,1,4,8))
>  multhist(l)
Error in barplot.default(c(1L, 2L, 4L, 3L, 2L, 1L, 1L, 2L, 0L, 2L, 2L,  : 
  object 'add' not found
Calls: multhist -> do.call -> barplot -> barplot.default
Execution halted
Running examples in ‘plotROC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GeomRoc
> ### Title: Empirical Receiver Operating Characteristic Curve
> ### Aliases: GeomRoc geom_roc
> ### Keywords: datasets
> 
> ### ** Examples
> 
> D.ex <- rbinom(50, 1, .5)
> rocdata <- data.frame(D = c(D.ex, D.ex), 
+                    M = c(rnorm(50, mean = D.ex, sd = .4), rnorm(50, mean = D.ex, sd = 1)), 
+                    Z = c(rep("A", 50), rep("B", 50)))
> 
> ggplot(rocdata, aes(m = M, d = D)) + geom_roc()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
Quitting from lines 99-101 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘examples.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bivarplots
> ### Title: Plots the bivariate relationship between two measures for each
> ###   group/unit
> ### Aliases: bivarplots
> 
> ### ** Examples
> 
> a <- runif(1000, min = 0, max = 1)
> b <- a + rnorm(1000, mean = 0, sd = 1)
> c <- rep(c(1:10), times = 100)
> data <- data.frame(a, b, c)
> bivarplots("a", "b", "c", data)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: bivarplots ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plotrr-vignette.Rmd’ using rmarkdown
Quitting from lines 30-36 (plotrr-vignette.Rmd) 
Error: processing vignette 'plotrr-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plotrr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
llla.bi: no visible global function definition for ‘as.formula’
llla.bi: no visible global function definition for ‘glm’
llla.bi: no visible global function definition for ‘binomial’
llla.bi: no visible binding for global variable ‘logit’
llla.bi: no visible global function definition for ‘vcov’
llla.bi: no visible global function definition for ‘coef’
llla.mc: no visible global function definition for ‘model.matrix’
llla.mc: no visible global function definition for ‘as.formula’
llla.mc: no visible global function definition for ‘coxph’
llla.mc: no visible global function definition for ‘vcov’
llla.mc: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘as.formula’
llla.mle: no visible global function definition for ‘glm’
llla.mle: no visible global function definition for ‘poisson’
llla.mle: no visible global function definition for ‘coef’
llla.mle: no visible global function definition for ‘vcov’
mclgen: no visible global function definition for ‘reshape’
simRasch.1D: no visible global function definition for ‘rnorm’
simRasch.1D: no visible global function definition for ‘runif’
vcov.sandwich.glm: no visible global function definition for
  ‘model.matrix’
vcov.sandwich.glm: no visible global function definition for ‘weights’
vcov.sandwich.glm: no visible global function definition for
  ‘residuals’
vcov.sandwich.glm: no visible global function definition for ‘vcov’
Undefined global functions or variables:
  as.formula binomial coef coxph glm logit model.matrix poisson reshape
  residuals rnorm runif vcov weights
Consider adding
  importFrom("stats", "as.formula", "binomial", "coef", "glm",
             "model.matrix", "poisson", "reshape", "residuals", "rnorm",
             "runif", "vcov", "weights")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘plspm_introduction.Rnw’ using knitr

Attaching package: 'ggplot2'

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

    alpha

Quitting from lines 310-329 (plspm_introduction.Rnw) 
Error: processing vignette 'plspm_introduction.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plspm_introduction.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plte_plot
> ### Title: Plot objects created by plte_builder
> ### Aliases: plte_plot
> 
> ### ** Examples
> 
> data('negative')
> 
> # BTSCS set the data
> neg_set <- btscs(df = negative, event = 'y', t_var = 'tim',
+                  cs_unit = 'group', pad_ts = FALSE)
>                  # Create temporal dependence variables
> neg_set$t <- neg_set$spell + 1
> 
> m1 <- glm(y ~ x + t + I(t^2) + I(t^3),
+           family = binomial(link = 'logit'),
+           data = neg_set)
> 
> counterfactual <- data.frame(x = 0.5)
> 
> sim1 <- plte_builder(obj = m1, obj_tvar = 't',
+                      cf = counterfactual, t_points = c(13, 25),
+                      cf_duration = 4, ci = 99)
> 
> # With time point labels
> plte_plot(sim1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
print.densityEHpi: no visible global function definition for ‘str’
Undefined global functions or variables:
  str
Consider adding
  importFrom("utils", "str")
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.
Running examples in ‘PMmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pl.histgg
> ### Title: Plot histograms for a data frame with ggplot2
> ### Aliases: pl.histgg
> 
> ### ** Examples
> 
> pl.histgg(as.data.frame(EuStockMarkets),1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: pl.histgg ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘pmpp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.pmpp
> ### Title: Plot method for objects of class 'pmpp'.
> ### Aliases: plot.pmpp
> 
> ### ** Examples
> 
> data(EmplUK, package = "plm")
> EmplUK <- dplyr::filter(EmplUK, year %in% c(1978, 1979, 1980, 1981, 1982))
> pmpp_model <- pmpp(dep_var = "emp", data = EmplUK)
> plot(pmpp_model)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
dbm: no visible global function definition for ‘optim’
dbm: no visible global function definition for ‘new’
destat: no visible global function definition for ‘weighted.mean’
local.knn: no visible global function definition for ‘sd’
local.knn: no visible global function definition for ‘optim’
mdpref: no visible global function definition for ‘sd’
mdpref: no visible global function definition for ‘text’
mdpref: no visible global function definition for ‘lines’
phicom: no visible global function definition for ‘optim’
phicom: no visible global function definition for ‘new’
pl: no visible global function definition for ‘optim’
pl: no visible global function definition for ‘new’
rol: no visible global function definition for ‘nlm’
rol: no visible global function definition for ‘new’
wdbm: no visible global function definition for ‘optim’
wdbm: no visible global function definition for ‘new’
Undefined global functions or variables:
  lines new nlm optim sd text weighted.mean
Consider adding
  importFrom("graphics", "lines", "text")
  importFrom("methods", "new")
  importFrom("stats", "nlm", "optim", "sd", "weighted.mean")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' call to ‘MASS’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pnmtrem1: no visible global function definition for ‘pnorm’
pnmtrem1: no visible global function definition for ‘dnorm’
pnmtrem1: no visible global function definition for ‘ginv’
pnmtrem1 : fun: no visible global function definition for ‘pnorm’
pnmtrem1 : derf: no visible global function definition for ‘dnorm’
pnmtrem1 : derf: no visible global function definition for ‘pnorm’
pnmtrem1 : fun: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm ginv pnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘rgenoud’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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 ‘POCRE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.pocre
> ### Title: Visualization of a 'pocre' Object
> ### Aliases: plot.pocre
> 
> ### ** Examples
> 
> data(simdata)
> xx <- scale(as.matrix(simdata[,-1]))
> yy <- scale(as.matrix(simdata[,1]))
> 
> ##Fit with pocre()
> pres <- pocre(yy, xx, lambda=0.9)
.....
> 
> # plot(pres,which=1)
> plot(pres)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
bipoilogMLE: no visible global function definition for ‘optim’
bipoilogMLE: no visible global function definition for ‘write.table’
poilogMLE: no visible global function definition for ‘optim’
rbipoilog : sim: no visible global function definition for ‘rnorm’
rbipoilog : sim: no visible global function definition for ‘rpois’
rpoilog : sim: no visible global function definition for ‘rnorm’
rpoilog : sim: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  optim rnorm rpois write.table
Consider adding
  importFrom("stats", "optim", "rnorm", "rpois")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running examples in ‘PointFore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estimate.functional
> ### Title: Estimate Functional
> ### Aliases: estimate.functional
> 
> ### ** Examples
> 
> # estimate constant quantile level of GDP forecast
> res <- estimate.functional(Y=GDP$observation, X=GDP$forecast,
+ model=constant)
Drop  1 case(s) because of chosen instruments
Choose parameter theta0 automatically.
> summary(res)
$call
estimate.functional(model = constant, Y = GDP$observation, X = GDP$forecast)

$coefficients
          Estimate Std. Error  t value     Pr(>|t|)
Theta[1] 0.5980637 0.04429534 13.50173 1.527435e-41

$Jtest

 ##  J-Test: degrees of freedom is 2  ## 

                J-test    P-value 
Test E(g)=0:    5.507506  0.063688


> plot(res)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GDP.Rmd’ using rmarkdown
Quitting from lines 26-35 (GDP.Rmd) 
Error: processing vignette 'GDP.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GDP.Rmd’

--- re-building ‘Precipitation.Rmd’ using rmarkdown
Quitting from lines 26-38 (Precipitation.Rmd) 
Error: processing vignette 'Precipitation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Precipitation.Rmd’

--- re-building ‘Tutorial.Rmd’ using rmarkdown
Quitting from lines 95-97 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Tutorial.Rmd’

SUMMARY: processing the following files failed:
  ‘GDP.Rmd’ ‘Precipitation.Rmd’ ‘Tutorial.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: event.plot
> ### Title: Plot event years for individual trees
> ### Aliases: event.plot
> 
> ### ** Examples
> 
> ## Plot event years from pointer.rgc output
> data(s033)
> py <- pointer.rgc(s033)
> event.plot(py, start.yr = 1950, end.yr = NULL) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pointRes_functionality.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 58-59 (pointRes_functionality.Rmd) 
Error: processing vignette 'pointRes_functionality.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pointRes_functionality.Rmd’

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

Error: Vignette re-building failed.
Execution halted
approxMargMLE: no visible global function definition for ‘optim’
approxMargMLECI : ciFunction: no visible global function definition for
  ‘qchisq’
approxMargMLECI: no visible global function definition for ‘uniroot’
margMLE: no visible global function definition for ‘optim’
margMLECI: no visible global function definition for ‘optim’
margMLECI : unNormLikeMinusVal: no visible global function definition
  for ‘qchisq’
margMLECI: no visible global function definition for ‘uniroot’
profMLECI : ciFunction: no visible global function definition for
  ‘qchisq’
profMLECI: no visible global function definition for ‘uniroot’
rtbinom: no visible global function definition for ‘rbinom’
rtpois: no visible global function definition for ‘rpois’
waldCI: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  optim qchisq qnorm rbinom rpois uniroot
Consider adding
  importFrom("stats", "optim", "qchisq", "qnorm", "rbinom", "rpois",
             "uniroot")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘combinat’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.Depth: no visible global function definition for ‘quantile’
PS.FDR: no visible global function definition for ‘quantile’
Permu.Ind: no visible global function definition for ‘permn’
Permu.Ind: no visible global function definition for ‘hcube’
Trans.Data: no visible global function definition for ‘write.table’
Trans.Data: no visible global function definition for ‘predict’
Trans.Data: no visible global function definition for ‘lm’
Undefined global functions or variables:
  hcube lm permn predict quantile write.table
Consider adding
  importFrom("stats", "lm", "predict", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
rpoistweedie: no visible global function definition for ‘runif’
testOmegaPT: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘scatterplot3d’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.poLCA: no visible global function definition for ‘layout’
plot.poLCA: no visible global function definition for ‘par’
poLCA: no visible global function definition for ‘model.frame’
poLCA: no visible global function definition for ‘model.response’
poLCA: no visible global function definition for ‘model.matrix’
poLCA: no visible global function definition for ‘runif’
poLCA: no visible global function definition for ‘ginv’
poLCA: no visible global function definition for ‘flush.console’
poLCA.makeplot.dich: no visible global function definition for
  ‘scatterplot3d’
poLCA.makeplot.poly: no visible global function definition for
  ‘scatterplot3d’
poLCA.se: no visible global function definition for ‘ginv’
poLCA.simdata: no visible global function definition for ‘runif’
poLCA.simdata: no visible global function definition for ‘rnorm’
poLCA.table: no visible global function definition for ‘model.frame’
print.poLCA: no visible global function definition for ‘pt’
print.poLCA: no visible global function definition for ‘flush.console’
rmulti: no visible global function definition for ‘runif’
Undefined global functions or variables:
  flush.console ginv layout model.frame model.matrix model.response par
  pt rnorm runif scatterplot3d
Consider adding
  importFrom("graphics", "layout", "par")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pt", "rnorm", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Running examples in ‘politeness-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: politenessPlot
> ### Title: Politeness plot
> ### Aliases: politenessPlot
> 
> ### ** Examples
> 
> 
> data("phone_offers")
> 
> polite.data<-politeness(phone_offers$message, parser="none", binary=FALSE, drop_blank=FALSE)
Warning: argument binary is deprecated; please use metric instead.
Note: Some features cannot be computed without part-of-speech tagging. See ?spacyr::spacyr for details.> 
> politeness::politenessPlot(polite.data,
+                            split=phone_offers$condition,
+                            split_levels = c("Tough","Warm"),
+                            split_name = "Condition",
+                            top_title = "Average Feature Counts")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘politeness.Rmd’ using rmarkdown
politeness v0.2.6 successfully loaded. See ?politeness for help.
Quitting from lines 105-109 (politeness.Rmd) 
Error: processing vignette 'politeness.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘politeness.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘pollimetrydata’
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.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

Parsed with column specification:
cols(
  Favorable = col_double(),
  Unfavorable = col_double(),
  Undecided = col_double(),
  poll_slug = col_character(),
  survey_house = col_character(),
  start_date = col_date(format = ""),
  end_date = col_date(format = ""),
  question_text = col_character(),
  sample_subpopulation = col_character(),
  observations = col_double(),
  margin_of_error = col_double(),
  mode = col_character(),
  partisanship = col_character(),
  partisan_affiliation = col_character()
)
Parsed with column specification:
cols(
  label = col_character(),
  date = col_date(format = ""),
  value = col_double(),
  low = col_logical(),
  high = col_logical()
)
Quitting from lines 36-46 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘examples.Rmd’

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

Error: Vignette re-building failed.
Execution halted
qPolyaAeppliSingle: no visible global function definition for ‘qgamma’
rPolyaAeppli: no visible global function definition for ‘rpois’
rPolyaAeppli: no visible global function definition for ‘rgeom’
Undefined global functions or variables:
  qgamma rgeom rpois
Consider adding
  importFrom("stats", "qgamma", "rgeom", "rpois")
to your NAMESPACE file.
Running examples in ‘polypoly-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: poly_plot
> ### Title: Plot a polynomial matrix
> ### Aliases: poly_plot poly_plot_data
> 
> ### ** Examples
> 
> # Defaults to plotting using the row number as x-axis
> m <- poly(1:100, degree = 3)
> poly_plot(m)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Quitting from lines 68-69 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘overview.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_iRAM_dist
> ### Title: Plot distribution of recovery time based on bootstrapped version
> ###   of iRAM
> ### Aliases: plot_iRAM_dist
> 
> ### ** Examples
> 
> ## Don't show: 
> plot_iRAM_dist(bootstrap_iRAM_3node$recovery.time.reps)
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_iRAM_dist ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Three_node_exmaple.Rmd’ using rmarkdown
Loading required package: reshape2
Quitting from lines 120-156 (Three_node_exmaple.Rmd) 
Error: processing vignette 'Three_node_exmaple.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Three_node_exmaple.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘matrixcalc’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘matrixcalc’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
print.mixed.pom: no visible global function definition for ‘pnorm’
print.pom: no visible global function definition for ‘pnorm’
siteocc : get.mod.matrix: no visible binding for global variable
  ‘na.pass’
siteocc : get.mod.matrix: no visible global function definition for
  ‘formula’
siteocc : get.mod.matrix: no visible global function definition for
  ‘model.matrix’
siteocc: no visible global function definition for ‘nlminb’
siteocc: no visible global function definition for
  ‘is.positive.definite’
Undefined global functions or variables:
  formula is.positive.definite model.matrix na.pass nlminb pnorm
Consider adding
  importFrom("stats", "formula", "model.matrix", "na.pass", "nlminb",
             "pnorm")
to your NAMESPACE file.
Running examples in ‘pooling-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_dfa
> ### Title: Plot Log-OR vs. X for Normal Discriminant Function Approach
> ### Aliases: plot_dfa
> 
> ### ** Examples
> 
> # Fit discriminant function model for poolwise Xtilde vs. (Y, C), without
> # assuming a constant log-OR. Ignoring processing errors for simplicity.
> data(pdat1)
> fit <- p_dfa_xerrors(g = pdat1$g, y = pdat1$numcases, xtilde = pdat1$xtilde,
+                      c = pdat1$c, errors = "neither", constant_or = FALSE)
> 
> # Plot estimated log-OR vs. X at mean value for C
> p <- plot_dfa(estimates = fit$estimates, varcov = fit$theta.var,
+               xrange = range(pdat1$xtilde / pdat1$g),
+               cvals = mean(pdat1$c / pdat1$g))
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
> p
Warning: Removed 1 rows containing missing values (geom_hline).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
Quitting from lines 169-172 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘examples.Rmd’

--- re-building ‘intro-poped.Rmd’ using rmarkdown
Quitting from lines 155-156 (intro-poped.Rmd) 
Error: processing vignette 'intro-poped.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro-poped.Rmd’

SUMMARY: processing the following files failed:
  ‘examples.Rmd’ ‘intro-poped.Rmd’

Error: Vignette re-building failed.
Execution halted
asymmetricIntervals: no visible global function definition for ‘stack’
bonferroniIntervals: no visible global function definition for ‘stack’
bonferroniIntervals: no visible global function definition for ‘lm’
bonferroniIntervals: no visible global function definition for
  ‘predict’
bootstrapIntervals: no visible global function definition for ‘stack’
component1a: no visible global function definition for ‘pnorm’
component1b: no visible global function definition for ‘pnorm’
component2: no visible global function definition for ‘dgamma’
eqnForMin: no visible global function definition for ‘pnorm’
eqnForMin: no visible global function definition for ‘integrate’
integrand : <anonymous>: no visible global function definition for
  ‘pnorm’
integrand: no visible global function definition for ‘dnorm’
integrate2: no visible global function definition for ‘integrate’
integrate2a: no visible global function definition for ‘integrate’
integrate2b: no visible global function definition for ‘integrate’
integrate4a: no visible global function definition for ‘integrate’
integrate4b: no visible global function definition for ‘integrate’
optimalCScalar2: no visible global function definition for ‘uniroot’
optimalLambda: no visible global function definition for ‘optimise’
optimalLambdaC: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dgamma dnorm integrate lm optimise pnorm predict stack uniroot
Consider adding
  importFrom("stats", "dgamma", "dnorm", "integrate", "lm", "optimise",
             "pnorm", "predict", "uniroot")
  importFrom("utils", "stack")
to your NAMESPACE file.
Running examples in ‘poppr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diversity_ci
> ### Title: Perform bootstrap statistics, calculate, and plot confidence
> ###   intervals.
> ### Aliases: diversity_ci
> 
> ### ** Examples
> 
> library(poppr)
> data(Pinf)
> diversity_ci(Pinf, n = 100L)

Confidence Intervals have been centered around observed statistic.
Please see ?diversity_ci for details.

Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: diversity_ci ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mlg.Rmd’ using rmarkdown
Loading required package: adegenet
Loading required package: ade4

   /// adegenet 2.1.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()


This is poppr version 2.8.2. To get started, type package?poppr
OMP parallel support: available
Loading required package: ape

Attaching package: 'phangorn'

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

    AICc

Quitting from lines 289-294 (mlg.Rmd) 
Error: processing vignette 'mlg.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘mlg.Rmd’

--- re-building ‘poppr_manual.Rmd’ using rmarkdown
Quitting from lines 845-848 (poppr_manual.Rmd) 
Error: processing vignette 'poppr_manual.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘poppr_manual.Rmd’

--- re-building ‘algo.Rnw’ using knitr
Loading required package: adegenet
Loading required package: ade4

   /// adegenet 2.1.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()


This is poppr version 2.8.2. To get started, type package?poppr
OMP parallel support: available
Warning in infinite_vals_replacement(D, warning) :
  Infinite values detected.
--- finished re-building ‘algo.Rnw’

SUMMARY: processing the following files failed:
  ‘mlg.Rmd’ ‘poppr_manual.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Quitting from lines 45-46 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
popRangeSim: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  write.table
Consider adding
  importFrom("utils", "write.table")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘burkina-faso-females.Rnw’ using Sweave
Loading required package: coda
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files
gdata: ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files
gdata: ENABLED.

Attaching package: ‘gdata’

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

    nobs

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

    object.size

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

    startsWith


Error: processing vignette 'burkina-faso-females.Rnw' failed with diagnostics:
 chunk 8 (label = PLOT-age-specific-fert-rate) 
Error in Summary.unit(structure(c(3.6, 3.6), unit = 8L, class = c("margin",  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘burkina-faso-females.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: map.marginal
> ### Title: Plot Marginal Distribution
> ### Aliases: map.marginal
> 
> ### ** Examples
> 
> data(iris)
> 
> ## set data frame and labels
> df <- subset(iris,select=-Species)
> labels <- subset(iris,select=Species)
> 
> ## build a map
> m <- map.build(df, labels, xdim=15, ydim=10, train=1000)
> 
> ## display marginal distribution of dimension 1
> map.marginal(m,1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' call to ‘methods’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘portfolioSim/R/AllClasses.R’:
  .onLoad calls:
    require(methods)

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

contributionSummaryDf,simResult : <anonymous>: no visible global
  function definition for ‘aggregate’
getSimTrades,stiFromSignal-orderable-portfolio-simData-logical: no
  visible binding for global variable ‘shares’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.freq’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.errors’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.type’
loadIn,simResult-character-missing: no visible binding for global
  variable ‘master.summary.interface’
loadIn,simResultSinglePeriod-character-missing: no visible binding for
  global variable ‘x’
plot,simResult-missing: no visible global function definition for
  ‘xyplot’
runSim,portfolioSim-logical: no visible binding for global variable
  ‘id’
runSim,portfolioSim-logical: no visible global function definition for
  ‘updateSummary’
securityPerfSummaryDf,simResult: no visible global function definition
  for ‘aggregate’
summary,simResult: no visible global function definition for ‘sd’
summary,simResult: no visible global function definition for ‘head’
summary,simResult: no visible global function definition for ‘tail’
Undefined global functions or variables:
  aggregate head id master.errors master.freq master.summary.interface
  master.type sd shares tail updateSummary x xyplot
Consider adding
  importFrom("stats", "aggregate", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-zoned.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    collapse

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 139-150 (getting-zoned.Rmd) 
Error: processing vignette 'getting-zoned.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘getting-zoned.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [635s/546s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("POUMM")
  Loading required package: POUMM
  Loading required package: Rcpp
    generate 10000 samples 
    generate 10000 samples 
    generate 10000 samples 
  Killed
Error(s) in re-building vignettes:
  ...
--- re-building ‘powdR_vignette.Rmd’ using rmarkdown
powdR: Full Pattern Summation of X-Ray Powder Diffraction Data
Quitting from lines 42-56 (powdR_vignette.Rmd) 
Error: processing vignette 'powdR_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘powdR_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

powell: no visible global function definition for ‘Quote’
Undefined global functions or variables:
  Quote
Consider adding
  importFrom("methods", "Quote")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘powell/libs/powell.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘powell.o’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dropout_manual
> ### Title: Manually specify dropout per time point
> ### Aliases: dropout_manual
> 
> ### ** Examples
> 
> dropout <- dropout_manual(0, 0, 0, 0, 0.2, 0.2, 0.3, 0.3, 0.4, 0.4, 0.45)
> 
> p <- study_parameters(n1 = 11,
+                       n2 = 5,
+                       n3 = 6,
+                       T_end = 10,
+                       icc_pre_subject = 0.5,
+                       icc_pre_cluster = 0,
+                       var_ratio = 0.03,
+                       icc_slope = 0.05,
+                       dropout = dropout,
+                       cohend = -0.8)
> plot(p, plot = 2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simulations.Rmd’ using rmarkdown
--- finished re-building ‘simulations.Rmd’

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

--- re-building ‘three-level.Rmd’ using rmarkdown
Scale for 'x' is already present. Adding another scale for 'x', which
will replace the existing scale.
Quitting from lines 197-200 (three-level.Rmd) 
Error: processing vignette 'three-level.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘three-level.Rmd’

--- re-building ‘two-level.Rmd’ using rmarkdown
Quitting from lines 163-164 (two-level.Rmd) 
Error: processing vignette 'two-level.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘two-level.Rmd’

SUMMARY: processing the following files failed:
  ‘three-level.Rmd’ ‘two-level.Rmd’

Error: Vignette re-building 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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘fcm.Rmd’ using rmarkdown
Loading required package: ggplot2
Welcome! Related Books: `Practical Guide To Cluster Analysis in R` at https://goo.gl/13EFCZ
Quitting from lines 202-207 (fcm.Rmd) 
Error: processing vignette 'fcm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘fcm.Rmd’

--- re-building ‘pcm.Rmd’ using rmarkdown
Loading required package: ggplot2
Welcome! Related Books: `Practical Guide To Cluster Analysis in R` at https://goo.gl/13EFCZ
Quitting from lines 188-193 (pcm.Rmd) 
Error: processing vignette 'pcm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pcm.Rmd’

--- re-building ‘upfc.Rmd’ using rmarkdown
Loading required package: ggplot2
Welcome! Related Books: `Practical Guide To Cluster Analysis in R` at https://goo.gl/13EFCZ
Quitting from lines 235-240 (upfc.Rmd) 
Error: processing vignette 'upfc.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘upfc.Rmd’

SUMMARY: processing the following files failed:
  ‘fcm.Rmd’ ‘pcm.Rmd’ ‘upfc.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCity
> ### Title: Visualizatio of all top cities.
> ### Aliases: plotCity
> ### Keywords: internal
> 
> ### ** Examples
> 
> 
> ## Don't show: 
> library(ppcSpatial)
> plotCity()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘PPforest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ternary_str
> ### Title: Data structure with the projected and boundary by node and
> ###   class.
> ### Aliases: ternary_str
> 
> ### ** Examples
> 
> #crab data set with all the observations used as training
> pprf.crab <- PPforest(data = crab, std =TRUE, class = "Type",
+  size.tr = 1, m = 100, size.p = .5, PPmethod = 'LDA')
>  require(dplyr)
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

> pl_ter <- function(dat, dx, dy ){
+   p1  <- dat[[1]] %>% dplyr::filter(pair %in% paste(dx, dy, sep = "-") ) %>%
+     dplyr::select(Class, x, y) %>%
+     ggplot2::ggplot(ggplot2::aes(x, y, color = Class)) +
+     ggplot2::geom_segment(data = dat[[2]], ggplot2::aes(x = x1, xend = x2,
+                                                y = y1, yend = y2), color = "black" ) +
+     ggplot2::geom_point(size = I(3), alpha = .5) +
+     ggplot2::labs(y = " ",  x = " ") +
+     ggplot2::theme(legend.position = "none", aspect.ratio = 1) +
+     ggplot2::scale_colour_brewer(type = "qual", palette = "Dark2") +
+     ggplot2::labs(x = paste0("T", dx, " "), y = paste0("T", dy, " ")) +
+     ggplot2::theme(aspect.ratio = 1)
+   p1
+ }
> #ternary plot in tree different selected dierections
>  pl_ter(ternary_str(pprf.crab, id = c(1, 2, 3), sp = 3, dx = 1, dy = 2), 1, 2 )
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPforest-vignette.Rmd’ using rmarkdown
Loading required package: PPforest
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: RColorBrewer
Loading required package: GGally
Loading required package: ggplot2

Attaching package: 'GGally'

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

    nasa

Loading required package: gridExtra

Attaching package: 'gridExtra'

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

    combine

Loading required package: PPtreeViz
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Quitting from lines 118-129 (PPforest-vignette.Rmd) 
Error: processing vignette 'PPforest-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PPforest-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ppgmmga
> ### Title: Projection pursuit based on Gaussian mixtures and evolutionary
> ###   algorithms for data visualisation
> ### Aliases: ppgmmga print.ppgmmga
> 
> ### ** Examples
> 
> 
> data(iris)
> X <- iris[,-5]
> Class <- iris$Species
> 
> # Unscented Transformation approximation (default)
> pp1 <- ppgmmga(data = X, d = 2, approx = "UT", seed = 123)
> summary(pp1, check = TRUE)
── ppgmmga ───────────────────────────── 

Data dimensions               = 150 x 4 
Data transformation           = center & scale 
Projection subspace dimension = 2 
GMM density estimate          = (VVV,2)
Negentropy approximation      = UT 
GA optimal negentropy         = 0.9461873 
GA encoded basis solution: 
          x1       x2         x3       x4       x5       x6
[1,] 1.62551 1.170375 0.07635218 0.564489 1.355774 2.316635

Estimated projection basis: 
                     PP1        PP2
Sepal.Length -0.07013906 -0.4841843
Sepal.Width   0.00384141 -0.6982979
Petal.Length -0.91821379  0.2345145
Petal.Width  -0.38980661 -0.4721744

Monte Carlo Negentropy approximation check: 
                           UT
Approx Negentropy 0.946187289
MC Negentropy     0.943898857
MC se             0.003331479
Relative accuracy 1.002424446
> plot(pp1, Class)
Warning in if (params$x != 0) { :
  the condition has length > 1 and only the first element will be used
Warning in if (params$y != 0) { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ppgmmga.Rmd’ using rmarkdown
Package 'ppgmmga' version 1.0.1
Quitting from lines 58-63 (ppgmmga.Rmd) 
Error: processing vignette 'ppgmmga.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ppgmmga.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PPQ.ggplot
> ### Title: Heatmap/Contour GGPlot for Dynamically Assessing Power of the
> ###   CQA PPQ Plan Using General Multiplier.
> ### Aliases: PPQ.ggplot
> 
> ### ** Examples
> 
> mu <- seq(95, 105, 0.1)
> sigma <- seq(0.1,1.7,0.1)
> PPQ.ggplot(attr.name = "Sterile Concentration Assay", attr.unit = "%", Llim=95, Ulim=105,
+ mu = mu, sigma = sigma, k=2.373, dynamic = FALSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
Quitting from lines 114-120 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PPQplan-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_pfit.Rmd’ using rmarkdown
PP package calling ...
Follow this project on github: https://github.com/manuelreif/PP.git
Quitting from lines 131-155 (intro_pfit.Rmd) 
Error: processing vignette 'intro_pfit.Rmd' failed with diagnostics:
'x' contains missing values
--- failed re-building ‘intro_pfit.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
pps1: no visible global function definition for ‘runif’
ppss: no visible global function definition for ‘runif’
ppswr: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
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.
Running examples in ‘PPtreeViz-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Huberplot
> ### Title: Huber plot
> ### Aliases: Huberplot
> ### Keywords: projection pursuit
> 
> ### ** Examples
> 
> data(iris)
> Huberplot(iris[,1:2],iris[,5],PPmethod="LDA")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: Huberplot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
TT.test : <anonymous>: no visible global function definition for
  ‘t.test’
TT.test: no visible binding for global variable ‘sd’
TT.test: no visible global function definition for ‘setNames’
kirjelda : combo: no visible binding for global variable ‘sd’
kor.tabel: no visible binding for global variable ‘cor.test’
Undefined global functions or variables:
  cor.test sd setNames t.test
Consider adding
  importFrom("stats", "cor.test", "sd", "setNames", "t.test")
to your NAMESPACE file.
Running examples in ‘prcbench-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.evalcurve
> ### Title: Plot the result of Precision-Recall curve evaluation
> ### Aliases: autoplot.evalcurve
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> ## Plot evaluation results on test datasets r1, r2, and r3
> testset <- create_testset("curve", c("c1", "c2", "c3"))
> toolset <- create_toolset(set_names = "crv5")
> eres1 <- run_evalcurve(testset, toolset)
> autoplot(eres1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: autoplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [183s/245s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(prcbench)
  > 
  > test_check("prcbench")
  ── 1. Failure: autoplot.evalcurve (@test_plot_autoplot.R#16)  ──────────────────
  `suppressWarnings(autoplot(evalcrv1))` threw an error.
  Message: VECTOR_ELT() can only be applied to a 'list', not a 'double'
  Class:   simpleError/error/condition
  
  ── 2. Failure: autoplot.evalcurve (@test_plot_autoplot.R#22)  ──────────────────
  `suppressWarnings(autoplot(evalcrv2))` threw an error.
  Message: VECTOR_ELT() can only be applied to a 'list', not a 'double'
  Class:   simpleError/error/condition
  
  ── 3. Failure: autoplot.evalcurve ret_grob (@test_plot_autoplot.R#36)  ─────────
  `suppressWarnings(grid.draw(pp))` threw an error.
  Message: VECTOR_ELT() can only be applied to a 'list', not a 'double'
  Class:   simpleError/error/condition
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 752 SKIPPED: 0 FAILED: 3
  1. Failure: autoplot.evalcurve (@test_plot_autoplot.R#16) 
  2. Failure: autoplot.evalcurve (@test_plot_autoplot.R#22) 
  3. Failure: autoplot.evalcurve ret_grob (@test_plot_autoplot.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 156-169 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_r_squared
> ### Title: Plot R^2 (r-squared) values for a range of number of profiles
> ### Aliases: plot_r_squared
> 
> ### ** Examples
> 
> df <- mtcars
> plot_r_squared(df, mpg, wt, hp, qsec, to_center = TRUE, lower_bound = 2, upper_bound = 4)
################################
Clustering data for iteration 2
Clustering data for iteration 3
Clustering data for iteration 4
################################
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_r_squared
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_to_prcr.Rmd’ using rmarkdown
Quitting from lines 23-37 (introduction_to_prcr.Rmd) 
Error: processing vignette 'introduction_to_prcr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction_to_prcr.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pplot.deciles
> ### Title: Plot deciles
> ### Aliases: pplot.deciles precintcon.plot.deciles
> ### Keywords: deciles precipitation
> 
> ### ** Examples
> 
> ## Loading the monthly precipitation serie.
> #
> data(monthly)
> 
> ## Performing the a set of statistical analysis
> #
> pplot.deciles(monthly)
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: pplot.deciles ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 61-69 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- 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 ‘predict3d.Rmd’ using rmarkdown
Loading required package: predict3d
Loading required package: rgl
Quitting from lines 46-49 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘predict3d.Rmd’

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

Error: Vignette re-building failed.
Execution halted
gausspred: no visible global function definition for ‘qt’
mvapred: no visible global function definition for ‘qt’
Undefined global functions or variables:
  qt
Consider adding
  importFrom("stats", "qt")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘DESCRIPTION.bck’
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘predmixcor/R/firstlib.r’:
  .First.lib calls:
    cat("predmixcor loaded\n", "COPY RIGHT: Longhai Li\n", "http://math.usask.ca/~longhai\n",     "Type ?begin.predmixcor for help\n", sep = "")

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

Predict.mix: no visible global function definition for ‘dbinom’
abs_cor: no visible global function definition for ‘cor’
gen.alpha.IGamma: no visible global function definition for ‘qgamma’
gendata.mix: no visible global function definition for ‘runif’
gendata.mix: no visible global function definition for ‘rbeta’
mh1.unif: no visible global function definition for ‘runif’
train_predict_mix: no visible global function definition for ‘dbinom’
training: no visible global function definition for ‘runif’
training: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  cor dbinom qgamma rbeta runif
Consider adding
  importFrom("stats", "cor", "dbinom", "qgamma", "rbeta", "runif")
to your NAMESPACE file.
Running examples in ‘PredPsych-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DimensionRed
> ### Title: Generic Dimensionallity Reduction Function
> ### Aliases: DimensionRed
> 
> ### ** Examples
> 
> # reducing dimension of Grip aperture from 10 to 2
> GripAperture <- DimensionRed(KinData,selectedCols = 12:21,
+ outcome = KinData[,"Object.Size"],plot = TRUE)

Performing Dimensionality Reduction analysis 

Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: DimensionRed ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘preference-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.preference.trial
> ### Title: Plot the effect sizes of a preference trial
> ### Aliases: plot.preference.trial
> 
> ### ** Examples
> 
> 
> # Plot trials with fixed power and varying preference effect.
> trials <- pt_from_power(power = 0.8, pref_effect = seq(0.5, 2, by = 0.1), 
+                         selection_effect = 1, treatment_effect = 1, 
+                         sigma2 = 1, pref_prop = 0.6)
> plot(trials)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘prepplotOverview.Rmd’ using rmarkdown
Quitting from lines 31-62 (prepplotOverview.Rmd) 
Error: processing vignette 'prepplotOverview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘prepplotOverview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘preprosim.Rmd’ using rmarkdown
Loading required package: lattice
Loading required package: ggplot2
Warning: Continuous x aesthetic -- did you forget aes(group=...)?
Quitting from lines 63-65 (preprosim.Rmd) 
Error: processing vignette 'preprosim.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘preprosim.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘preproviz.Rmd’ using rmarkdown
Quitting from lines 35-37 (preproviz.Rmd) 
Error: processing vignette 'preproviz.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘preproviz.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Non-standard file/directory found at top level:
  ‘COPYRIGHTS’
Copyright information should be in file inst/COPYRIGHTS
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting_started_with_preText.Rmd’ using rmarkdown
Quitting from lines 140-141 (getting_started_with_preText.Rmd) 
Error: processing vignette 'getting_started_with_preText.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘getting_started_with_preText.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sigplot
> ### Title: sigplot
> ### Aliases: sigplot
> 
> ### ** Examples
> 
> 
> #Load the iris dataset
> data(iris)
> 
> #Set up the predictors object
> 
> predictors=iris[,c(1:4)]
> colnames(predictors)<-colnames(iris[1:4])
> 
> #Execute the main pRF function
> p.test<-pRF(response=factor(iris$Species),
+ predictors=iris[,c(1:4)],n.perms=20,mtry=3,
+ type="classification",alpha=0.05)
Checking if response variable is valid
fitting original random forest
populating permuted importance table
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
[1] 11
[1] 12
[1] 13
[1] 14
[1] 15
[1] 16
[1] 17
[1] 18
[1] 19
[1] 20
calculating permutation p.values
adjusting for FDR using two-step BH
> 
> #Plot
> 
> sigplot(pRF.list=p.test,threshold=0.1)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘interpolation-in-small-samples.Rmd’ using rmarkdown
Quitting from lines 50-91 (interpolation-in-small-samples.Rmd) 
Error: processing vignette 'interpolation-in-small-samples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘interpolation-in-small-samples.Rmd’

--- re-building ‘visualizing-psm-results.Rmd’ using rmarkdown
Quitting from lines 83-147 (visualizing-psm-results.Rmd) 
Error: processing vignette 'visualizing-psm-results.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘visualizing-psm-results.Rmd’

SUMMARY: processing the following files failed:
  ‘interpolation-in-small-samples.Rmd’ ‘visualizing-psm-results.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following hidden files and directories:
  data/.Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘deSolve’ which was already attached by Depends.
  Please remove these calls from your code.
LVCompGames: no visible global function definition for ‘runif’
LVCompGames: no visible global function definition for ‘plot’
LVCompGames: no visible global function definition for ‘axis’
LVCompGames: no visible global function definition for ‘box’
LVCompGames: no visible global function definition for ‘lines’
LVCompGames: no visible global function definition for ‘points’
MetaSim: no visible global function definition for ‘runif’
chesson: no visible global function definition for ‘rbeta’
chesson: no visible global function definition for ‘dbeta’
chesson : rhof: no visible global function definition for ‘dbeta’
chesson: no visible global function definition for ‘integrate’
pimmlawton: no visible global function definition for ‘runif’
Undefined global functions or variables:
  axis box dbeta integrate lines plot points rbeta runif
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot", "points")
  importFrom("stats", "dbeta", "integrate", "rbeta", "runif")
to your NAMESPACE file.
Running examples in ‘primerTree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.primerTree
> ### Title: plot function for a primerTree object, calls plot_tree_ranks
> ### Aliases: plot.primerTree
> 
> ### ** Examples
> 
> library(gridExtra)
> library(directlabels)
> #plot with all common ranks
> plot(mammals_16S)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following significant warnings:
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 2 equals destination size [-Wstringop-truncation]
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 3 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PRIMME.Rcheck/00install.out’ for details.
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.
pr.conditional: no visible global function definition for ‘qnorm’
pr.marginal: no visible global function definition for ‘qnorm’
prLogisticDelta: no visible global function definition for ‘glm’
prLogisticDelta: no visible binding for global variable ‘binomial’
Undefined global functions or variables:
  binomial glm qnorm
Consider adding
  importFrom("stats", "binomial", "glm", "qnorm")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘equivocal-zones.Rmd’ using rmarkdown

Attaching package: 'probably'

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

    as.factor, as.ordered


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 ‘equivocal-zones.Rmd’

--- re-building ‘where-to-use.Rmd’ using rmarkdown

Attaching package: 'probably'

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

    as.factor, as.ordered


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: tidyr
Quitting from lines 170-196 (where-to-use.Rmd) 
Error: processing vignette 'where-to-use.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘where-to-use.Rmd’

SUMMARY: processing the following file failed:
  ‘where-to-use.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggroc.roc
> ### Title: Plot a ROC curve with ggplot2
> ### Aliases: ggroc.roc ggroc.list ggroc
> 
> ### ** Examples
> 
> # Create a basic roc object
> data(aSAH)
> rocobj <- roc(aSAH$outcome, aSAH$s100b)
> rocobj2 <- roc(aSAH$outcome, aSAH$wfns)
> 
> library(ggplot2)
> g <- ggroc(rocobj)
> g
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
Running examples in ‘productplots-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: prodplot
> ### Title: Create a product plot
> ### Aliases: prodplot
> 
> ### ** Examples
> 
> if (require("ggplot2")) {
+ prodplot(happy, ~ happy, "hbar")
+ prodplot(happy, ~ happy, "hspine")
+ 
+ prodplot(happy, ~ sex + happy, c("vspine", "hbar"))
+ prodplot(happy, ~ sex + happy, stacked())
+ 
+ prodplot(happy, ~ happy + sex | health, mosaic("h")) + aes(fill=happy)
+ # The levels argument can be used to extract a given level of the plot
+ prodplot(happy, ~ sex + happy, stacked(), level = 1)
+ prodplot(happy, ~ sex + happy, stacked(), level = 2)
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
profBinary: no visible global function definition for ‘model.frame’
profBinary: no visible global function definition for ‘model.matrix’
profLinear: no visible global function definition for ‘model.frame’
profLinear: no visible global function definition for ‘model.matrix’
profLinear: no visible global function definition for ‘model.response’
profLinear: no visible global function definition for ‘model.extract’
summary.profBinary: no visible global function definition for ‘terms’
summary.profBinary: no visible global function definition for ‘qbeta’
summary.profLinear: no visible global function definition for ‘terms’
Undefined global functions or variables:
  model.extract model.frame model.matrix model.response qbeta terms
Consider adding
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "model.response", "qbeta", "terms")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘nlme’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘profr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot.profr
> ### Title: Visualise profiling data with ggplot2. Visualise profiling data
> ###   stored in a 'profr' data.frame.
> ### Aliases: ggplot.profr
> ### Keywords: hplot
> 
> ### ** Examples
> 
> if (require("ggplot2")) {
+   ggplot(nesting_prof)
+   ggplot(reshape_prof)
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Packages in Depends field not imported from:
  ‘splines’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
IndividualPROC: no visible global function definition for ‘survfit’
IndividualPROC: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile survfit
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Running examples in ‘projections-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cumulate.projections
> ### Title: Compute cumulative projections
> ### Aliases: cumulate.projections
> 
> ### ** Examples
> 
> 
> if (require(distcrete) &&
+     require(incidence)) {
+ 
+   ## simulate basic epicurve
+   dat <- c(0, 2, 2, 3, 3, 5, 5, 5, 6, 6, 6, 6)
+   i <- incidence(dat)
+ 
+ 
+   ## example with a function for SI
+   si <- distcrete("gamma", interval = 1L,
+                   shape = 1.5,
+                   scale = 2, w = 0)
+   set.seed(1)
+   pred_1 <- project(i, runif(100, 0.8, 1.9), si, n_days = 30)
+   plot_1 <- plot(pred_1)
+ 
+   ## cumulative predictions
+   pred_1_cum <- cumulate(pred_1)
+   pred_1_cum
+   plot(pred_1_cum)
+ }
Loading required package: distcrete
Loading required package: incidence
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Loading required package: Rcpp
rstanarm (Version 2.18.2, packaged: 2018-11-08 22:19:38 UTC)
- Do not expect the default priors to remain the same in future rstanarm versions.
Thus, R scripts should specify priors explicitly, even if they are just the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())
- Plotting theme set to bayesplot::theme_default().
This is projpred version 1.1.1.
This is bayesplot version 1.6.0
- Online documentation and vignettes at mc-stan.org/bayesplot
- bayesplot theme set to bayesplot::theme_default()
   * Does _not_ affect other ggplot2 plots
   * See ?bayesplot_theme_set for details on theme setting
Quitting from lines 62-64 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_start.Rmd’ using rmarkdown
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 51-52 (quick_start.Rmd) 
Error: processing vignette 'quick_start.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quick_start.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotciAAS
> ### Title: Plot of CI estimation of adjusted ArcSine
> ### Aliases: PlotciAAS
> 
> ### ** Examples
> 
> n=5; alp=0.05;h=2
> PlotciAAS(n,alp,h)
Warning: Ignoring unknown aesthetics: x
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
Cul: no visible global function definition for ‘qf’
blockScale: no visible binding for global variable ‘sd’
cochranTest: no visible global function definition for ‘prcomp’
cochranTest: no visible binding for global variable ‘var’
cochranTest: no visible global function definition for ‘matplot’
cochranTest: no visible global function definition for ‘legend’
continuumRemoval : crfun: no visible global function definition for
  ‘chull’
continuumRemoval : crfun: no visible global function definition for
  ‘approx’
continuumRemoval : crfun: no visible global function definition for
  ‘splinefun’
detrend: no visible binding for global variable ‘sd’
duplex: no visible global function definition for ‘prcomp’
e2m: no visible global function definition for ‘cov’
kenStone: no visible global function definition for ‘prcomp’
naes: no visible global function definition for ‘prcomp’
naes: no visible global function definition for ‘kmeans’
puchwein: no visible global function definition for ‘prcomp’
readASD: no visible global function definition for ‘read.table’
resample : resfun: no visible global function definition for ‘approx’
resample : resfun: no visible global function definition for
  ‘splinefun’
shenkWest: no visible global function definition for ‘prcomp’
spliceCorrection : extrapfun: no visible global function definition for
  ‘lm’
standardNormalVariate: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  approx chull cov kmeans legend lm matplot prcomp qf read.table sd
  splinefun var
Consider adding
  importFrom("grDevices", "chull")
  importFrom("graphics", "legend", "matplot")
  importFrom("stats", "approx", "cov", "kmeans", "lm", "prcomp", "qf",
             "sd", "splinefun", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
addIonSatistics: no visible binding for global variable ‘median’
adjustOne: no visible binding for global variable ‘median’
attachModifications: no visible global function definition for
  ‘na.omit’
avrgLoadingCalculation: no visible binding for global variable ‘median’
channelResponses : estimate: no visible binding for global variable
  ‘var’
responseStatisics : func: no visible global function definition for
  ‘aggregate’
testing: no visible global function definition for ‘aov’
testingOneshot: no visible global function definition for ‘anova’
testingTukey: no visible global function definition for ‘TukeyHSD’
Undefined global functions or variables:
  TukeyHSD aggregate anova aov median na.omit var
Consider adding
  importFrom("stats", "TukeyHSD", "aggregate", "anova", "aov", "median",
             "na.omit", "var")
to your NAMESPACE file.
estimateLSEparam: no visible global function definition for ‘lm’
estimateMLEparam: no visible global function definition for ‘optim’
getCCnlL: no visible global function definition for ‘dnorm’
iterateScampi: no visible global function definition for ‘quantile’
plot.scampi: no visible global function definition for ‘hist’
plot.scampiVal: no visible global function definition for ‘par’
plot.scampiVal: no visible global function definition for ‘hist’
plot.scampiVal: no visible global function definition for ‘abline’
plot.scampiVal: no visible global function definition for ‘qqnorm’
plot.scampiVal: no visible global function definition for ‘qqline’
sampleInitialVector: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline dnorm hist lm optim par qqline qqnorm quantile runif
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "dnorm", "lm", "optim", "qqline", "qqnorm",
             "quantile", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘class’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘class’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Extract_plant_grapevine_function: no visible global function definition
  for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Package suggested but not available for checking: ‘rdt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRROC.Rnw’ using Sweave
Error: processing vignette 'PRROC.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PRROC.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Package in Depends field not imported from: ‘rpart’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
mahalanobisComposite: no visible global function definition for
  ‘princomp’
prepareComposite: no visible global function definition for ‘cov’
winsorizor : f: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov princomp quantile
Consider adding
  importFrom("stats", "cov", "princomp", "quantile")
to your NAMESPACE file.
Running examples in ‘pscore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: distanceScores
> ### Title: Calculate distance scores on data in preparation for composite
> ###   scoring
> ### Aliases: distanceScores
> 
> ### ** Examples
> 
> # this example creates distances for the built in mtcars data
> # see ?mtcars for more details
> # The distances are calculated from the "best" in the dataset
> # defined by these thresholds
> thresholds <- with(mtcars, c(
+   mpg = max(mpg),
+   hp = max(hp),
+   wt = min(wt),
+   qsec = min(qsec)))
> 
> # higher mpg and hp are better,
> # whereas lower wt and qsec are better
> dres <- distanceScores(mtcars[, c("mpg", "hp", "wt", "qsec")],
+   thresholds = list(thresholds),
+   higherisbetter = c(TRUE, TRUE, FALSE, FALSE),
+   saveall = TRUE)
> 
> # see a density plot of the distance scores
> dres$Density
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘psda-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pplot
> ### Title: Plot polygonal symbolic variable
> ### Aliases: pplot
> 
> ### ** Examples
> 
> x <- psim(10, 10) #simulate 10 polygons of 10 sides
> pplot(x)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 403-408 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
candidate.overlap: no visible global function definition for
  ‘write.table’
fisher: no visible global function definition for ‘fisher.test’
fisher.iteration: no visible global function definition for
  ‘download.file’
fisher.iteration: no visible global function definition for
  ‘read.table’
pSI.list: no visible global function definition for ‘write.table’
specificity.index: no visible global function definition for ‘png’
specificity.index: no visible global function definition for ‘par’
specificity.index: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off download.file fisher.test par png read.table write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "par")
  importFrom("stats", "fisher.test")
  importFrom("utils", "download.file", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to ‘numDeriv’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
test.problem : g: no visible global function definition for ‘grad’
test.problem: no visible global function definition for ‘new’
psoptim,test.problem-missing-missing-missing-missing: no visible global
  function definition for ‘new’
show,test.result: no visible global function definition for ‘show’
show,test.result: no visible global function definition for ‘sd’
Undefined global functions or variables:
  grad new sd show
Consider adding
  importFrom("methods", "new", "show")
  importFrom("stats", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pspearman: no visible global function definition for ‘pt’
spearman.test: no visible global function definition for
  ‘complete.cases’
spearman.test: no visible global function definition for ‘cor’
Undefined global functions or variables:
  complete.cases cor pt
Consider adding
  importFrom("stats", "complete.cases", "cor", "pt")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘orig’
Error(s) in re-building vignettes:
  ...
--- re-building ‘pstr-vignette.Rmd’ using rmarkdown
Quitting from lines 129-132 (pstr-vignette.Rmd) 
Error: processing vignette 'pstr-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pstr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘EffectsRelBaseline’ ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
catEffectBootAdaptor: no visible binding for global variable ‘sumSqCat’
compExclusionFraction: no visible global function definition for
  ‘rpois’
compExclusionFraction: no visible global function definition for
  ‘t.test’
compExclusionFraction: no visible global function definition for ‘glm’
compExclusionFraction: no visible global function definition for
  ‘anova’
compPowerCatSelectivity: no visible binding for global variable
  ‘fRatioStat’
compPowerGeneralRespDetection: no visible binding for global variable
  ‘sumSqCat’
compPowerRespDetection: no visible binding for global variable
  ‘sumSqCat’
compRejectionFraction: no visible global function definition for
  ‘rpois’
compRejectionFraction: no visible global function definition for
  ‘t.test’
compRejectionFraction: no visible global function definition for ‘glm’
compRejectionFraction: no visible global function definition for
  ‘anova’
simCatResp: no visible global function definition for ‘rpois’
simNormCatResp: no visible global function definition for ‘rnorm’
testCatEffectBoot: no visible global function definition for ‘boot’
Undefined global functions or variables:
  anova boot fRatioStat glm rnorm rpois sumSqCat t.test
Consider adding
  importFrom("stats", "anova", "glm", "rnorm", "rpois", "t.test")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Quitting from lines 668-680 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘overview.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘multilevel’ ‘nlme’
A package should be listed in only one of these fields.
Non-standard file/directory found at top level:
  ‘README.txt’
'library' or 'require' calls to packages already attached by Depends:
  ‘multilevel’ ‘nlme’
  Please remove these calls from your code.
Found the following significant warnings:
  Warning: replacing previous import ‘loo::kfold’ by ‘rstanarm::kfold’ when loading ‘psycho’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/psycho.Rcheck/00install.out’ for details.
Running examples in ‘psycho-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HDI
> ### Title: Highest Density Intervals (HDI).
> ### Aliases: HDI
> 
> ### ** Examples
> 
> library(psycho)
> 
> distribution <- rnorm(1000, 0, 1)
> HDI_values <- HDI(distribution)
> print(HDI_values)
95% CI [-2.10, 2.03]
> plot(HDI_values)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘psychotree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bttree
> ### Title: Bradley-Terry Trees
> ### Aliases: bttree plot.bttree print.bttree predict.bttree itempar.bttree
> ### Keywords: tree
> 
> ### ** Examples
> 
> o <- options(digits = 4)
> 
> ## Germany's Next Topmodel 2007 data
> data("Topmodel2007", package = "psychotree")
> 
> ## BT tree
> tm_tree <- bttree(preference ~ ., data = Topmodel2007, minsize = 5, ref = "Barbara")
> plot(tm_tree, abbreviate = 1, yscale = c(0, 0.5))
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
Errors in running code in vignettes:
when running code in ‘raschtree.Rnw’
  ...

> library("psychotree")
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: psychotools

> data("SPISA", package = "psychotree")

> if (file.exists("raschtree-spisa.rda")) load("raschtree-spisa.rda") else {
+     my_first_raschtree <- raschtree(spisa ~ age + gender + semester + 
 .... [TRUNCATED] 

> file.remove("raschtree-spisa.rda")
[1] TRUE

> plot(my_first_raschtree)

  When sourcing ‘raschtree.R’:
Error: no string supplied for 'strwidth/height' unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘raschtree.Rnw’ using Sweave
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Loading required package: psychotools

Error: processing vignette 'raschtree.Rnw' failed with diagnostics:
 chunk 9 (label = plot_raschtree) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_CalibratedMSErr
> ### Title: Plot bargraph of uncalibrated mass errors for each Raw file.
> ### Aliases: plot_CalibratedMSErr
> 
> ### ** Examples
> 
>   n = c(150, 1000, 1000, 1000)
>   data = data.frame(fc.raw.file = repEach(letters[4:1], n),
+                     mass.error..ppm. = c(rnorm(n[1], 1, 2.4),
+                                          rnorm(n[2], 0.5, 0.5),
+                                          rnorm(n[3], 0.1, 0.7),
+                                          rnorm(n[4], 0.3, 0.8)))
>   stats = data.frame(fc.raw.file = letters[4:1],
+                      sd = c(2.4, 0.5, 0.7, 0.8),
+                      outOfCal = c(TRUE, FALSE, FALSE, FALSE))           
>   plot_CalibratedMSErr(data, MQBug_raw_files = letters[1], stats, y_lim = c(-20,20), 15, "subtitle")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Packages in Depends field not imported from:
  ‘R.utils’ ‘rmeta’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChisqTest_expect: no visible global function definition for ‘pchisq’
plot_chase_observed_expected: no visible global function definition for
  ‘meta.MH’
plot_chase_observed_expected: no visible global function definition for
  ‘txtProgressBar’
plot_chase_observed_expected: no visible global function definition for
  ‘setTxtProgressBar’
test.one.treated: no visible global function definition for
  ‘fisher.test’
test_one: no visible global function definition for ‘rbinom’
test_one: no visible global function definition for ‘fisher.test’
Undefined global functions or variables:
  fisher.test meta.MH pchisq rbinom setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "fisher.test", "pchisq", "rbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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.
CandidateBio.getBio : <anonymous>: no visible global function
  definition for ‘na.omit’
Committee.getCommittee : <anonymous>: no visible global function
  definition for ‘na.omit’
getAllBios: no visible global function definition for ‘txtProgressBar’
getAllBios: no visible global function definition for
  ‘setTxtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘txtProgressBar’
getAllLocalOfficials: no visible global function definition for
  ‘setTxtProgressBar’
getAllVotes: no visible global function definition for ‘txtProgressBar’
getAllVotes: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  na.omit setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Running examples in ‘pwr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.power.htest
> ### Title: Plot diagram of sample size vs. test power
> ### Aliases: plot.power.htest
> ### Keywords: htest
> 
> ### ** Examples
> 
> 
> ## Two-sample t-test
> p.t.two <- pwr.t.test(d=0.3, power=0.8, type="two.sample", alternative="two.sided")
> plot(p.t.two)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pwr-vignette.Rmd’ using rmarkdown
Quitting from lines 62-67 (pwr-vignette.Rmd) 
Error: processing vignette 'pwr-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pwr-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
.grid.matrix: no visible global function definition for ‘slot’
.matrix2grid: no visible global function definition for ‘as’
.poly2grid: no visible global function definition for ‘is’
.poly2grid: no visible global function definition for ‘slot’
.poly2grid: no visible global function definition for ‘as’
.pycno.core : smooth2D : s1d: no visible global function definition for
  ‘filter’
.pycno.core: no visible global function definition for ‘flush.console’
.pycno2matrix: no visible global function definition for ‘slot’
Undefined global functions or variables:
  as filter flush.console is slot
Consider adding
  importFrom("methods", "as", "is", "slot")
  importFrom("stats", "filter")
  importFrom("utils", "flush.console")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
pyramid: no visible global function definition for ‘plot’
pyramid: no visible global function definition for ‘segments’
pyramid: no visible global function definition for ‘lines’
pyramid: no visible global function definition for ‘text’
pyramid: no visible global function definition for ‘rect’
pyramidf: no visible global function definition for ‘segments’
pyramidf: no visible global function definition for ‘lines’
pyramidf: no visible global function definition for ‘text’
pyramidf: no visible global function definition for ‘rect’
Undefined global functions or variables:
  lines plot rect segments text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "segments", "text")
to your NAMESPACE file.
Running examples in ‘qad-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_density
> ### Title: Plot density of empirical checkerboard copula
> ### Aliases: plot_density
> 
> ### ** Examples
> 
> n <- 1000
> x <- runif(n,0,1)
> y <- runif(n,0,1)
> sample <- data.frame(x,y)
> plot(sample)
> 
> mass <- emp_c_copula(sample, resolution=8)
> plot_density(mass, density=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
Running examples in ‘QCAtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xyplot
> ### Title: Plot fuzzy set score of two sets against each other
> ### Aliases: xyplot
> 
> ### ** Examples
> 
> require(QCA)
Loading required package: QCA

To cite this package in publications, please use:
  Dusa, Adrian (2019) QCA with R. A Comprehensive Resource.
  Springer International Publishing.

To run the graphical user interface, use: runGUI()

NOTE: Found multiple functions and object type conflicts in the fork package QCApro.
      To avoid confusion, please uninstall it before using this software, with:
      uninstall("QCApro")

> data(d.urban)
> xyplot("MLC", "WSR", d.urban)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
dmm_fn: no visible global function definition for ‘dnorm’
dmm_noweights_fn: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Running examples in ‘qcQpcr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: qcQpcr-package
> ### Title: Histone ChIP-Seq qPCR Analyzer Histone ChIP-Seq qPCR Analyzer
> ### Aliases: qcQpcr-package
> ### Keywords: qpcr
> 
> ### ** Examples
> 
> 
> 
>   library(ggplot2)
>   data(SampleTest)
>   qcQpcr(SampleTest,'Title for your graph')
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘QCSimulator-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SWAPQ0Q1
> ### Title: SWAP Q0 Q1
> ### Aliases: SWAPQ0Q1
> 
> ### ** Examples
> 
> # Initialze global variables
> init()
> SWAPQ0Q1(q110_)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘qdap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: type_token_ratio
> ### Title: Type-Token Ratio
> ### Aliases: type_token_ratio
> 
> ### ** Examples
> 
> with(raj, type_token_ratio(dialogue, person))
            person   wc   ttr
1            Nurse 2206 0.426
2     Lady Capulet  872 0.436
3           Juliet 4263 0.454
4            Romeo 4665 0.462
5   Friar Laurence 2727 0.470
6          Abraham   24 0.500
7          Sampson  259 0.502
8            Paris  539 0.509
9          Capulet 2123 0.509
10           Peter  245 0.510
11          Prince  585 0.520
12        Mercutio 2094 0.533
13         Servant  183 0.573
14          Tybalt  262 0.574
15       Balthasar  232 0.575
16        Benvolio 1153 0.582
17        Montague  316 0.641
18         Gregory  149 0.664
19   First Servant   79 0.679
20  First Watchman  134 0.679
21  Second Capulet   17 0.706
22            Page   81 0.728
23          Chorus  113 0.730
24      Friar John   96 0.735
25  Second Servant   96 0.740
26   First Citizen   43 0.744
27  First Musician   62 0.750
28 Second Musician   34 0.824
29  Third Watchman   26 0.846
30      Apothecary   53 0.849
31   Lady Montague   28 0.897
32        Musician    8 1.000
33 Second Watchman    9 1.000
34  Third Musician    7 1.000

Type-token ratio for entire text: 0.448
> plot(with(raj, type_token_ratio(dialogue, person)))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘qgcomp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.qgcompfit
> ### Title: plot.qgcompfit: default plotting method for a qgcompfit object
> ### Aliases: plot.qgcompfit
> 
> ### ** Examples
> 
> set.seed(12)
> dat <- data.frame(x1=(x1 <- runif(100)), x2=runif(100), x3=runif(100), z=runif(100),
+                   y=runif(100)+x1+x1^2)
> ft <- qgcomp.noboot(y ~ z + x1 + x2 + x3, expnms=c('x1','x2','x3'), data=dat, q=4)
> ft
Scaled effect size (positive direction, sum of positive coefficients = 0.515)
    x1     x2 
0.9759 0.0241 

Scaled effect size (negative direction, sum of negative coefficients = -0.0163)
x3 
 1 

Mixture slope parameters (Delta method CI):

     Estimate Std. Error Lower CI Upper CI t value Pr(>|t|)
psi1 0.499201   0.050285  0.40064  0.59776  9.9275 2.22e-16
> plot(ft)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘qgcomp-vignette.Rmd’ using knitr
Loading required package: ggplot2
Loading required package: grid
Loading required package: gridExtra
Quitting from lines 171-186 (qgcomp-vignette.Rmd) 
Error: processing vignette 'qgcomp-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘qgcomp-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘qicharts2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: paretochart
> ### Title: Paretochart
> ### Aliases: paretochart
> 
> ### ** Examples
> 
> # Generate categorical vector
> x <- rep(LETTERS[1:9], c(256, 128, 64, 32, 16, 8, 4, 2, 1))
> 
> # Make paretochart
> paretochart(x)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘qicharts2.Rmd’ using rmarkdown
Quitting from lines 33-39 (qicharts2.Rmd) 
Error: processing vignette 'qicharts2.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘qicharts2.Rmd’

SUMMARY: processing the following file failed:
  ‘qicharts2.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.tcc
> ### Title: Summarise Trellis Control Charts
> ### Aliases: summary.tcc
> 
> ### ** Examples
> 
> # Build data frame for example
> d <- data.frame(x = rep(1:24, 4),
+                 mo = (rep(seq(as.Date('2014-1-1'),
+                               length.out = 24,
+                               by = 'month'),
+                           4)),
+                 n = rbinom(4 * 24, 100, 0.5),
+                 d = round(runif(4 * 24, 90, 110)),
+                 g1 = rep(c('a', 'b'), each = 48),
+                 g2 = rep(c('A', 'B'), each = 24))
> 
> # P chart
> p <- tcc(n, d, mo, g1 = g1, g2 = g2, breaks = 12, data = d, chart = 'p')
> plot(p)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Package suggested but not available for checking: ‘biom’
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.matrix’
chooseMDoubleBootstrap: no visible global function definition for
  ‘as.formula’
chooseMDoubleBootstrap: no visible global function definition for
  ‘model.frame’
chooseMDoubleBootstrap: no visible global function definition for ‘lm’
chooseMDoubleBootstrap: no visible global function definition for
  ‘coef’
chooseMDoubleBootstrap: no visible global function definition for
  ‘quantile’
chooseMDoubleBootstrap: no visible global function definition for
  ‘qnorm’
getModel: no visible global function definition for ‘lm’
getModel: no visible global function definition for ‘model.matrix’
getModel: no visible global function definition for ‘as.formula’
getModel: no visible global function definition for ‘model.frame’
getModel: no visible global function definition for ‘model.response’
getModel: no visible global function definition for ‘coef’
getModel: no visible global function definition for ‘qnorm’
qLearn: no visible global function definition for ‘model.matrix’
qLearn: no visible global function definition for ‘as.formula’
qLearn: no visible global function definition for ‘model.frame’
qLearn: no visible global function definition for ‘coef’
qLearn: no visible global function definition for ‘lm’
qLearn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  as.formula coef lm model.frame model.matrix model.response qnorm
  quantile
Consider adding
  importFrom("stats", "as.formula", "coef", "lm", "model.frame",
             "model.matrix", "model.response", "qnorm", "quantile")
to your NAMESPACE file.
pcAxisCubeMake: no visible global function definition for ‘aggregate’
pcAxisCubeToCSV: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  aggregate write.csv
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Running examples in ‘qqplotr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_pp_band
> ### Title: Probability-probability confidence bands
> ### Aliases: stat_pp_band
> 
> ### ** Examples
> 
> # generate random Normal data
> set.seed(0)
> smp <- data.frame(norm = rnorm(100), exp = rexp(100))
> 
> # Normal P-P plot of Normal data
> gg <- ggplot(data = smp, mapping = aes(sample = norm)) +
+  stat_pp_band() +
+  stat_pp_line() +
+  stat_pp_point() +
+  labs(x = "Probability Points", y = "Cumulative Probability")
> gg
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Loading required package: qqplotr
Loading required package: ggplot2

Attaching package: 'qqplotr'

The following objects are masked from 'package:ggplot2':

    StatQqLine, stat_qq_line

Quitting from lines 101-107 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘compileMetaObject’
File ‘qtbase/libs/qtbase.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘Rf_EncodeInteger’,
    ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’, ‘Rf_formatInteger’,
    ‘Rf_formatLogical’, ‘Rf_formatReal’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ci.length: no visible global function definition for ‘qexp’
detectable.bc: no visible global function definition for ‘uniroot’
detectable.f2: no visible global function definition for ‘uniroot’
detectable.ri: no visible global function definition for ‘uniroot’
nu: no visible global function definition for ‘pnorm’
nullinfo: no visible global function definition for ‘qnorm’
nullinfo: no visible global function definition for ‘dnorm’
optselection.bc: no visible global function definition for ‘optimize’
optselection.f2: no visible global function definition for ‘optimize’
optspacing.bc: no visible global function definition for ‘optim’
optspacing.bc: no visible global function definition for ‘optimize’
optspacing.f2: no visible global function definition for ‘optim’
optspacing.f2: no visible global function definition for ‘optimize’
powercalc.bc: no visible global function definition for ‘pchisq’
powercalc.f2: no visible global function definition for ‘pchisq’
samplesize.bc: no visible global function definition for ‘uniroot’
samplesize.f2: no visible global function definition for ‘uniroot’
samplesize.ri: no visible global function definition for ‘uniroot’
tailprob: no visible global function definition for ‘pchisq’
thresh: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dnorm optim optimize pchisq pnorm qexp qnorm uniroot
Consider adding
  importFrom("stats", "dnorm", "optim", "optimize", "pchisq", "pnorm",
             "qexp", "qnorm", "uniroot")
to your NAMESPACE file.
'library' or 'require' call to ‘Rmpfr’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
adjacencyMatrix: no visible global function definition for ‘as’
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard files/directories found at top level:
  ‘LICENSE.GPL-2’ ‘LICENSE.GPL-3’
quadp: no visible global function definition for ‘var’
Undefined global functions or variables:
  var
Consider adding
  importFrom("stats", "var")
to your NAMESPACE file.
Running examples in ‘quadrupen-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bounded.reg
> ### Title: Fit a linear model with infinity-norm plus ridge-like
> ###   regularization
> ### Aliases: bounded.reg
> ### Keywords: models, regression
> 
> ### ** Examples
> 
> ## Simulating multivariate Gaussian with blockwise correlation
> ## and piecewise constant vector of parameters
> beta <- rep(c(0,1,0,-1,0), c(25,10,25,10,25))
> cor <- 0.75
> Soo <- toeplitz(cor^(0:(25-1))) ## Toeplitz correlation for irrelevant variables
> Sww  <- matrix(cor,10,10) ## bloc correlation between active variables
> Sigma <- bdiag(Soo,Sww,Soo,Sww,Soo)
> diag(Sigma) <- 1
> n <- 50
> x <- as.matrix(matrix(rnorm(95*n),n,95) %*% chol(Sigma))
> y <- 10 + x %*% beta + rnorm(n,0,10)
> 
> ## Infinity norm without/with an additional l2 regularization term
> ## and with structuring prior
> labels <- rep("irrelevant", length(beta))
> labels[beta != 0] <- "relevant"
> plot(bounded.reg(x,y,lambda2=0) , label=labels) ## a mess
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
Running examples in ‘QualInt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: QualInt-package
> ### Title: R-package for qualitative interaction test
> ### Aliases: QualInt-package
> 
> ### ** Examples
> 
> test9 <- qualval(effect = c(1.0, 0.5, -2.0), se = c(0.86, 0.64, 0.32))
> print(test9)

Call:
qualval(effect = c(1, 0.5, -2), se = c(0.86, 0.64, 0.32))

Type:
unknown

Estimating Results for treatment effects:
  Estimate Std. Error Lower CI Upper CI
1      1.0       0.86  -0.6856    2.686
2      0.5       0.64  -0.7544    1.754
3     -2.0       0.32  -2.6272   -1.373

Test:
IBGA

p-value:
0.2299

Power:
0.3088

Alpha:
0.05

> plot(test9)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘qualint.Rnw’ using Sweave
Loading required package: survival
Loading required package: ggplot2

Error: processing vignette 'qualint.Rnw' failed with diagnostics:
 chunk 4 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘qualint.Rnw’

--- re-building ‘qualval.Rnw’ using Sweave
Loading required package: survival
Loading required package: ggplot2

Error: processing vignette 'qualval.Rnw' failed with diagnostics:
 chunk 3 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘qualval.Rnw’

SUMMARY: processing the following files failed:
  ‘qualint.Rnw’ ‘qualval.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    nasa

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 111-120 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘wilcox1973.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addSpecialProteins
> ### Title: add special labels
> ### Aliases: addSpecialProteins
> 
> ### ** Examples
> 
> 
> foldchange <- rnorm(1000)
> pvals <-rexp(1000)
> names <- sample(colors(),1000,replace=TRUE)
> 
> dataX <- data.frame(
+   q.mod = pvals,
+   log2FC = foldchange,
+   names = names
+ )
> library(rlang)
> foldchange = "log2FC"
> p <- volcano2GB(dataX, pthresh=0.1, log2FCThresh=0.5 , main='test',
+                 repel.segment.size=0.3,
+                 repel.text.size=2)
> special <- sample(colors(),5)
> p <- addSpecialProteins(p, dataX, special)
> p
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning: Removed 993 rows containing missing values (geom_text_repel).
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘quanteda-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: textplot_keyness
> ### Title: Plot word keyness
> ### Aliases: textplot_keyness
> ### Keywords: textplot
> 
> ### ** Examples
> 
> # compare Trump speeches to other Presidents by chi^2
> dfmat1 <- data_corpus_inaugural %>%
+      corpus_subset(Year > 1980) %>%
+      dfm(groups = "President", remove = stopwords("english"), remove_punct = TRUE)
> tstat1 <- textstat_keyness(dfmat1, target = "Trump")
> textplot_keyness(tstat1, margin = 0.2, n = 10)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Package version: 1.4.1
Parallel computing: 2 of 32 threads used.
See https://quanteda.io for tutorials and examples.

Attaching package: 'quanteda'

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

    View

Quitting from lines 158-166 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following calls to attach():
File ‘quantmod/R/attachSymbols.R’:
  attach(NULL, pos = pos, name = DB$name)
  attach(NULL, pos = pos, name = DB$name)
See section ‘Good practice’ in ‘?attach’.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Release.Rmd’ using rmarkdown
--- finished re-building ‘Release.Rmd’

--- re-building ‘Use_case.Rmd’ using rmarkdown
Quitting from lines 119-120 (Use_case.Rmd) 
Error: processing vignette 'Use_case.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Use_case.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.queue_list
> ### Title: ggplot2 method for output from queueing model
> ### Aliases: plot.queue_list
> 
> ### ** Examples
> 
> if(require(ggplot2, quietly = TRUE)){
+ 
+ n_customers <- 50
+ arrival_rate <- 1.8
+ service_rate <- 1
+ arrivals <- cumsum(rexp(n_customers, arrival_rate))
+ service <- rexp(n_customers, service_rate)
+ queue_obj <- queue_step(arrivals, service, servers = 2)
+ plot(queue_obj)
+ 
+ }
[[1]]
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘iii-plotting.Rmd’ using rmarkdown

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: sp

Attaching package: 'raster'

The following object is masked from 'package:data.table':

    shift

Quitting from lines 128-134 (iii-plotting.Rmd) 
Error: processing vignette 'iii-plotting.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘iii-plotting.Rmd’

SUMMARY: processing the following file failed:
  ‘iii-plotting.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cum_normal_fun
> ### Title: Cumulative normal function
> ### Aliases: cum_normal_fun
> 
> ### ** Examples
> 
> xseq <- seq(0,4,.01)
> yseq <- cum_normal_fun(xseq, c(2, .5))
> curve <- data.frame(x = xseq, y = yseq)
> ggplot(curve, aes(x = x, y = y)) + geom_line()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘quickReg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.reg
> ### Title: plot the result of regression result
> ### Aliases: plot.reg plot_reg
> 
> ### ** Examples
> 
> reg_glm<-reg(data = diabetes, y = 5, factor = c(1, 3, 4), model = 'glm')
> plot(reg_glm)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickReg.Rmd’ using rmarkdown
Quitting from lines 131-162 (quickReg.Rmd) 
Error: processing vignette 'quickReg.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickReg.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘QUIC/libs/QUIC.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘quokar.Rmd’ using rmarkdown
Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


Attaching package: 'dplyr'

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

    combine

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 62-63 (quokar.Rmd) 
Error: processing vignette 'quokar.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quokar.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘qwraps2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot2_extract_legend
> ### Title: ggplot2 tools
> ### Aliases: ggplot2_extract_legend
> 
> ### ** Examples
> 
> # a simple plot
> my_plot <- 
+   ggplot2::ggplot(mtcars) + 
+   ggplot2::aes(x = wt, y = mpg, color = wt, shape = factor(cyl)) + 
+   ggplot2::geom_point()
> 
> my_plot
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
mutualCoherence : .setOneMutualP: no visible global function definition
  for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘R2admb.Rnw’ using knitr
Loading required package: stats4

Attaching package: 'bbmle'

The following object is masked from 'package:R2admb':

    stdEr

Quitting from lines 153-164 (R2admb.Rnw) 
Error: processing vignette 'R2admb.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘R2admb.Rnw’

SUMMARY: processing the following file failed:
  ‘R2admb.Rnw’

Error: Vignette re-building failed.
Execution halted
conf2d.default: no visible global function definition for ‘polygon’
conf2d_int: no visible global function definition for ‘contourLines’
Undefined global functions or variables:
  contourLines polygon
Consider adding
  importFrom("grDevices", "contourLines")
  importFrom("graphics", "polygon")
to your NAMESPACE file.
'library' or 'require' call to ‘rgdal’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘matrixStats’ ‘rgdal’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘r2glmm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.R2
> ### Title: Visualize standardized effect sizes and model R squared
> ### Aliases: plot.R2
> 
> ### ** Examples
> 
> library(nlme)
> library(r2glmm)
> 
> data(Orthodont)
> 
> # Linear mixed model
> lmemod = lme(distance ~ age*Sex, random = ~1|Subject, data = Orthodont)
> 
> r2 = r2beta(model=lmemod,partial=TRUE,method='sgv')
Warning in model.matrix.default(~b$groups[[n.levels - i + 1]] - 1, contrasts.arg = c("contr.treatment",  :
  non-list contrasts argument ignored
> 
> plot(x=r2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following calls to attach():
File ‘R2OpenBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
Non-standard file/directory found at top level:
  ‘readme’
r2stl: no visible global function definition for ‘persp’
Undefined global functions or variables:
  persp
Consider adding
  importFrom("graphics", "persp")
to your NAMESPACE file.
Found the following calls to attach():
File ‘R2WinBUGS/R/attach.all.R’:
  attach(x, name = name)
See section ‘Good practice’ in ‘?attach’.
'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘leaps’ ‘rgl’ ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  R4dfp-object.c:253:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  R4dfp-object.c:260:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/R4dfp.Rcheck/00install.out’ for details.
Running examples in ‘r4lineups-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make_roc
> ### Title: Compute and plot ROC curve for lineup accuracy ~ confidence
> ### Aliases: make_roc
> 
> ### ** Examples
> 
> #Data:
> data(mickwick)
> 
> #Call:
> make_roc(mickwick)
Warning in roc.default(response, m[[predictors]], ...) :
  'response' has more than two levels. Consider setting 'levels' explicitly or using 'multiclass.roc' instead
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette.Rmd’ using rmarkdown
Warning in roc.default(response, m[[predictors]], ...) :
  'response' has more than two levels. Consider setting 'levels' explicitly or using 'multiclass.roc' instead
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Quitting from lines 398-400 (Vignette.Rmd) 
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.clt
> ### Title: Plot method for the Central Limit Theorem simulation
> ### Aliases: plot.clt
> 
> ### ** Examples
> 
> clt("Uniform", 100, 100, unif_min = 10, unif_max = 20) %>% plot()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: %>% ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘radiant.data-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.pivotr
> ### Title: Plot method for the pivotr function
> ### Aliases: plot.pivotr
> 
> ### ** Examples
> 
> pivotr(diamonds, cvars = "cut") %>% plot()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘radiant.design-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.sample_size_comp
> ### Title: Plot method for the sample_size_comp function
> ### Aliases: plot.sample_size_comp
> 
> ### ** Examples
> 
> sample_size_comp(
+   type = "proportion", p1 = 0.1, p2 = 0.15,
+   conf_lev = 0.95, power = 0.8
+ ) %>% plot()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘radiant.model-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.confusion
> ### Title: Plot method for the confusion matrix
> ### Aliases: plot.confusion
> 
> ### ** Examples
> 
> data.frame(buy = dvd$buy, pred1 = runif(20000), pred2 = ifelse(dvd$buy == "yes", 1, 0)) %>%
+   confusion(c("pred1", "pred2"), "buy") %>%
+   plot()
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘radiant.multivariate-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.conjoint
> ### Title: Plot method for the conjoint function
> ### Aliases: plot.conjoint
> 
> ### ** Examples
> 
> result <- conjoint(mp3, rvar = "Rating", evar = "Memory:Shape")
> plot(result, scale_plot = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot -> plot.conjoint -> %>% -> eval -> eval -> sshhr
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘programming.Rmd’ using rmarkdown
Quitting from lines 39-44 (programming.Rmd) 
Error: processing vignette 'programming.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘programming.Rmd’

SUMMARY: processing the following file failed:
  ‘programming.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.
RnDif.het: no visible global function definition for ‘runif’
RnDif.hom: no visible global function definition for ‘runif’
RnDifAdv.hom: no visible global function definition for ‘runif’
SoilAdv.hom: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘rags2ridges-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: edgeHeat
> ### Title: Visualize (precision) matrix as a heatmap
> ### Aliases: edgeHeat
> 
> ### ** Examples
> 
> ## Obtain some (high-dimensional) data
> p = 25
> n = 10
> set.seed(333)
> X = matrix(rnorm(n*p), nrow = n, ncol = p)
> colnames(X)[1:25] = letters[1:25]
> Cx <- covML(X)
> 
> ## Obtain regularized precision matrix
> P <- ridgeP(Cx, lambda = 10, type = "Alt")
> 
> ## Obtain sparsified partial correlation matrix
> PC0 <- sparsify(P, threshold = "localFDR", FDRcut = .8)$sparseParCor
Step 1... determine cutoff point
Step 2... estimate parameters of null distribution and eta0
Step 3... compute p-values and estimate empirical PDF/CDF
Step 4... compute q-values and local fdr
Step 5... prepare for plotting

- Retained elements:  11 
- Corresponding to 3.67 % of possible edges 
 
> 
> ## Visualize sparsified partial correlation matrix as heatmap
> edgeHeat(PC0)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ragt2ridges-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sparsifyVAR2
> ### Title: Function that determines the support of autoregression
> ###   parameters of the VAR(2) model.
> ### Aliases: sparsifyVAR2
> 
> ### ** Examples
> 
> # set dimensions (p=covariates, n=individuals, T=time points)
> p <- 3; n <- 12; T <- 10
> 
> # set model parameters
> SigmaE <- diag(p)/4
> A1 <- -createA(p, "clique", nCliques=1, nonzeroA=0.1)
> A2 <- t(createA(p, "chain", nBands=1, nonzeroA=0.1))
> 
> # generate data
> Y <- dataVAR2(n, T, A1, A2, SigmaE)
> 
> # fit VAR(1) model
> VAR2hat <- ridgeVAR2(Y, 1, 1, 1)
> 
> # obtain support of adjacancy matrix
> A1nullornot <- matrix(0, p, p)
> A1nullornot[sparsifyVAR2(VAR2hat$A1, VAR2hat$A2, solve(VAR1hat$P), 
+                          threshold="top", top=c(3,3))$nonzerosA1] <- 1
-> Retained elements of A1:  3 
-> Corresponding to 33.33 % of possible A1 elements 
-> Retained elements of A2:  3 
-> Corresponding to 33.33 % of possible A2 elements 
> 
> ## plot non-null structure of A1 
> edgeHeat(A1nullornot)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ragtop_convertibles_in_r.Rmd’ using rmarkdown
Warning: Removed 39 rows containing missing values (geom_path).
Quitting from lines 408-418 (ragtop_convertibles_in_r.Rmd) 
Error: processing vignette 'ragtop_convertibles_in_r.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ragtop_convertibles_in_r.Rmd’

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

Error: Vignette re-building failed.
Execution halted
cpc_get_rawdata: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘raincpc_demo.Rmd’ using knitr
Loading required package: sp

Attaching package: 'raster'

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

    distance

Quitting from lines 103-117 (raincpc_demo.Rmd) 
Error: processing vignette 'raincpc_demo.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘raincpc_demo.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: OTU.recap
> ### Title: Summarize OTU
> ### Aliases: OTU.recap
> ### Keywords: math
> 
> ### ** Examples
> 
> data(ITS1, ITS2)
> ranks <- c("p", "c", "o", "f", "g")
> df <- OTU.recap(data=list(ITS1=ITS1, ITS2=ITS2), ranks=ranks)
Using ind as id variables
Using ind as id variables
Warning in brewer.pal(len, brewer.pal) :
  n too large, allowed maximum for palette Pastel1 is 9
Returning the palette you asked for with that many colors

Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: OTU.recap ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘randomForestExplainer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_importance_ggpairs
> ### Title: Plot importance measures with ggpairs
> ### Aliases: plot_importance_ggpairs
> 
> ### ** Examples
> 
> forest <- randomForest::randomForest(Species ~ ., data = iris, localImp = TRUE, ntree = 200)
> frame <- measure_importance(forest, measures = c("mean_min_depth", "times_a_root"))
Warning: Factor `split var` contains implicit NA, consider using `forcats::fct_explicit_na`
> plot_importance_ggpairs(frame, measures = c("mean_min_depth", "times_a_root"))
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘randomForestExplainer.Rmd’ using rmarkdown
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Quitting from lines 68-70 (randomForestExplainer.Rmd) 
Error: processing vignette 'randomForestExplainer.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘randomForestExplainer.Rmd’

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

Error: Vignette re-building failed.
Execution halted
.disableThreads: no visible global function definition for
  ‘stopCluster’
.enableThreads: no visible global function definition for ‘detectCores’
.enableThreads: no visible global function definition for
  ‘makePSOCKcluster’
.enableThreads: no visible global function definition for
  ‘clusterExport’
.enableThreads: no visible global function definition for ‘clusterCall’
.forwardSelection: no visible binding for global variable ‘var’
.forwardSelection: no visible global function definition for ‘glm’
.forwardSelection: no visible global function definition for ‘formula’
.forwardSelection: no visible global function definition for ‘binomial’
.forwardSelection: no visible global function definition for ‘lm’
.forwardSelection: no visible global function definition for ‘predict’
.predict.internal: no visible global function definition for ‘predict’
randomGLM: no visible binding for global variable ‘cor’
randomGLM: no visible binding for global variable ‘sd’
randomGLM: no visible global function definition for ‘var’
thinRandomGLM: no visible global function definition for ‘glm’
thinRandomGLM: no visible global function definition for ‘binomial’
thinRandomGLM: no visible global function definition for ‘lm’
Undefined global functions or variables:
  binomial clusterCall clusterExport cor detectCores formula glm lm
  makePSOCKcluster predict sd stopCluster var
Consider adding
  importFrom("stats", "binomial", "cor", "formula", "glm", "lm",
             "predict", "sd", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘randomGLM/R/randomGLM.R’:
  assign(".randomGLMparallelCluster", cluster, pos = ".GlobalEnv")
anovaF: no visible global function definition for ‘anova’
anovaF: no visible global function definition for ‘lm’
randInterval: no visible global function definition for ‘quantile’
randInterval : <anonymous>: no visible global function definition for
  ‘quantile’
randPlot: no visible global function definition for ‘par’
randPlot: no visible global function definition for ‘hist’
randPlot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline anova hist lm par quantile
Consider adding
  importFrom("graphics", "abline", "hist", "par")
  importFrom("stats", "anova", "lm", "quantile")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘article.Rnw’ using knitr
Warning in remind_sweave(if (in.file) input, sweave_lines) :
  It seems you are using the Sweave-specific syntax in line(s) 766; you may need Sweave2knitr("article.Rnw") to convert it to knitr
Loading required package: ggplot2
Loading required package: plotrix
Quitting from lines 927-929 (article.Rnw) 
Error: processing vignette 'article.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘article.Rnw’

--- re-building ‘comparison-example.Rnw’ using knitr
Loading required package: ggplot2
Loading required package: plotrix
Quitting from lines 153-154 (comparison-example.Rnw) 
Error: processing vignette 'comparison-example.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘comparison-example.Rnw’

--- re-building ‘desirability-example.Rnw’ using knitr
Loading required package: ggplot2
Loading required package: plotrix
--- finished re-building ‘desirability-example.Rnw’

--- re-building ‘randomizeR-refCard.Rnw’ using knitr
--- finished re-building ‘randomizeR-refCard.Rnw’

SUMMARY: processing the following files failed:
  ‘article.Rnw’ ‘comparison-example.Rnw’

Error: Vignette re-building failed.
Execution halted
bartels.rank.test: no visible global function definition for ‘na.omit’
bartels.rank.test: no visible global function definition for ‘pbeta’
bartels.rank.test: no visible global function definition for ‘pnorm’
cox.stuart.test: no visible global function definition for ‘pbinom’
difference.sign.test: no visible global function definition for
  ‘na.omit’
difference.sign.test: no visible global function definition for ‘pnorm’
rank.test: no visible global function definition for ‘na.omit’
rank.test: no visible global function definition for ‘pnorm’
rruns: no visible global function definition for ‘runif’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘na.omit’
runs.test: no visible global function definition for ‘points’
runs.test: no visible global function definition for ‘abline’
runs.test: no visible global function definition for ‘gray’
runs.test: no visible global function definition for ‘pnorm’
turning.point.test: no visible global function definition for ‘embed’
turning.point.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline embed gray median na.omit pbeta pbinom pnorm points runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "points")
  importFrom("stats", "embed", "median", "na.omit", "pbeta", "pbinom",
             "pnorm", "runif")
to your NAMESPACE file.
Running examples in ‘rangeMapper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot,rmap.frame,missing-method
> ### Title: Plot a rmap.frame
> ### Aliases: plot,rmap.frame,missing-method
> 
> ### ** Examples
> 
> require(rangeMapper)
> breding_ranges = rgdal::readOGR(system.file(package = "rangeMapper",
+      "extdata", "wrens", "vector_combined"), "wrens", verbose = FALSE)[1:70, ]
> data(wrens)
> d = subset(wrens, select = c('sci_name', 'body_mass', 'clutch_size') )
> con = ramp("wrens.sqlite", gridSize = 4, spdf = breding_ranges, biotab = d, ID = "sci_name",
+             FUN = "median", overwrite = TRUE)
New session 2019-03-29 21:25:35
PROJECT: wrens.sqlite 
DIRECTORY: /home/hornik/tmp/scratch/RtmpGyrq80
Grid size set to 4 map units.
Canvas uploaded.
Writing overlay output to project...
70 out of 70 ranges updated; Elapsed time: 0 mins
Table biotab saved as a  BIO_ table
+______________+
class            rangeMap
Project_location /home/hornik/tmp/scratch/RtmpGyrq80/wrens.sqlite
Proj4            +proj=longlat +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +no_defs
CellSize         4
Extent           xmin=-126.1848,xmax=-34.79333,ymin=-55.72056,ymax=59.32195
BIO_tables       biotab
MAP_tables       species_richness;median_body_mass;median_clutch_size
METADATA_RANGES  
+______________+
> m = rangeMap.fetch(con, c('median_body_mass', 'median_clutch_size'), spatial = FALSE)
> plot(m, ncol = 2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rangemodelR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rangemod2d
> ### Title: Range Cohesion Models for Spatial Polygon Grids
> ### Aliases: rangemod2d
> 
> ### ** Examples
> 
> if(require(rgdal)&&require(maptools)&&require(rgeos)&&require(ggplot2)){
+ data(shp)
+ data(neigh_ob)
+ data(spmat)
+ mod.out <- rangemod2d(spmat,shp,"ID",nb = neigh_ob,rsize = "observed",
+                        var = NULL,reps = 5)
+ shp.out <- mod.out$out.shp
+ shp.out.df <- shp.out@data
+ shp.out.fort <- fortify(shp.out,region = "ID")
+ seq <- match(shp.out.fort$id,shp.out.df$ID)
+ shp.out.gg <- data.frame(shp.out.fort,shp.out.df[seq,])
+ ggplot(shp.out.gg)+
+   geom_map(map=shp.out.gg,aes_string(map_id="id",
+                                      fill = "mod.rich"))+
+   geom_path(aes(x = long,y = lat,group = group),colour = "white")+
+   coord_equal() + theme_bw()+
+   scale_fill_continuous(low = "white",high = "black")
+ }
Loading required package: rgdal
Loading required package: sp
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
 Path to GDAL shared files: /usr/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: 1.3-1 
Loading required package: maptools
Checking rgeos availability: TRUE
Loading required package: rgeos
rgeos version: 0.4-2, (SVN revision 581)
 GEOS runtime version: 3.7.1-CAPI-1.11.1 
 Linking to sp version: 1.3-1 
 Polygon checking: TRUE 

Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
src/Makevars: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
  src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_LIBS but not in PKG_CXXFLAGS
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
rank.L2R: no visible global function definition for ‘kmeans’
rank.L2R: no visible global function definition for ‘pnorm’
rank.LN: no visible global function definition for ‘kmeans’
rank.LN: no visible global function definition for ‘pnorm’
rank.gs: no visible global function definition for ‘qnorm’
rank.wald: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  kmeans pnorm qnorm
Consider adding
  importFrom("stats", "kmeans", "pnorm", "qnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘BSgenome.Hsapiens.UCSC.hg19’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
freq: no visible global function definition for ‘xtabs’
freq: no visible binding for global variable ‘na.pass’
freq: no visible global function definition for ‘melt’
freq: no visible global function definition for ‘complete.cases’
freq: no visible global function definition for ‘tail’
kurtosis: no visible global function definition for ‘na.omit’
label: no visible global function definition for ‘tail’
name: no visible global function definition for ‘tail’
nvalid : <anonymous>: no visible global function definition for
  ‘na.omit’
rp.desc: no visible global function definition for ‘melt.data.frame’
rp.desc: no visible global function definition for ‘cast’
rp.desc: no visible global function definition for ‘na.omit’
rp.desc : <anonymous>: no visible global function definition for ‘tail’
rp.desc : <anonymous>: no visible global function definition for ‘head’
rp.freq: no visible global function definition for ‘xtabs’
rp.freq: no visible binding for global variable ‘na.pass’
rp.freq: no visible global function definition for ‘melt’
rp.freq: no visible global function definition for ‘complete.cases’
rp.freq: no visible global function definition for ‘tail’
rp.label: no visible global function definition for ‘tail’
rp.name: no visible global function definition for ‘tail’
rp.outlier : lundcrit: no visible global function definition for ‘qf’
rp.outlier: no visible global function definition for ‘lm’
rp.outlier: no visible global function definition for ‘rstandard’
rp.valid : <anonymous>: no visible global function definition for
  ‘na.omit’
skewness: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  cast complete.cases head lm melt melt.data.frame na.omit na.pass qf
  rstandard tail xtabs
Consider adding
  importFrom("stats", "complete.cases", "lm", "na.omit", "na.pass", "qf",
             "rstandard", "xtabs")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
fnRAP: no visible global function definition for ‘chisq.test’
fnRAP: no visible global function definition for ‘combn’
Undefined global functions or variables:
  chisq.test combn
Consider adding
  importFrom("stats", "chisq.test")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running examples in ‘raptr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: space.plot
> ### Title: Plot space
> ### Aliases: space.plot space.plot.RapData space.plot.RapUnsolved
> ###   space.plot.RapSolved
> 
> ### ** Examples
> 
> # load RapSolved objects
> data(sim_ru, sim_rs)
> 
> # plot first species in first attribute space
> space.plot(sim_ru, 1, 1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following significant warnings:
  avc_binwr.c:166:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:173:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:180:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:187:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: ‘%4.4d’ directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: ‘%s’ directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: ‘-ID’ directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: ‘%s’ directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RArcInfo.Rcheck/00install.out’ for details.
plotarc: no visible global function definition for ‘par’
plotarc: no visible global function definition for ‘plot’
plotarc: no visible global function definition for ‘lines’
plotpoly: no visible global function definition for ‘par’
plotpoly: no visible global function definition for ‘plot’
plotpoly: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  lines par plot polygon
Consider adding
  importFrom("graphics", "lines", "par", "plot", "polygon")
to your NAMESPACE file.
INT_FIX: no visible global function definition for ‘rbinom’
INT_FIX: no visible global function definition for ‘glm’
INT_FIX: no visible global function definition for ‘as.formula’
INT_FIX: no visible global function definition for ‘residuals’
INT_FIX: no visible global function definition for ‘var’
INT_RAN: no visible global function definition for ‘rbinom’
INT_RAN: no visible global function definition for ‘as.formula’
INT_RAN: no visible global function definition for ‘predict’
JOINT: no visible global function definition for ‘rbinom’
JOINT: no visible global function definition for ‘glm’
JOINT: no visible global function definition for ‘as.formula’
JOINT: no visible global function definition for ‘var’
JOINT: no visible global function definition for ‘residuals’
pKuonen: no visible global function definition for ‘pchisq’
pKuonen: no visible global function definition for ‘uniroot’
pKuonen: no visible global function definition for ‘pnorm’
rareGE: no visible global function definition for ‘rbinom’
rareGE: no visible global function definition for ‘as.formula’
rareGE: no visible global function definition for ‘predict’
rareGE: no visible global function definition for ‘glm’
rareGE: no visible global function definition for ‘residuals’
rareGE: no visible global function definition for ‘var’
rareGE_joint_mc: no visible global function definition for ‘pchisq’
rareGE_joint_mc: no visible global function definition for ‘qchisq’
wuweights: no visible global function definition for ‘dbeta’
Undefined global functions or variables:
  as.formula dbeta glm pchisq pnorm predict qchisq rbinom residuals
  uniroot var
Consider adding
  importFrom("stats", "as.formula", "dbeta", "glm", "pchisq", "pnorm",
             "predict", "qchisq", "rbinom", "residuals", "uniroot",
             "var")
to your NAMESPACE file.
BiogTest.individual: no visible global function definition for ‘combn’
BiogTest.individual: no visible global function definition for ‘runif’
BiogTest.individual: no visible global function definition for ‘rlnorm’
BiogTest.individual: no visible global function definition for
  ‘rnbinom’
BiogTest.sample: no visible global function definition for ‘combn’
BiogTest.sample: no visible global function definition for ‘runif’
BiogTest.sample: no visible global function definition for ‘rlnorm’
BiogTest.sample: no visible global function definition for ‘rnbinom’
BiogTest.sample: no visible global function definition for ‘aggregate’
EcoTest.individual: no visible global function definition for ‘xtabs’
plot.BiogTest: no visible global function definition for ‘quantile’
plot.BiogTest: no visible global function definition for ‘combn’
plot.EcoTest: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate combn quantile rlnorm rnbinom runif xtabs
Consider adding
  importFrom("stats", "aggregate", "quantile", "rlnorm", "rnbinom",
             "runif", "xtabs")
  importFrom("utils", "combn")
to your NAMESPACE file.
rateratio.test: no visible global function definition for
  ‘complete.cases’
rateratio.test: no visible global function definition for ‘pbinom’
rateratio.test : p.L: no visible global function definition for ‘qbeta’
rateratio.test : p.U: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  complete.cases pbinom qbeta
Consider adding
  importFrom("stats", "complete.cases", "pbinom", "qbeta")
to your NAMESPACE file.
concordance: no visible global function definition for ‘quantile’
concordance : Normal: no visible global function definition for ‘qnorm’
concordance : Normal: no visible global function definition for ‘pnorm’
concordance : MC: no visible global function definition for ‘rmultinom’
concordance : MC: no visible global function definition for ‘quantile’
concordance: no visible global function definition for ‘qnorm’
concordance: no visible global function definition for ‘pnorm’
concordance : Chisq: no visible global function definition for ‘qchisq’
concordance : Chisq: no visible global function definition for ‘pchisq’
concordance : Normal2: no visible global function definition for
  ‘qnorm’
concordance : Normal2: no visible global function definition for
  ‘pnorm’
concordance : MC2: no visible global function definition for
  ‘rmultinom’
concordance : MC2: no visible global function definition for ‘quantile’
wlin.conc: no visible global function definition for ‘quantile’
wlin.conc : MC: no visible global function definition for ‘rmultinom’
wlin.conc : MC: no visible global function definition for ‘quantile’
wquad.conc: no visible global function definition for ‘quantile’
wquad.conc : MC: no visible global function definition for ‘rmultinom’
wquad.conc : MC: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  pchisq pnorm qchisq qnorm quantile rmultinom
Consider adding
  importFrom("stats", "pchisq", "pnorm", "qchisq", "qnorm", "quantile",
             "rmultinom")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘RDperm.Rnw’ using knitr
Loading required package: RATest
Loading required package: ggplot2
Loading required package: gridExtra
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Quitting from lines 616-651 (RDperm.Rnw) 
Error: processing vignette 'RDperm.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RDperm.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rsr
> ### Title: Rating scale reduction
> ### Aliases: rsr
> 
> ### ** Examples
> 
> #creating the matrix of attributes and the decision vector
> #must be as.numeric()
> data(aSAH)
> attach(aSAH)
> is.numeric(aSAH)
[1] FALSE
> 
> attribute <-data.frame(as.numeric(gender), 
+ as.numeric(age), as.numeric(wfns), as.numeric(s100b), as.numeric(ndka))
> colnames(attribute) <-c("a1", "a2", "a3", "a4", "a5")
> decision <-as.numeric(outcome)
> 
> #rating scale reduction procedure
> rsred <-rsr(attribute, decision, plotRSR=TRUE)
> rsred
$rsr.auc
[1] 0.8236789 0.8241870

$rsr.label
[1] "a3" "a4"

$summary
   AUC one variable AUC running total
a3        0.8236789         0.8236789
a4        0.7313686         0.8241870

[[4]]
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
.GCD: no visible global function definition for ‘as.polynomial’
.LCM: no visible global function definition for ‘as.polynomial’
.is_zero_polynomial: no visible global function definition for ‘coef’
.poly2expr: no visible global function definition for ‘coef’
integral.rationalfun: no visible global function definition for ‘coef’
integraterf.transcendent: no visible global function definition for
  ‘coef’
rationalfun: no visible global function definition for ‘polynomial’
rationalfun.poly: no visible global function definition for
  ‘polynomial’
rationalfun.poly: no visible global function definition for
  ‘is.polynomial’
rfun: no visible global function definition for ‘polynomial’
rfun.poly: no visible global function definition for ‘polynomial’
rfun.poly: no visible global function definition for ‘is.polynomial’
simplify: no visible global function definition for ‘coef’
simplify: no visible global function definition for ‘polynomial’
Undefined global functions or variables:
  as.polynomial coef is.polynomial polynomial
Consider adding
  importFrom("stats", "coef")
to your NAMESPACE file.
Package suggested but not available for checking: ‘playwith’
.avisApiBusAvanzada: no visible global function definition for
  ‘read.csv’
.avisRenderMapAdmin: no visible global function definition for ‘points’
.avisRenderMapAdmin: no visible global function definition for ‘rect’
.avisRenderMapPhysical: no visible global function definition for
  ‘points’
avisMap: no visible global function definition for ‘par’
avisMap: no visible global function definition for ‘layout’
Undefined global functions or variables:
  layout par points read.csv rect
Consider adding
  importFrom("graphics", "layout", "par", "points", "rect")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Running examples in ‘RBesT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: forest_plot
> ### Title: Forest Plot
> ### Aliases: forest_plot
> 
> ### ** Examples
> 
> # we consider the example AS MAP analysis
> example(AS)

AS> set.seed(34563)

AS> map_AS <- gMAP(cbind(r, n-r) ~ 1 | study,
AS+                family=binomial,
AS+                data=AS,
AS+                tau.dist="HalfNormal", tau.prior=1,
AS+                beta.prior=2,
AS+                ## ensure fast example runtime
AS+                thin=1, chains=1)
Assuming default prior location   for beta: 0
Final MCMC sample equivalent to less than 1000 independent draws.
Please consider increasing the MCMC simulation size.
> 
> # default forest plot for a gMAP analysis
> forest_plot(map_AS)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rbin-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rbin_equal_length
> ### Title: Equal length binning
> ### Aliases: rbin_equal_length plot.rbin_equal_length
> 
> ### ** Examples
> 
> bins <- rbin_equal_length(mbank, y, age, 10)
> bins
Binning Summary
---------------------------------
Method               Equal Length 
Response             y 
Predictor            age 
Bins                 10 
Count                4521 
Goods                517 
Bads                 4004 
Entropy              0.5 
Information Value    0.17 


# A tibble: 10 x 7
   cut_point bin_count  good   bad     woe       iv entropy
   <chr>         <int> <int> <int>   <dbl>    <dbl>   <dbl>
 1 < 24.6           85    24    61 -1.11   0.0347     0.859
 2 < 31.2          822   106   716 -0.137  0.00358    0.555
 3 < 37.8         1133   115  1018  0.134  0.00425    0.474
 4 < 44.4          943    82   861  0.304  0.0172     0.426
 5 < 51            623    52   571  0.349  0.0147     0.414
 6 < 57.6          612    66   546  0.0660 0.000574   0.493
 7 < 64.2          229    43   186 -0.582  0.0214     0.697
 8 < 70.8           34    12    22 -1.44   0.0255     0.937
 9 < 77.4           25    13    12 -2.13   0.0471     0.999
10 >= 77.4          15     4    11 -1.04   0.00517    0.837
> 
> # plot
> plot(bins)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 59-61 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
GetHistoricTradeData: no visible global function definition for
  ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
bn2nbn: no visible binding for global variable ‘bn.fit’
chain4chain: no visible binding for global variable ‘head’
chain4chain: no visible binding for global variable ‘tail’
estimate8arcs: no visible global function definition for ‘lm’
estimate8arcs: no visible global function definition for ‘coefficients’
estimate8nbn: no visible global function definition for ‘lm’
estimate8nbn: no visible global function definition for ‘as.formula’
estimate8nbn: no visible global function definition for ‘anova’
estimate8nbn: no visible global function definition for ‘coefficients’
generate8chain: no visible global function definition for ‘runif’
generate8chain: no visible global function definition for ‘rbinom’
generate8nbn: no visible global function definition for ‘runif’
generate8nbn: no visible global function definition for ‘rbinom’
nbn2bnfit: no visible global function definition for ‘model2network’
nbn2bnfit: no visible global function definition for ‘custom.fit’
simulate8gema: no visible global function definition for ‘rnorm’
simulate8mn: no visible global function definition for ‘mvrnorm’
simulate8nbn: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  anova as.formula bn.fit coefficients custom.fit head lm model2network
  mvrnorm rbinom rnorm runif tail
Consider adding
  importFrom("stats", "anova", "as.formula", "coefficients", "lm",
             "rbinom", "rnorm", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Running examples in ‘RBMRB-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HSQC_13C
> ### Title: Simulates H1-C13 HSQC spectra for a given entry or list of
> ###   entries from BMRB
> ### Aliases: HSQC_13C
> 
> ### ** Examples
> 
> plot_hsqc<-HSQC_13C(c(17074,17076,17077))
Error in rjson::fromJSON(httr::content(rawdata, "text", encoding = "UTF-8")) : 
  unexpected character '<'
Calls: HSQC_13C ... fetch_entry_chemical_shifts -> fetch_entry_cs -> <Anonymous>
Execution halted
SumTestSens: no visible global function definition for ‘pnorm’
binarysens: no visible global function definition for ‘dbinom’
hlsens: no visible global function definition for ‘wilcox.test’
iv_sens: no visible global function definition for ‘pnorm’
mcontrol: no visible global function definition for ‘pnorm’
psens: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dbinom pnorm wilcox.test
Consider adding
  importFrom("stats", "dbinom", "pnorm", "wilcox.test")
to your NAMESPACE file.
find_available_versions: no visible global function definition for
  ‘contrib.url’
find_available_versions: no visible global function definition for
  ‘available.packages’
install_version: no visible global function definition for
  ‘contrib.url’
install_version: no visible global function definition for
  ‘available.packages’
install_version: no visible global function definition for
  ‘install_url’
load_available_packages: no visible global function definition for
  ‘contrib.url’
validate_installed_package: no visible global function definition for
  ‘installed.packages’
Undefined global functions or variables:
  available.packages contrib.url install_url installed.packages
Consider adding
  importFrom("utils", "available.packages", "contrib.url",
             "installed.packages")
to your NAMESPACE file.
Running examples in ‘rcartocolor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_color_carto_c
> ### Title: CARTO color scales
> ### Aliases: scale_color_carto_c scale_color_carto_d scale_colour_carto_c
> ###   scale_colour_carto_d scale_fill_carto_c scale_fill_carto_d
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> ggplot(msleep, aes(vore, sleep_total, fill = vore)) +
+         geom_boxplot() +
+         scale_fill_carto_d(palette = 6, direction = -1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘RColorBrewer’ ‘classInt’ ‘maptools’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘classInt’ ‘maptools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
RC.read.table: no visible global function definition for ‘type.convert’
Undefined global functions or variables:
  type.convert
Consider adding
  importFrom("utils", "type.convert")
to your NAMESPACE file.
Running examples in ‘rchess-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggchessboard
> ### Title: Plot a fen representation chessboard via ggplot2
> ### Aliases: ggchessboard
> 
> ### ** Examples
> 
> ggchessboard()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
.onAttach: no visible global function definition for
  ‘packageDescription’
rselect.list: no visible global function definition for ‘select.list’
Undefined global functions or variables:
  packageDescription select.list
Consider adding
  importFrom("utils", "packageDescription", "select.list")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘ec_climate.Rmd’ using rmarkdown
Warning: Removed 14 rows containing missing values (geom_path).
Quitting from lines 96-107 (ec_climate.Rmd) 
Error: processing vignette 'ec_climate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ec_climate.Rmd’

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

Error: Vignette re-building failed.
Execution halted
climdex.data.frame: no visible global function definition for
  ‘as.PCICt’
Undefined global functions or variables:
  as.PCICt
get_ClinicalCodes: no visible global function definition for ‘read.csv’
get_ClinicalCodes : <anonymous>: no visible global function definition
  for ‘read.csv’
Undefined global functions or variables:
  read.csv
Consider adding
  importFrom("utils", "read.csv")
to your NAMESPACE file.
cmaOptimDP: no visible global function definition for ‘flush.console’
Undefined global functions or variables:
  flush.console
Consider adding
  importFrom("utils", "flush.console")
to your NAMESPACE file.
enterTableMHTest : onOK: no visible global function definition for
  ‘na.omit’
startStop: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Namespace with empty importFrom: ‘tcltk’
'library' or 'require' calls to packages already attached by Depends:
  ‘depthTools’ ‘tcltk’
  Please remove these calls from your code.
computeMBD : OnOutput: no visible global function definition for
  ‘tkbutton’
computeMBD: no visible global function definition for ‘tkbutton’
computeMBD : OnPlot: no visible global function definition for
  ‘tkcanvas’
computeMBD : OnPlot: no visible global function definition for
  ‘tkbutton’
computeTmean: no visible global function definition for ‘tkcanvas’
computeTmean: no visible global function definition for ‘tkbutton’
computeTmean : onOK: no visible global function definition for ‘par’
plotCentralCurves: no visible global function definition for ‘tkcanvas’
plotCentralCurves: no visible global function definition for ‘tkbutton’
plotCentralCurves : onOK: no visible global function definition for
  ‘par’
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
'library' or 'require' call to ‘FrF2.catlg128’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
managedata: no visible binding for global variable ‘data’
Undefined global functions or variables:
  data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘fuzzyrcmdrplugin.Rmd’ using rmarkdown
Quitting from lines 72-73 (fuzzyrcmdrplugin.Rmd) 
Error: processing vignette 'fuzzyrcmdrplugin.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘fuzzyrcmdrplugin.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘RcmdrPlugin.KMggplot2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_stepribbon
> ### Title: Step ribbon plots.
> ### Aliases: GeomStepribbon geom_stepribbon
> ### Keywords: datasets
> 
> ### ** Examples
> 
> huron <- data.frame(year = 1875:1972, level = as.vector(LakeHuron))
> h <- ggplot(huron, aes(year))
> h + geom_stepribbon(aes(ymin = level - 1, ymax = level + 1), fill = "grey70") +
+     geom_step(aes(y = level))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘extrafont.Rmd’ using rmarkdown
--- finished re-building ‘extrafont.Rmd’

--- re-building ‘geom-stepribbon.Rmd’ using rmarkdown
Quitting from lines 38-84 (geom-stepribbon.Rmd) 
Error: processing vignette 'geom-stepribbon.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘geom-stepribbon.Rmd’

--- re-building ‘plot-km-requirement.Rmd’ using rmarkdown
--- finished re-building ‘plot-km-requirement.Rmd’

SUMMARY: processing the following file failed:
  ‘geom-stepribbon.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘ENmisc’ ‘Hmisc’ ‘Rcmdr’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
.onAttach: no visible global function definition for ‘getRcmdr’
.onAttach: no visible global function definition for ‘closeCommander’
.onAttach: no visible global function definition for ‘Commander’
mosaicMenuItem: no visible global function definition for
  ‘mosaicSelectDialog’
mosaicMenuItem: no visible global function definition for ‘Message’
Undefined global functions or variables:
  Commander Message closeCommander getRcmdr mosaicSelectDialog
BOXWP: no visible binding for global variable ‘top’
BOXWP: no visible binding for global variable ‘buttonsFrame’
HIST: no visible binding for global variable ‘top’
HIST: no visible binding for global variable ‘buttonsFrame’
QQN: no visible binding for global variable ‘top’
QQN: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  buttonsFrame top
Namespaces with empty importFrom:
  ‘stats’ ‘tcltk’
fncLRpROC: no visible global function definition for ‘palette’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘rgb’
fncPairedpROC: no visible global function definition for ‘palette’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncUnpairedpROC: no visible global function definition for ‘palette’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncvpROC: no visible global function definition for ‘palette’
fncvpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncvpROC : onOK : convert: no visible global function definition for
  ‘rgb’
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
SampleSizes: no visible global function definition for ‘xtabs’
SampleSizes: no visible global function definition for ‘weighted.mean’
SampleSizes: no visible global function definition for ‘reshape’
stage1Sample.fn: no visible global function definition for ‘runif’
stage2Sample.fn: no visible global function definition for ‘runif’
strata.options : onOK: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
'library' or 'require' call to ‘SLC’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘SLC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.steeptestDij : onOK: no visible binding for global variable
  ‘replications’
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  ‘replications’
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ROpenOffice’
Running examples in ‘RCMIP5-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: worldPlot
> ### Title: Plot global data
> ### Aliases: worldPlot
> 
> ### ** Examples
> 
> d <- cmip5data(1970:1975)   # sample data
> worldPlot(d)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
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.
addLine: no visible global function definition for ‘abline’
ellipse: no visible global function definition for ‘approx’
ellipse: no visible global function definition for ‘tail’
Undefined global functions or variables:
  abline approx tail
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "approx")
  importFrom("utils", "tail")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘RcppDynProg.Rmd’ using rmarkdown
Quitting from lines 63-84 (RcppDynProg.Rmd) 
Error: processing vignette 'RcppDynProg.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RcppDynProg.Rmd’

--- re-building ‘Segmentation.Rmd’ using rmarkdown
Quitting from lines 16-41 (Segmentation.Rmd) 
Error: processing vignette 'Segmentation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Segmentation.Rmd’

--- re-building ‘SegmentationL.Rmd’ using rmarkdown
Quitting from lines 16-47 (SegmentationL.Rmd) 
Error: processing vignette 'SegmentationL.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘SegmentationL.Rmd’

SUMMARY: processing the following files failed:
  ‘RcppDynProg.Rmd’ ‘Segmentation.Rmd’ ‘SegmentationL.Rmd’

Error: Vignette re-building failed.
Execution halted
Gauss: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dnorm
Consider adding
  importFrom("stats", "dnorm")
to your NAMESPACE file.
Compilation used the following non-portable flag(s):
  ‘-mrtm’
Files which contain pragma(s) suppressing diagnostics:
  ‘inst/include/ql/math/distributions/normaldistribution.hpp’
  ‘inst/include/ql/math/matrix.hpp’
  ‘inst/include/ql/math/optimization/levenbergmarquardt.hpp’
  ‘inst/include/ql/math/statistics/incrementalstatistics.hpp’
  ‘inst/include/ql/time/date.hpp’ ‘inst/include/ql/time/imm.hpp’
  ‘inst/include/ql/utilities/dataparsers.hpp’
  ‘inst/include/ql/utilities/null.hpp’
Package suggested but not available for checking: ‘Rcompression’
Non-standard files/directories found at top level:
  ‘Changes.html’ ‘CodeGeneration’ ‘README.windows’ ‘Todo.html’
  ‘dynGC.R’ ‘encoding.R’ ‘exampleCode’ ‘getURL.html’ ‘libcurlLicense’
  ‘post.R’ ‘postForm.html’
Packages in Depends field not imported from:
  ‘MASS’ ‘Matrix’ ‘lattice’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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').
get.datamarket.csv: no visible global function definition for
  ‘read.csv’
getUserAgent: no visible global function definition for ‘sessionInfo’
Undefined global functions or variables:
  read.csv sessionInfo
Consider adding
  importFrom("utils", "read.csv", "sessionInfo")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rdbnomics.Rmd’ using rmarkdown
Quitting from lines 182-185 (rdbnomics.Rmd) 
Error: processing vignette 'rdbnomics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rdbnomics.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rdplotdensity
> ### Title: Density Plot
> ### Aliases: rdplotdensity
> 
> ### ** Examples
> 
> # density being discontinuous
> set.seed(42)
> x <- rnorm(2000, mean = -0.5); x[x>0] <- x[x>0] * 2
> rdd <- rddensity(X = x)
> plot <- rdplotdensity(rdd, x, plotRange = c(-2, 2), plotN = 25)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: rdplotdensity ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rddtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotPlacebo
> ### Title: Draw a (density) plot of placebo tests
> ### Aliases: computePlacebo plotPlacebo plotPlacebo.rdd_reg plotPlaceboDens
> ###   plotPlaceboDens.rdd_reg
> 
> ### ** Examples
> 
> data(house)
> house_rdd <- rdd_data(y=house$y, x=house$x, cutpoint=0)
> reg_nonpara <- rdd_reg_np(rdd_object=house_rdd)
> plotPlacebo(reg_nonpara)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotPlacebo ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘morocco.Rmd’ using rmarkdown
Quitting from lines 99-100 (morocco.Rmd) 
Error: processing vignette 'morocco.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘morocco.Rmd’

--- re-building ‘rddtools.Rmd’ using rmarkdown
Quitting from lines 69-70 (rddtools.Rmd) 
Error: processing vignette 'rddtools.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rddtools.Rmd’

SUMMARY: processing the following files failed:
  ‘morocco.Rmd’ ‘rddtools.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
sumry_categorical: no visible global function definition for ‘freq’
sumry_continous: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  freq quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
Running examples in ‘rdi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convertRDI
> ### Title: Convert RDI measures
> ### Aliases: convertRDI
> 
> ### ** Examples
> 
> 
> #create genes
> genes = sample(letters, 10000, replace=TRUE)
> #create sequence annotations
> seqAnnot = data.frame(donor = sample(1:4, 10000, replace=TRUE))
> #calculate RDI
> d = rdi(genes, seqAnnot)
> 
> ##convert RDI to actual 'lfc' estimates and compare
> dtrue = convertRDI(d)$pred
> plot(d, dtrue)
> 
> ##look at SD ranges around lfc estimates
> dtrue = convertRDI(d, calcSD=TRUE)
> 
> ##plot using ggplot2
> library(ggplot2)
> x = as.numeric(d)
> y = as.numeric(dtrue$pred)
> sd = as.numeric(dtrue$sd)
> qplot(x,y)+geom_errorbar(aes(x=x, ymin=y-sd, ymax=y+sd))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rdiversity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_diversity
> ### Title: Plot diversity
> ### Aliases: plot_diversity
> 
> ### ** Examples
> 
> # Define metacommunity
> pop <- data.frame(a = c(1,3), b = c(1,1))
> row.names(pop) <- paste0("sp", 1:2)
> pop <- pop/sum(pop)
> meta <- metacommunity(pop)
> 
> # Calculate subcommunity beta diversity (takes the relative entropy)
> b <- raw_beta(meta)
> res <- subdiv(b, 0:2)
> plot_diversity(res)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CreateRDML.Rmd’ using rmarkdown
Loading required package: robustbase
Warning: Removed 29 rows containing missing values (geom_point).
Quitting from lines 56-63 (CreateRDML.Rmd) 
Error: processing vignette 'CreateRDML.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CreateRDML.Rmd’

--- re-building ‘RDML.Rmd’ using rmarkdown
knitr hook "anchor" is now available
Quitting from lines 246-259 (RDML.Rmd) 
Error: processing vignette 'RDML.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RDML.Rmd’

--- re-building ‘usingRDML_with_other_R_packages.Rmd’ using rmarkdown
Quitting from lines 96-107 (usingRDML_with_other_R_packages.Rmd) 
Error: processing vignette 'usingRDML_with_other_R_packages.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘usingRDML_with_other_R_packages.Rmd’

SUMMARY: processing the following files failed:
  ‘CreateRDML.Rmd’ ‘RDML.Rmd’ ‘usingRDML_with_other_R_packages.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
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-devel-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 172-174 (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:
VECTOR_ELT() can only be applied to a 'list', not a '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
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘synchronicity’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘RDS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bottleneck.plot
> ### Title: Bottleneck Plot
> ### Aliases: bottleneck.plot
> 
> ### ** Examples
> 
> data(fauxmadrona)
> bottleneck.plot(fauxmadrona,"disease")
[1] "194"
[1] "298"
[1] "164"
[1] "617"
[1] "586"
[1] "322"
[1] "729"
[1] "925"
[1] "992"
[1] "356"
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
ip2coordinates: no visible global function definition for ‘URLencode’
street2coordinates: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
Files which contain pragma(s) suppressing diagnostics:
  ‘inst/include/re2/prog.h’ ‘inst/include/re2/re2.h’
  ‘inst/include/re2/regexp.h’ ‘src/dfa.cc’ ‘src/onepass.cc’
Error(s) in re-building vignettes:
  ...
--- re-building ‘realestateDK.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 82-86 (realestateDK.Rmd) 
Error: processing vignette 'realestateDK.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘realestateDK.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Non-standard file/directory found at top level:
  ‘devel’
'library' or 'require' calls to packages already attached by Depends:
  ‘leaps’ ‘mgcv’
  Please remove these calls from your code.
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of ‘env’ to ‘envir’
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of ‘env’ to ‘envir’
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘reams/R/xy.R’:
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
ReCiPa: no visible global function definition for ‘count.fields’
ReCiPa: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  count.fields read.table
Consider adding
  importFrom("utils", "count.fields", "read.table")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Custom_Steps.Rmd’ using rmarkdown
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


Attaching package: 'recipes'

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

    step

Quitting from lines 49-54 (Custom_Steps.Rmd) 
Error: processing vignette 'Custom_Steps.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Custom_Steps.Rmd’

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

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

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

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


Attaching package: 'recipes'

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

    step

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

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


Attaching package: 'recipes'

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

    step

Loading required package: tidyr
--- finished re-building ‘Simple_Example.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mcf
> ### Title: Mean Cumulative Function (MCF)
> ### Aliases: mcf mcf,formula-method mcf,rateReg-method
> 
> ### ** Examples
> 
> library(reda)
> 
> ### sample MCF
> ## Example 1. valve-seat data
> ## the default variance estimates by Lawless and Nadeau (1995) method
> valveMcf0 <- mcf(Survr(ID, Days, No.) ~ 1, data = valveSeats)
> plot(valveMcf0, conf.int = TRUE, mark.time = TRUE, addOrigin = TRUE) +
+     ggplot2::xlab("Days") + ggplot2::theme_bw()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘reda-intro.Rmd’ using rmarkdown
Quitting from lines 122-128 (reda-intro.Rmd) 
Error: processing vignette 'reda-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘reda-intro.Rmd’

--- re-building ‘reda-simulate.Rmd’ using rmarkdown
--- finished re-building ‘reda-simulate.Rmd’

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

Error: Vignette re-building 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.
S3 methods shown with full name in documentation object 'fitted.REEMtree':
  ‘fitted.REEMtree’

S3 methods shown with full name in documentation object 'logLik':
  ‘logLik.REEMtree’

S3 methods shown with full name in documentation object 'plot':
  ‘plot.REEMtree’

S3 methods shown with full name in documentation object 'predict':
  ‘predict.REEMtree’

S3 methods shown with full name in documentation object 'print':
  ‘print.REEMtree’

S3 methods shown with full name in documentation object 'ranef.REEMtree':
  ‘ranef.REEMtree’

S3 methods shown with full name in documentation object 'residuals.REEMtree':
  ‘residuals.REEMtree’

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.
cook.outliers: no visible global function definition for ‘lm’
cook.outliers: no visible global function definition for
  ‘cooks.distance’
nonparRI: no visible global function definition for ‘quantile’
plot.interval: no visible global function definition for ‘par’
plot.interval: no visible global function definition for ‘plot.new’
plot.interval: no visible global function definition for ‘plot.window’
plot.interval: no visible global function definition for ‘segments’
plot.interval: no visible global function definition for ‘axis’
plot.interval: no visible global function definition for ‘title’
plot.interval: no visible global function definition for ‘legend’
plot.interval: no visible global function definition for ‘box’
plot.interval: no visible global function definition for ‘text’
robust: no visible global function definition for ‘qt’
singleRefLimit: no visible global function definition for ‘qnorm’
singleRefLimit: no visible global function definition for
  ‘shapiro.test’
singleRefLimit: no visible global function definition for ‘ks.test’
Undefined global functions or variables:
  axis box cooks.distance ks.test legend lm par plot.new plot.window
  qnorm qt quantile segments shapiro.test text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "par", "plot.new",
             "plot.window", "segments", "text", "title")
  importFrom("stats", "cooks.distance", "ks.test", "lm", "qnorm", "qt",
             "quantile", "shapiro.test")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 27-67 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
cluster.reg: no visible global function definition for ‘rnorm’
cluster.reg: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
.area.my: no visible global function definition for ‘density’
optimalGT : <anonymous>: no visible global function definition for
  ‘median’
optimalGT: no visible global function definition for ‘png’
optimalGT: no visible global function definition for ‘dev.off’
permutation: no visible global function definition for ‘flush.console’
plot.wls: no visible global function definition for ‘par’
plot.wls: no visible global function definition for ‘plot’
plot.wls: no visible global function definition for ‘text’
plot.wls: no visible global function definition for ‘abline’
reGenotyper: no visible global function definition for ‘flush.console’
reGenotyper: no visible binding for global variable ‘var’
reGenotyper: no visible global function definition for ‘plot’
Undefined global functions or variables:
  abline density dev.off flush.console median par plot png text var
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "par", "plot", "text")
  importFrom("stats", "density", "median", "var")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Running examples in ‘reghelper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: graph_model
> ### Title: Graph interactions for fitted models.
> ### Aliases: graph_model graph_model.lm graph_model.aov graph_model.glm
> ###   graph_model.lme graph_model.merMod
> 
> ### ** Examples
> 
> # iris data
> model <- lm(Sepal.Width ~ Sepal.Length * Species, data=iris)
> graph_model_q(model, y='Sepal.Width', x='Sepal.Length', lines='Species')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘regrrr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_effect
> ### Title: plotting the marginal effect of X on Y, with or without one or
> ###   multiple interaction terms
> ### Aliases: plot_effect
> 
> ### ** Examples
> 
> data(mtcars)
> m1 <- lm(mpg ~ vs + carb + hp + wt + wt * hp , data = mtcars)
> plot_effect(reg.coef = summary(m1)$coefficients, 
+                  data = mtcars, model = m1, 
+                  x_var.name = "wt", y_var.name = "mpg", moderator.name = "hp", 
+                  confidence_interval = TRUE,  CI_Ribbon = TRUE, 
+                  xlab = "Weight", ylab = "MPG", moderator.lab = "Horsepower")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Non-standard files/directories found at top level:
  ‘prebuild.sh’ ‘regtest-Ex.R’
binregtest: no visible global function definition for ‘str’
binregtest: no visible binding for global variable ‘str’
binregtest: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif str
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "str")
to your NAMESPACE file.
Running examples in ‘reinsureR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw
> ### Title: Claims: Plot function
> ### Aliases: draw draw,Claims-method
> 
> ### ** Examples
> 
> c <- data.frame(year = unlist(sapply(2000:2017, function(x) rep(x, rpois(1,3)))))
> c$amount <- pmax(rnorm(nrow(c), 200000, 100000), 0)
> p <- aggregate(amount ~ year, c, sum)
> claims <- claims(c, p)
> treaty_1 <- xl(ded = 100000, lim = 20000, aad = 5000,
+                aal = 200000, prm = 0.01, rns = 1)
> claims <- apply_treaty(claims, treaty_1)
> draw(claims)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
.onAttach: no visible global function definition for
  ‘packageDescription’
.relax.cv.elnet: no visible global function definition for ‘predict’
.relax.cv.elnet: no visible binding for global variable ‘weighted.mean’
.relax.cv.lognet: no visible global function definition for ‘predict’
.relax.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
.relax.cvcompute: no visible binding for global variable
  ‘weighted.mean’
.single.column: no visible global function definition for ‘glm’
.single.column: no visible global function definition for ‘coef’
cv.alpha.relaxnet: no visible global function definition for
  ‘mc.reset.stream’
cv.alpha.relaxnet: no visible global function definition for ‘mclapply’
cv.relaxnet: no visible global function definition for ‘predict’
cv.relaxnet: no visible global function definition for
  ‘mc.reset.stream’
cv.relaxnet: no visible global function definition for ‘mclapply’
predict.cv.alpha.relaxnet: no visible global function definition for
  ‘predict’
predict.cv.relaxnet: no visible global function definition for
  ‘predict’
predict.relaxnet: no visible global function definition for ‘predict’
Undefined global functions or variables:
  coef glm mc.reset.stream mclapply packageDescription predict
  weighted.mean
Consider adding
  importFrom("stats", "coef", "glm", "predict", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
'library' or 'require' call to ‘lars’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
relaxo: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
print.summary.rem: no visible global function definition for
  ‘printCoefmat’
print.summary.rem: no visible global function definition for ‘pnorm’
print.summary.rem: no visible binding for global variable ‘quantile’
print.summary.rem: no visible global function definition for ‘pchisq’
print.summary.rem.dyad: no visible global function definition for
  ‘printCoefmat’
print.summary.rem.dyad: no visible global function definition for
  ‘pnorm’
print.summary.rem.dyad: no visible global function definition for
  ‘pchisq’
rem: no visible global function definition for ‘rnorm’
rem: no visible global function definition for ‘dnorm’
rem: no visible global function definition for ‘runif’
rem: no visible global function definition for ‘rchisq’
rem: no visible global function definition for ‘cov’
rem.dyad: no visible global function definition for ‘rnorm’
rem.dyad: no visible global function definition for ‘optim’
rem.dyad: no visible global function definition for ‘rchisq’
rem.dyad: no visible global function definition for ‘quantile’
rem.dyad: no visible global function definition for ‘sd’
rem.dyad: no visible global function definition for ‘var’
rem.dyad.lprior: no visible global function definition for ‘dnorm’
rem.dyad.lprior: no visible global function definition for ‘dt’
Undefined global functions or variables:
  cov dnorm dt optim pchisq pnorm printCoefmat quantile rchisq rnorm
  runif sd var
Consider adding
  importFrom("stats", "cov", "dnorm", "dt", "optim", "pchisq", "pnorm",
             "printCoefmat", "quantile", "rchisq", "rnorm", "runif",
             "sd", "var")
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.
GlobTestMissing: no visible global function definition for ‘lme’
GlobTestMissing: no visible global function definition for ‘anova’
TestStatSP: no visible global function definition for ‘pf’
TestStatSimple: no visible global function definition for ‘ginv’
TestStatSimple: no visible global function definition for ‘pf’
Undefined global functions or variables:
  anova ginv lme pf
Consider adding
  importFrom("stats", "anova", "pf")
to your NAMESPACE file.
Running examples in ‘Repliscope-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotBed
> ### Title: A function to boxplot 'score' column of a BED dataframe, per
> ###   unique chromosome name in the <e2><80><98>chrom<e2><80><99> column.
> ###   The resulting plot also highlights outliers based on the inter
> ###   quartile range (IQR). The genome wide median is plotted as a pink
> ###   line through the boxplots.
> ### Aliases: plotBed
> ### Keywords: BED bioinformatics boxplot genomics
> 
> ### ** Examples
> 
> plotBed(W303_S)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DependencySorting.Rmd’ using rmarkdown
--- finished re-building ‘DependencySorting.Rmd’

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

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

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

--- re-building ‘letExample.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

Loading required package: wrapr

Attaching package: 'wrapr'

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

    coalesce

Quitting from lines 111-115 (letExample.Rmd) 
Error: processing vignette 'letExample.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘letExample.Rmd’

--- re-building ‘replyr.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 ‘replyr.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
delete: no visible global function definition for ‘menu’
doc_temp: no visible global function definition for ‘menu’
html5: no visible global function definition for ‘na.omit’
install_pandoc: no visible global function definition for
  ‘download.file’
new_report: no visible global function definition for ‘tail’
new_report: no visible global function definition for ‘head’
new_report: no visible global function definition for ‘menu’
presentation: no visible global function definition for ‘head’
presentation: no visible global function definition for ‘tail’
presentation: no visible global function definition for ‘menu’
repo2github: no visible global function definition for ‘download.file’
repo2github: no visible global function definition for ‘unzip’
reveal.js: no visible global function definition for ‘na.omit’
update_bib: no visible global function definition for ‘tail’
update_bib: no visible global function definition for ‘menu’
Undefined global functions or variables:
  download.file head menu na.omit tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "tail", "unzip")
to your NAMESPACE file.
MBoxtest: no visible global function definition for ‘var’
jrparams: no visible global function definition for ‘prcomp’
jrparams: no visible global function definition for ‘predict’
jrparams: no visible global function definition for ‘qchisq’
jrparams: no visible global function definition for ‘qf’
Undefined global functions or variables:
  prcomp predict qchisq qf var
Consider adding
  importFrom("stats", "prcomp", "predict", "qchisq", "qf", "var")
to your NAMESPACE file.
Running examples in ‘reproducer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: boxplotAndDensityCurveOnHistogram
> ### Title: boxplotAndDensityCurveOnHistogram
> ### Aliases: boxplotAndDensityCurveOnHistogram
> 
> ### ** Examples
> 
> library(ggplot2)
> library(grid)
> library(gridExtra)
> boxplotAndDensityCurveOnHistogram(Madeyski15EISEJ.PropProjects, "STUD", 0, 100)
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 2 rows containing missing values (geom_bar).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: boxplotAndDensityCurveOnHistogram ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
call.eqs: no visible global function definition for ‘write.table’
read.eqs: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf write.table
Consider adding
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Running examples in ‘reReg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.reReg
> ### Title: Plotting Baseline Cumulative Rate Function and Baseline
> ###   Cumulative Hazard Function
> ### Aliases: plot.reReg
> ### Keywords: Plots
> 
> ### ** Examples
> 
> data(readmission, package = "frailtypack")
> fit <- reReg(reSurv(t.stop, id, event, death) ~ sex + chemo,
+              data = subset(readmission, id < 50))
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Warning in regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
> plot(fit)
Baseline cumulative hazard function is not available for method = cox.LWYY.
Only the baseline cumulative rate function is plotted.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rERR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: f_plot_linERR_ef
> ### Title: plot likelihood function from ef
> ### Aliases: f_plot_linERR_ef
> 
> ### ** Examples
> 
> # set the formulas for the models
> formula1  <- Surv(entry_age,exit_age,outcome) ~ lin(dose_cum) + strata(sex)
> 
> # fit the model
> fit1 <- f_fit_linERR_ef(formula1,data=cohort_ef,id_name="id",dose_name="dose",
+                         time_name="age",covars_names=c("sex"),lag=2,exclusion_done=TRUE)
>                         
> # plot the partial loglikelihood function
> f_plot_linERR_ef(fit1,formula1,data=cohort_ef,id_name="id",dose_name="dose",
+                         time_name="age",covars_names=c("sex"),lag=2,exclusion_done=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
.resampleMakeFunction: no visible global function definition for ‘is’
.resampleSetSeed: no visible global function definition for ‘runif’
CI.bca: no visible global function definition for ‘is’
CI.bca: no visible global function definition for ‘qnorm’
CI.bca: no visible global function definition for ‘pnorm’
CI.t: no visible global function definition for ‘qt’
ExpandProbs: no visible global function definition for ‘pnorm’
ExpandProbs: no visible global function definition for ‘qt’
colVars : f: no visible global function definition for ‘var’
colVars: no visible global function definition for ‘var’
hist.resample: no visible global function definition for ‘density’
hist.resample: no visible global function definition for ‘lines’
hist.resample: no visible global function definition for ‘points’
hist.resample: no visible global function definition for ‘approx’
hist.resample: no visible global function definition for ‘segments’
resample: no visible global function definition for ‘is’
samp.bootknife: no visible global function definition for ‘runif’
samp.bootstrap: no visible global function definition for ‘runif’
Undefined global functions or variables:
  approx density is lines pnorm points qnorm qt runif segments var
Consider adding
  importFrom("graphics", "lines", "points", "segments")
  importFrom("methods", "is")
  importFrom("stats", "approx", "density", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-standard file/directory found at top level:
  ‘load.r’
Packages in Depends field not imported from:
  ‘gWidgets’ ‘gWidgetsRGtk2’ ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
reshapeGUI: no visible global function definition for ‘gwindow’
reshapeGUI: no visible global function definition for ‘gnotebook’
reshapeGUI: no visible global function definition for ‘size<-’
reshapeGUI: no visible global function definition for ‘ggroup’
reshapeGUI: no visible global function definition for ‘gtable’
reshapeGUI: no visible global function definition for ‘addSpring’
reshapeGUI: no visible global function definition for ‘gbutton’
reshapeGUI: no visible global function definition for ‘glabel’
reshapeGUI: no visible global function definition for ‘gedit’
reshapeGUI: no visible global function definition for ‘gcheckbox’
reshapeGUI: no visible global function definition for ‘gdf’
reshapeGUI: no visible global function definition for ‘visible<-’
reshapeGUI: no visible global function definition for
  ‘addHandlerClicked’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘gmessage’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘svalue’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘svalue<-’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘delete’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘add’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘gdf’
reshapeGUI : <anonymous>: no visible global function definition for
  ‘visible<-’
reshapeGUI: no visible global function definition for
  ‘addHandlerChanged’
updateMeltCodeBox: no visible global function definition for ‘svalue<-’
Undefined global functions or variables:
  add addHandlerChanged addHandlerClicked addSpring delete gbutton
  gcheckbox gdf gedit ggroup glabel gmessage gnotebook gtable gwindow
  size<- svalue svalue<- visible<-
GUI_template : onHelp: no visible global function definition for ‘help’
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘retimes’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
dexgauss: no visible global function definition for ‘pnorm’
loglik: no visible global function definition for ‘pnorm’
mexgauss: no visible global function definition for ‘sd’
rexgauss: no visible global function definition for ‘rnorm’
rexgauss: no visible global function definition for ‘rexp’
timefit: no visible global function definition for ‘optim’
timefit: no visible global function definition for ‘sd’
timefit: no visible global function definition for ‘par’
timefit: no visible global function definition for ‘hist’
timefit: no visible global function definition for ‘density’
timefit: no visible global function definition for ‘curve’
timefit: no visible global function definition for ‘new’
plot,timefit: no visible global function definition for ‘density’
plot,timefit: no visible global function definition for ‘par’
plot,timefit: no visible global function definition for ‘curve’
Undefined global functions or variables:
  curve density hist new optim par pnorm rexp rnorm sd
Consider adding
  importFrom("graphics", "curve", "hist", "par")
  importFrom("methods", "new")
  importFrom("stats", "density", "optim", "pnorm", "rexp", "rnorm", "sd")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘retrodesign-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim_plot
> ### Title: sim_plot: visualize type S/M errors
> ### Aliases: sim_plot
> 
> ### ** Examples
> 
> sim_plot(1,3.28)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_To_retrodesign.Rmd’ using rmarkdown
Quitting from lines 91-92 (Intro_To_retrodesign.Rmd) 
Error: processing vignette 'Intro_To_retrodesign.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Intro_To_retrodesign.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using knitr
Loading required package: rivr
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
Quitting from lines 73-74 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘revdbayes-a-vignette.Rmd’ using rmarkdown
--- finished re-building ‘revdbayes-a-vignette.Rmd’

--- re-building ‘revdbayes-b-using-rcpp-vignette.Rmd’ using rmarkdown
--- finished re-building ‘revdbayes-b-using-rcpp-vignette.Rmd’

--- re-building ‘revdbayes-c-predictive-vignette.Rmd’ using rmarkdown
Quitting from lines 98-101 (revdbayes-c-predictive-vignette.Rmd) 
Error: processing vignette 'revdbayes-c-predictive-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘revdbayes-c-predictive-vignette.Rmd’

--- re-building ‘revdbayes-d-kgaps-vignette.Rmd’ using rmarkdown
--- finished re-building ‘revdbayes-d-kgaps-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘revdbayes-c-predictive-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
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 ‘log_parsing.Rmd’ using rmarkdown
Read 1000 items
Quitting from lines 69-71 (log_parsing.Rmd) 
Error: processing vignette 'log_parsing.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘log_parsing.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
FDSNGetTimeSeries: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
fs_author_ids : <anonymous>: no visible global function definition for
  ‘select.list’
fs_download : <anonymous>: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file select.list
Consider adding
  importFrom("utils", "download.file", "select.list")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘XML’ ‘xts’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
quoteFXTsData : function.fx: no visible global function definition for
  ‘xmlValue’
quoteFundTsData : function.fund: no visible global function definition
  for ‘xmlValue’
quoteStockTsData : function.stock: no visible global function
  definition for ‘xmlSize’
quoteStockTsData : function.stock: no visible global function
  definition for ‘xmlValue’
quoteTsData: no visible global function definition for ‘xmlRoot’
quoteTsData: no visible global function definition for ‘htmlTreeParse’
quoteTsData: no visible global function definition for
  ‘xmlErrorCumulator’
quoteTsData: no visible global function definition for ‘xmlSize’
toXts: no visible global function definition for ‘as.xts’
Undefined global functions or variables:
  as.xts htmlTreeParse xmlErrorCumulator xmlRoot xmlSize xmlValue
Running examples in ‘rfm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rfm_bar_chart
> ### Title: RFM bar chart
> ### Aliases: rfm_bar_chart
> 
> ### ** Examples
> 
> # using transaction data
> analysis_date <- lubridate::as_date('2006-12-31', tz = 'UTC')
> rfm_order <- rfm_table_order(rfm_data_orders, customer_id, order_date,
+ revenue, analysis_date)
> 
> # bar chart
> rfm_bar_chart(rfm_order)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: rfm_bar_chart ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rfm-customer-level-data.Rmd’ using rmarkdown

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 116-117 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rfm-customer-level-data.Rmd’

--- re-building ‘rfm-transaction-level-data.Rmd’ using rmarkdown

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 113-114 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rfm-transaction-level-data.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: impHeatmap
> ### Title: Importance Heatmap
> ### Aliases: impHeatmap
> 
> ### ** Examples
> 
> data(mtcars)
> 
> # A randomForest model
> rf <- randomForest(factor(am) ~ ., mtcars, importance = TRUE)
> importance(rf)
              0          1 MeanDecreaseAccuracy MeanDecreaseGini
mpg   3.6085439  4.8299920            5.1570120        1.0513643
cyl   1.1006672  1.8752027            2.0963503        0.2128961
disp  5.2145802  8.0631572            8.4476655        1.8481357
hp    1.9174919  4.9738587            5.0371940        0.8768533
drat  5.5743157  9.0046005            9.0753230        2.0552791
wt   12.6460573 16.7371824           17.2904661        3.8012383
qsec  5.9572770  3.7329653            5.4690146        1.3975243
vs    3.6146152  0.5608144            2.9643967        0.1430843
gear  9.4788534 13.9098472           13.9703043        3.1261030
carb  0.3580251 -0.9342927           -0.5446649        0.4398967
> impHeatmap(rf, xlab = "Transmission", ylab = "Predictor")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: impHeatmap ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
.testLTS: no visible binding for global variable ‘stackloss’
Undefined global functions or variables:
  stackloss
Consider adding
  importFrom("datasets", "stackloss")
to your NAMESPACE file.
gabriel.plot: no visible global function definition for ‘barplot’
gabriel.plot: no visible global function definition for ‘arrows’
rgabriel: no visible binding for global variable ‘sd’
rgabriel : psmm_x: no visible global function definition for ‘pnorm’
rgabriel : psmm: no visible global function definition for ‘integrate’
rgabriel : qsmm: no visible global function definition for ‘qnorm’
rgabriel : qsmm: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  arrows barplot integrate pnorm qnorm sd uniroot
Consider adding
  importFrom("graphics", "arrows", "barplot")
  importFrom("stats", "integrate", "pnorm", "qnorm", "sd", "uniroot")
to your NAMESPACE file.
Package in Depends field not imported from: ‘gsl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
gammaIntegral: no visible global function definition for ‘integrate’
gammaIntegral : <anonymous>: no visible global function definition for
  ‘hyperg_1F1’
gammaMLE: no visible global function definition for ‘weighted.mean’
gammaMME: no visible binding for global variable ‘sd’
gammaMME: no visible binding for global variable ‘var’
Undefined global functions or variables:
  hyperg_1F1 integrate sd var weighted.mean
Consider adding
  importFrom("stats", "integrate", "sd", "var", "weighted.mean")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_RGCCA.Rmd’ using rmarkdown
Quitting from lines 737-753 (vignette_RGCCA.Rmd) 
Error: processing vignette 'vignette_RGCCA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette_RGCCA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
genoud: multiple local function definitions for ‘fn1.bfgs’ with
  different formal arguments
genoud: multiple local function definitions for ‘gr1’ with different
  formal arguments
genoud: multiple local function definitions for ‘hess.fn’ with
  different formal arguments
genoud_transform: multiple local function definitions for ‘fn1.bfgs’
  with different formal arguments
genoud_transform: multiple local function definitions for ‘gr1’ with
  different formal arguments
gexf.to.igraph: no visible global function definition for ‘rgb’
igraph.to.gexf: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
  col2rgb rgb
Consider adding
  importFrom("grDevices", "col2rgb", "rgb")
to your NAMESPACE file.
'library' or 'require' call to ‘gWidgetsRGtk2’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘RGtk2’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘RGtk2Extras-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gtkDfEditDoTask
> ### Title: Editor change handling.
> ### Aliases: gtkDfEditDoTask
> 
> ### ** Examples
> 
> 
> win = gtkWindowNew("gtkDfEdit Demo")
Error in .RGtkCall("S_gtk_window_new", type, PACKAGE = "RGtk2") : 
  Could not parse enum value gtkDfEdit Demo
Calls: gtkWindowNew -> .RGtkCall
Execution halted
File ‘RGtk2/libs/RGtk2.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_new_custom_connection’,
    ‘Rf_EncodeInteger’, ‘Rf_EncodeLogical’, ‘Rf_EncodeReal’,
    ‘Rf_formatInteger’, ‘Rf_formatLogical’, ‘Rf_formatReal’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.quick_fetch: no visible global function definition for ‘POST’
.quick_fetch: no visible global function definition for ‘add_headers’
.quick_fetch: no visible global function definition for
  ‘stop_for_status’
.quick_fetch: no visible global function definition for ‘content’
fetch_healthdata: no visible binding for global variable ‘resources’
fetch_healthdata : <anonymous>: no visible binding for global variable
  ‘filters’
Undefined global functions or variables:
  POST add_headers content filters resources stop_for_status
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
ggtree v1.15.6  For help: https://guangchuangyu.github.io/software/ggtree

If you use ggtree in published research, please cite the most appropriate paper(s):

[36m-[39m Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194[36m-[39m Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628


Loading required package: ape

Attaching package: 'ape'

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

    rotate

Loading required package: maps

Attaching package: 'phytools'

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

    read.newick

Warning in load_fasta(fasta.file.name) :
  Characters not in acgtnACGTN- will be treated as missing (-)...
Warning in load_fasta(woodmouse) :
  Characters not in acgtnACGTN- will be treated as missing (-)...
Read 1 item
Quitting from lines 106-110 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ECL: no visible global function definition for ‘new’
ECLDataset: no visible global function definition for ‘new’
ECLDedUp: no visible global function definition for ‘new’
ECLDistribute: no visible global function definition for ‘new’
ECLIterate: no visible global function definition for ‘new’
ECLJoin: no visible global function definition for ‘new’
ECLOutput: no visible global function definition for ‘new’
ECLProject: no visible global function definition for ‘new’
ECLRecord: no visible global function definition for ‘new’
ECLRollUp: no visible global function definition for ‘new’
ECLSort: no visible global function definition for ‘new’
ECLTOPN: no visible global function definition for ‘new’
ECLTable: no visible global function definition for ‘new’
ECLTransform: no visible global function definition for ‘new’
eclDirectCall: no visible global function definition for ‘postForm’
parseResults: no visible global function definition for ‘xmlRoot’
parseResults: no visible global function definition for ‘xmlTreeParse’
parseResults: no visible global function definition for ‘getNodeSet’
parseResults: no visible global function definition for ‘xmlGetAttr’
parseResults: no visible global function definition for ‘xmlValue’
parseResults: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  getNodeSet new postForm write.table xmlGetAttr xmlRoot xmlTreeParse
  xmlValue
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  RhpcMPI.c:301:5: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rhpc.Rcheck/00install.out’ for details.
RHT.2samp : my.HotellingT2 : my.InvCov2: no visible global function
  definition for ‘cov’
RHT.2samp : get.lambda : get.para: no visible global function
  definition for ‘optimize’
RHT.2samp : get.lambda : gg: no visible global function definition for
  ‘qchisq’
RHT.2samp : get.lambda : ggl: no visible global function definition for
  ‘qnorm’
RHT.2samp : <anonymous>: no visible global function definition for
  ‘cov’
RHT.fun : my.HotellingT : my.InvCov: no visible global function
  definition for ‘cov’
RHT.fun : get.lambda : get.para: no visible global function definition
  for ‘optimize’
RHT.fun : get.lambda : gg: no visible global function definition for
  ‘qchisq’
RHT.fun : get.lambda : ggl: no visible global function definition for
  ‘qnorm’
RHT.fun : <anonymous>: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optimize qchisq qnorm
Consider adding
  importFrom("stats", "cov", "optimize", "qchisq", "qnorm")
to your NAMESPACE file.
Running examples in ‘ri2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: conduct_ri
> ### Title: Conduct Randomization Inference
> ### Aliases: conduct_ri
> 
> ### ** Examples
> 
> 
> # Data from Gerber and Green Table 2.2
> 
> 
> # Randomization Inference for the Average Treatment Effect
> 
> table_2.2 <-
+     data.frame(d = c(1, 0, 0, 0, 0, 0, 1),
+                y = c(15, 15, 20, 20, 10, 15, 30))
> 
> ## Declare randomization procedure
> declaration <- declare_ra(N = 7, m = 2)
> 
> ## Conduct Randomization Inference
> out <- conduct_ri(y ~ d,
+                       declaration = declaration,
+                       assignment = "d",
+                       sharp_hypothesis = 0,
+                       data = table_2.2)
> 
> summary(out)
  term estimate two_tailed_p_value
1    d      6.5          0.3809524
> plot(out)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ri2_vignette.Rmd’ using rmarkdown
Quitting from lines 42-57 (ri2_vignette.Rmd) 
Error: processing vignette 'ri2_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ri2_vignette.Rmd’

--- re-building ‘ri2_vs_ri.Rmd’ using rmarkdown
--- finished re-building ‘ri2_vs_ri.Rmd’

SUMMARY: processing the following file failed:
  ‘ri2_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
FusedQDA : <anonymous>: no visible global function definition for ‘cov’
RidgeFused: no visible binding for global variable ‘cov2cor’
RidgeFusedCV : <anonymous>: no visible global function definition for
  ‘cov’
SSRidgeFused : <anonymous>: no visible global function definition for
  ‘cov’
Undefined global functions or variables:
  cov cov2cor
Consider adding
  importFrom("stats", "cov", "cov2cor")
to your NAMESPACE file.
ridit.raw: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
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 examples in ‘RImagePalette-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_color_image
> ### Title: Image color scales
> ### Aliases: scale_color_image scale_colour_image scale_fill_image
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> # ripped from the pages of ggplot2
> your_image <- jpeg::readJPEG(system.file("img", "Rlogo.jpg", package="jpeg"))
> display_image(your_image)
> 
> #Discrete scale example
> p <- ggplot(mtcars, aes(wt, mpg))
> p + geom_point(size=4, aes(colour = factor(cyl))) +
+     scale_color_image(image = your_image) +
+     theme_bw()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rinatVignette.Rmd’ using rmarkdown
Quitting from lines 180-188 (rinatVignette.Rmd) 
Error: processing vignette 'rinatVignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rinatVignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘RInside/libs/RInside.so’:
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  cornellout.cpp:101:20: warning: ‘%2d’ directive writing between 2 and 11 bytes into a region of size between 0 and 931 [-Wformat-overflow=]
  cornellout.cpp:139:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  cornellout.cpp:131:26: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 988 and 995 [-Wformat-overflow=]
  mat.cpp:2352:11: warning: passing NULL to non-pointer argument 1 of ‘dMat::dMat(int, int, double)’ [-Wconversion-null]
  mat.cpp:2382:11: warning: passing NULL to non-pointer argument 1 of ‘dMat::dMat(int, int, double)’ [-Wconversion-null]
  mat.cpp:2428:11: warning: passing NULL to non-pointer argument 1 of ‘dMat::dMat(int, int, double)’ [-Wconversion-null]
  mat.cpp:2500:11: warning: passing NULL to non-pointer argument 1 of ‘dMat::dMat(int, int, double)’ [-Wconversion-null]
  mat.cpp:2518:11: warning: passing NULL to non-pointer argument 1 of ‘dMat::dMat(int, int, double)’ [-Wconversion-null]
  mat.cpp:315:4: warning: ‘*<unknown>.dataMat::p’ is used uninitialized in this function [-Wuninitialized]
  tilia.cpp:179:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 61 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:180:10: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 19 bytes from a string of length 19 [-Wstringop-truncation]
  tilia.cpp:225:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:228:17: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 29 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rioja.Rcheck/00install.out’ for details.
desmat.sanitize: no visible global function definition for ‘aggregate’
dispdist: no visible global function definition for ‘quantile’
dispdist: no visible global function definition for ‘hist’
dispdist: no visible global function definition for ‘lines’
estate: no visible global function definition for ‘weighted.mean’
estate: no visible global function definition for ‘lm’
genperms: no visible global function definition for ‘combn’
genprobexact: no visible global function definition for ‘ave’
invert.ci: no visible global function definition for ‘quantile’
invert.ci: no visible global function definition for ‘uniroot’
omni.ate: no visible global function definition for ‘hist’
omni.ate: no visible global function definition for ‘lines’
omni.ate: no visible global function definition for ‘quantile’
resresplot: no visible global function definition for ‘lm’
resresplot: no visible global function definition for ‘symbols’
resresplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline aggregate ave combn hist lines lm quantile symbols uniroot
  weighted.mean
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "symbols")
  importFrom("stats", "aggregate", "ave", "lm", "quantile", "uniroot",
             "weighted.mean")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running examples in ‘rise-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rise
> ### Title: RISE Analysis
> ### Aliases: rise
> 
> ### ** Examples
> 
> library(ggplot2)
> rise(sample_df, visual = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘riskRegression-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.predictCSC
> ### Title: Plot Predictions From a Cause-specific Cox Proportional Hazard
> ###   Regression
> ### Aliases: autoplot.predictCSC
> 
> ### ** Examples
> 
> library(survival)
> library(rms)
Loading required package: Hmisc
Loading required package: lattice
Loading required package: Formula

Attaching package: ‘Hmisc’

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

    format.pval, units

Loading required package: SparseM

Attaching package: ‘SparseM’

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

    backsolve

> 
> #### simulate data ####
> set.seed(10)
> d <- sampleData(1e2, outcome = "competing.risks")
> 
> #### CSC model ####
> m.CSC <- CSC(Hist(time,event)~ X1 + X2 + X6, data = d)
> 
> pred.CSC <- predict(m.CSC, newdata = d[1:2,], time = 1:5, cause = 1)#'
> autoplot(pred.CSC)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: autoplot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
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.
Alg2: no visible global function definition for ‘uniroot’
Alg3: no visible global function definition for ‘optim’
NVCopula: no visible global function definition for ‘rnorm’
NVCopula: no visible global function definition for ‘rgamma’
NVCopula: no visible global function definition for ‘var’
NVCopula: no visible global function definition for ‘cov’
NVCopula: no visible global function definition for ‘qnorm’
NVCopulaMT: no visible global function definition for ‘rnorm’
NVCopulaMT: no visible global function definition for ‘rgamma’
NVCopulaMT: no visible global function definition for ‘var’
NVCopulaMT: no visible global function definition for ‘cov’
NVCopulaMT: no visible global function definition for ‘qnorm’
R2X: no visible global function definition for ‘write.table’
ReturnCopula: no visible global function definition for ‘qt’
ReturnCopula: no visible global function definition for ‘pt’
SISCopula: no visible global function definition for ‘runif’
SISCopula: no visible global function definition for ‘qnorm’
SISCopula: no visible global function definition for ‘rnorm’
SISCopula: no visible global function definition for ‘qgamma’
SISCopula: no visible global function definition for ‘var’
SISCopula: no visible global function definition for ‘cov’
SISCopulaMT: no visible global function definition for ‘runif’
SISCopulaMT: no visible global function definition for ‘qnorm’
SISCopulaMT: no visible global function definition for ‘rnorm’
SISCopulaMT: no visible global function definition for ‘qgamma’
SISCopulaMT: no visible global function definition for ‘var’
SISCopulaMT: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov optim pt qgamma qnorm qt rgamma rnorm runif uniroot var
  write.table
Consider adding
  importFrom("stats", "cov", "optim", "pt", "qgamma", "qnorm", "qt",
             "rgamma", "rnorm", "runif", "uniroot", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘compiler’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
NumConv: no visible global function definition for ‘pchip’
NumConv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘pchip’
NumDeconv : error_function: no visible global function definition for
  ‘pchip’
NumDeconv: no visible global function definition for ‘cmpfun’
NumDeconv: no visible global function definition for ‘optim’
RivivcA: no visible global function definition for ‘lm’
Undefined global functions or variables:
  cmpfun lm optim pchip
Consider adding
  importFrom("stats", "lm", "optim")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘publication-reproduction.Rmd’ using rmarkdown
--- finished re-building ‘publication-reproduction.Rmd’

--- re-building ‘quickstart.Rmd’ using rmarkdown
Loading required package: rivr
M1 profile specified. Computing upstream profile
Loading required package: ggplot2
Quitting from lines 100-104 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickstart.Rmd’

--- re-building ‘technical-vignette.Rmd’ using rmarkdown
--- finished re-building ‘technical-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Non-standard files/directories found at top level:
  ‘getsp.class’ ‘getsp.java’ ‘install-sh’ ‘jri’ ‘version’
Found the following possibly unsafe calls:
File ‘rJava/R/import.R’:
  unlockBinding(IMPORTER, env = env)
  assignInNamespace(IMPORTER, importer, envir = env)
File ‘rJava/R/jinit.R’:
  unlockBinding(x, .env)
  unlockBinding(x, pe)
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-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.
cubeHelix : <anonymous>: no visible global function definition for
  ‘rgb’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  rgamma rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("stats", "rgamma")
to your NAMESPACE file.
'library' or 'require' call to ‘rJava’ which was already attached by Depends.
  Please remove these calls from your code.
Running examples in ‘rKIN-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estEllipse
> ### Title: Estimate Bivariate Normal Ellipse Isotope Niche
> ### Aliases: estEllipse
> 
> ### ** Examples
> 
> library(rKIN)
> data("rodents")
> #estimate niche overlap between 2 species using bivariate ellipse
> test.elp<- estEllipse(data=rodents, x="Ave_C", y="Ave_N", group="Species",
+                      levels=c(50, 75, 95))
> #determine polygon overlap for all polygons
> plotKIN(test.elp, scaler=2, title="Ellipse Estimates", xlab="Ave_C", ylab="Ave_N")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
':::' calls which should be '::':
  ‘stats:::dexp’ ‘stats:::dgamma’ ‘stats:::dweibull’ ‘stats:::pexp’
  ‘stats:::pgamma’ ‘stats:::pweibull’ ‘stats:::qexp’ ‘stats:::qgamma’
  ‘stats:::qweibull’ ‘stats:::rexp’ ‘stats:::rgamma’ ‘stats:::rweibull’
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rlecuyer.Rcheck/00install.out’ for details.
Found the following Makefile(s) without a final LF:
  src/Makevars.in
Some ‘make’ programs ignore lines not ending in LF.
Package in Depends field not imported from: ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘EMSRb_internal’ ‘EM_internal’ ‘PD_internal’
EMSRb_internal: no visible global function definition for ‘qnorm’
EM_internal: no visible global function definition for ‘dnorm’
EM_internal: no visible global function definition for ‘pnorm’
PD_internal: no visible global function definition for ‘qtnorm’
PD_internal: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dnorm pnorm qnorm qtnorm sd
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "sd")
to your NAMESPACE file.
ma.filter: no visible global function definition for ‘par’
ma.filter: no visible global function definition for ‘lines’
ma.filter: no visible global function definition for ‘abline’
qn: no visible global function definition for ‘lm’
qn: no visible global function definition for ‘var’
qn: no visible global function definition for ‘resid’
ss.filter: no visible global function definition for ‘smooth.spline’
ss.filter: no visible global function definition for ‘par’
ss.filter: no visible global function definition for ‘lines’
ss.filter: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline lines lm par resid smooth.spline var
Consider adding
  importFrom("graphics", "abline", "lines", "par")
  importFrom("stats", "lm", "resid", "smooth.spline", "var")
to your NAMESPACE file.
Found an obsolete/platform-specific call in the following function:
  ‘Mallows’
Found the platform-specific device:
  ‘x11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
Mallows: no visible global function definition for ‘runif’
Mallows: no visible global function definition for ‘x11’
Mallows: no visible global function definition for ‘plot’
Mallows: no visible global function definition for ‘dev.off’
UpdateLambda: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  DbResult.cpp:81:41: warning: catching polymorphic type ‘class MariaResultPrep::UnsupportedPS’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RMariaDB.Rcheck/00install.out’ for details.
Running examples in ‘rmcorr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.rmc
> ### Title: Plot the repeated measures correlation coefficient.
> ### Aliases: plot.rmc
> 
> ### ** Examples
> 
> ## Bland Altman 1995 data
> my.rmc <- rmcorr(participant = Subject, measure1 = PacO2, measure2 = pH, dataset = bland1995)
Warning in rmcorr(participant = Subject, measure1 = PacO2, measure2 = pH,  :
  'Subject' coerced into a factor
> plot(my.rmc, overall = TRUE)
> 
> #using ggplot instead
> ggplot2::ggplot(bland1995, ggplot2::aes(x = PacO2, y = pH, group = factor(Subject),
+       color = factor(Subject))) +
+       ggplot2::geom_point(ggplot2::aes(colour = factor(Subject))) +
+       ggplot2::geom_line(ggplot2::aes(y = my.rmc$model$fitted.values), linetype = 1) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘RMCriteria-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RPrometheeI
> ### Title: RPrometheeI
> ### Aliases: RPrometheeI RPrometheeI,RPrometheeArguments-method
> ### Keywords: decision-analysis decision-method mcda promethee
> 
> ### ** Examples
> 
> library(RMCriteria)
> ## Create objects for each argument
> data <-matrix(c(5.2, -3.5,
+                 4.3, -1.2,
+                 6.7, -2.0), byrow = TRUE, ncol = 2, nrow = 3)
> 
> parms <- matrix(c(NA, NA), byrow = TRUE, ncol = 1, nrow = 2)
> vecWeights <- c(0.3, 0.7)
> vecMaximiz <- c(FALSE, TRUE)
> prefFunction <- c(0, 0)
> normalize <- FALSE
> alternatives <- c("Alt 1", "Alt 2", "Alt 3")
> 
> ## Create RPrometheeArguments object
> PromObj <- RPrometheeConstructor(datMat = data, vecWeights = vecWeights,
+ vecMaximiz = vecMaximiz, prefFunction = prefFunction,
+ parms = parms, normalize = normalize, alternatives = alternatives)
> 
> ## Run RPrometheeI
> (result <- RPrometheeI(PromObj))
Promethee I object with 3 alternatives. 
Phi Plus: 0.095 0.738 0.237 
Phi Minus: 0.710 0.000 0.360 
The alternatives are: 1 2 3> 
> ## There are two alternatives two plot a RPrometheeI object:
> plot(result)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rmetalog-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.metalog
> ### Title: Plot of the metalog object
> ### Aliases: plot.metalog
> 
> ### ** Examples
> 
> # Load example data
> data("fishSize")
> 
> # Create a bounded metalog object
> myMetalog <- metalog(fishSize$FishSize,
+                      bounds=c(0, 60),
+                      boundedness = 'b',
+                      term_limit = 13)
> 
> plot(myMetalog)
$pdf
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rmetalog-vignette.Rmd’ using rmarkdown
Quitting from lines 70-71 (rmetalog-vignette.Rmd) 
Error: processing vignette 'rmetalog-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rmetalog-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
CI: no visible global function definition for ‘sd’
CI: no visible global function definition for ‘qt’
L: no visible global function definition for ‘sd’
L: no visible global function definition for ‘residuals’
Qa: no visible global function definition for ‘logLik’
Qb: no visible global function definition for ‘residuals’
Qc: no visible global function definition for ‘residuals’
Qc: no visible global function definition for ‘logLik’
STDERR: no visible global function definition for ‘sd’
group.UCL: no visible global function definition for ‘aggregate’
lr.glover: no visible binding for global variable ‘logLik’
lr.glover: no visible binding for global variable ‘update’
lr.glover : nobs0: no visible binding for global variable ‘nobs’
lr.glover : nobs0 : nobs2: no visible global function definition for
  ‘residuals’
lr.glover : tlab: no visible global function definition for ‘terms’
lr.glover : name: no visible global function definition for ‘formula’
lr.glover : modelUpdate: no visible global function definition for
  ‘as.formula’
lr.glover: no visible global function definition for ‘model.frame’
lr.glover: no visible binding for global variable ‘AIC’
lr.glover: no visible binding for global variable ‘BIC’
summarySE : <anonymous>: no visible global function definition for ‘sd’
summarySE: no visible global function definition for ‘qt’
Undefined global functions or variables:
  AIC BIC aggregate as.formula formula logLik model.frame nobs qt
  residuals sd terms update
Consider adding
  importFrom("stats", "AIC", "BIC", "aggregate", "as.formula", "formula",
             "logLik", "model.frame", "nobs", "qt", "residuals", "sd",
             "terms", "update")
to your NAMESPACE file.
Combi: no visible global function definition for ‘new’
barplotMixCluster: no visible global function definition for ‘is’
barplotMixCluster: no visible global function definition for ‘par’
barplotMixCluster: no visible global function definition for ‘lines’
barplotMixCluster: no visible global function definition for ‘text’
barplotMixCluster: no visible global function definition for ‘title’
barplotMixCluster: no visible global function definition for ‘mtext’
histMixCluster: no visible global function definition for ‘is’
histMixCluster: no visible global function definition for ‘par’
histMixCluster: no visible global function definition for ‘dnorm’
histMixCluster: no visible global function definition for ‘lines’
mixmodEntPlot: no visible global function definition for ‘par’
mixmodEntPlot: no visible global function definition for ‘lines’
mixmodEntPlot: no visible global function definition for ‘axis’
mixmodEntPlot: no visible global function definition for ‘title’
mixmodEntPlot: no visible binding for global variable ‘par’
plot,MixmodCombi: no visible global function definition for ‘par’
plot,MixmodCombi: no visible global function definition for ‘plot.new’
plot,MixmodCombi: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis dnorm is lines mtext new par plot.new text title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot.new",
             "text", "title")
  importFrom("methods", "is", "new")
  importFrom("stats", "dnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.pLGP_qvec: no visible global function definition for ‘ppois’
.qLGP_pvec: no visible global function definition for ‘qpois’
.rLGP.failsafe: no visible global function definition for ‘runif’
.subdmg: no visible global function definition for ‘dbinom’
dnegbin: no visible global function definition for ‘dnbinom’
pLGP: no visible global function definition for ‘ppois’
qLGP: no visible global function definition for ‘qpois’
rLGP: no visible global function definition for ‘rpois’
rLGP: no visible global function definition for ‘rnorm’
rLGP: no visible global function definition for ‘runif’
rbinegbin: no visible global function definition for ‘rnbinom’
rmanaclash: no visible global function definition for ‘rbinom’
rmanaclash: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbinom dnbinom ppois qpois rbinom rnbinom rnorm rpois runif
Consider adding
  importFrom("stats", "dbinom", "dnbinom", "ppois", "qpois", "rbinom",
             "rnbinom", "rnorm", "rpois", "runif")
to your NAMESPACE file.
Found the following calls to attach():
File ‘Rmosek/R/builder.R’:
  attach(builderenv, pos, name, warn.conflicts)
See section ‘Good practice’ in ‘?attach’.
CoeffYWeq: no visible global function definition for ‘index’
fitdistrForPrecipitation: no visible global function definition for
  ‘fitdistr’
generate.CCGammaObject: no visible binding for global variable ‘rnorm’
generate.CCGammaObject: no visible global function definition for
  ‘pnorm’
generate.YuleWalkerCoefficientBlockmatrices: no visible binding for
  global variable ‘rnorm’
generate.YuleWalkerCoefficientBlockmatricesPerEachMonth: no visible
  binding for global variable ‘rnorm’
generatePrecipitationAmount: no visible global function definition for
  ‘str’
omega_inv: no visible global function definition for ‘uniroot’
qqfit: no visible binding for global variable ‘qexp’
qqfit: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  ecdf fitdistr index pnorm qexp rnorm str uniroot
Consider adding
  importFrom("stats", "ecdf", "pnorm", "qexp", "rnorm", "uniroot")
  importFrom("utils", "str")
to your NAMESPACE file.
Missing or unexported object: ‘base::shell.exec’
rms.pval: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘rms-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Function
> ### Title: Compose an S Function to Compute X beta from a Fit
> ### Aliases: Function.rms Function.cph sascode perlcode
> ### Keywords: regression methods interface models survival math
> 
> ### ** Examples
> 
> set.seed(1331)
> x1 <- exp(rnorm(100))
> x2 <- factor(sample(c('a','b'),100,rep=TRUE))
> dd <- datadist(x1, x2)
> options(datadist='dd')
> y  <- log(x1)^2+log(x1)*(x2=='b')+rnorm(100)/4
> f  <- ols(y ~ pol(log(x1),2)*x2)
> f$coef
   Intercept           x1         x1^2         x2=b    x1 * x2=b  x1^2 * x2=b 
-0.001885864 -0.019198566  1.017432226  0.047810769  1.037259829 -0.032005994 
> g  <- Function(f, digits=5)
> g
function (x1 = 1.0906, x2 = "b") 
{
    x1 <- log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1^2 + 0.047811 * (x2 == 
        "b") + (x2 == "b") * (1.0373 * x1 - 0.032006 * x1^2)
}
<environment: 0x55a6a5541060>
> sascode(g)
    x1 = log(x1)
    -0.0018859 - 0.019199 * x1 + 1.0174 * x1**2 + 0.047811 * (x2 = 
        "b") + (x2 = "b") * (1.0373 * x1 - 0.032006 * x1**2);
> cat(perlcode(g), '\n')
Error in expr[[3]] : subscript out of bounds
Calls: cat ... convert -> f -> paste -> convert -> f -> paste -> convert
Execution halted
dWishartSpike: no visible global function definition for ‘dnorm’
pWishartSpike: no visible global function definition for ‘pnorm’
qWishartSpike: no visible global function definition for ‘qnorm’
rWishartSpike: no visible global function definition for ‘qnorm’
rmp: no visible global function definition for ‘runif’
rtw: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm pnorm qnorm runif
Consider adding
  importFrom("stats", "dnorm", "pnorm", "qnorm", "runif")
to your NAMESPACE file.
Running examples in ‘rmweather-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rmw_plot_normalised
> ### Title: Function to plot the meteorologically normalised time series
> ###   after 'rmw_normalise'.
> ### Aliases: rmw_plot_normalised
> 
> ### ** Examples
> 
> 
> # Plot normalised example data
> rmw_plot_normalised(data_london_normalised)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' calls in package code:
  ‘DESeq’ ‘seqinr’ ‘topGO’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: ‘rnaturalearthhires’
Found the following significant warnings:
  nxsreader.cpp:659:22: warning: catching polymorphic type ‘class NxsException’ by value [-Wcatch-value=]
  nxsreader.cpp:709:25: warning: catching polymorphic type ‘class NxsException’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rncl.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘taxadb’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rngtools)
  Loading required package: pkgmaker
  Loading required package: registry
  
  Attaching package: 'pkgmaker'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  > 
  > test_check("rngtools")
  ── 1. Failure: RNGtype (@test-format.R#100)  ───────────────────────────────────
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  MISSING : result has correct length ( [ 2 ) ]
  
  ── 2. Failure: RNGtype (@test-format.R#101)  ───────────────────────────────────
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  numeric(1) : result has correct length ( [ 2 ) Valid single numeric seed ]
  
  ── 3. Failure: RNGtype (@test-format.R#102)  ───────────────────────────────────
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  integer(3) : result has correct length ( [ 2 ) Valid seed ]
  
  ── 4. Failure: RNGtype (@test-format.R#103)  ───────────────────────────────────
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  integer(1) : result has correct length ( [ 2 ) Valid encoded kind ]
  
  ── 5. Failure: RNGtype (@test-format.R#106)  ───────────────────────────────────
  length(d) not identical to `expL`.
  1/1 mismatches
  [1] 3 - 2 == 1
  list(2) : result has correct length ( [ 2 ) list with rng slot ]
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 225 SKIPPED: 0 FAILED: 5
  1. Failure: RNGtype (@test-format.R#100) 
  2. Failure: RNGtype (@test-format.R#101) 
  3. Failure: RNGtype (@test-format.R#102) 
  4. Failure: RNGtype (@test-format.R#103) 
  5. Failure: RNGtype (@test-format.R#106) 
  
  Error: testthat unit tests failed
  Execution halted
well19937.validate: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Nnls.trimW : fun1: no visible global function definition for ‘runif’
initM: no visible global function definition for ‘runif’
rnmf: no visible global function definition for ‘txtProgressBar’
rnmf: no visible global function definition for ‘setTxtProgressBar’
see: no visible global function definition for ‘heat.colors’
see: no visible global function definition for ‘colorRampPalette’
see: no visible global function definition for ‘grey’
see: no visible global function definition for ‘par’
see: no visible global function definition for ‘image’
see: no visible global function definition for ‘mtext’
simtum: no visible global function definition for ‘runif’
simtum: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  colorRampPalette grey heat.colors image mtext par rnorm runif
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "image", "mtext", "par")
  importFrom("stats", "rnorm", "runif")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rnmr1D.Rmd’ using knitr
Quitting from lines 213-219 (Rnmr1D.Rmd) 
Error: processing vignette 'Rnmr1D.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Rnmr1D.Rmd’

SUMMARY: processing the following file failed:
  ‘Rnmr1D.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [8s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rnn)
  > 
  > test_check("rnn")
  ── 1. Failure: (unknown) (@test_rnn.R#66)  ─────────────────────────────────────
  sum(bin2int(B)) not equal to 888626.
  1/1 mismatches
  [1] 258488 - 888626 == -630138
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test_rnn.R#66) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘RNOmni.Rmd’ using rmarkdown
Quitting from lines 40-50 (RNOmni.Rmd) 
Error: processing vignette 'RNOmni.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RNOmni.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clustCoDa
> ### Title: Cluster analysis for compositional data
> ### Aliases: clustCoDa plot.clustCoDa
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(expenditures)
> x <- expenditures
> rr <- clustCoDa(x, k=6, scale = "robust", transformation = "pivotCoord")

 *** running Mclust cluster algorithm...

 *** calculating validity measure... 

 finished
> rr2 <- clustCoDa(x, k=6, distMethod = "Aitchison", scale = "none", 
+                  transformation = "identity")

 *** running Mclust cluster algorithm...

 *** calculating validity measure... 

 finished
> rr3 <- clustCoDa(x, k=6, distMethod = "Aitchison", method = "single",
+                  transformation = "identity", scale = "none")

 *** running single cluster algorithm...

 *** calculating validity measure... 

 finished
> plot(rr)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
'library' or 'require' calls in package code:
  ‘robustbase’ ‘sfsmisc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.BuildPartial: no visible global function definition for ‘as.formula’
.BuildPartial: no visible global function definition for ‘residuals’
.PairwiseCorrelation : .Standardize : <anonymous>: no visible global
  function definition for ‘na.omit’
.PairwiseCorrelation : .Standardize: no visible binding for global
  variable ‘median’
.PairwiseCorrelation: no visible global function definition for
  ‘complete.cases’
.yw: no visible global function definition for ‘toeplitz’
FastQn: no visible global function definition for ‘median’
FastQn: no visible global function definition for ‘mad’
fqn: no visible global function definition for ‘median’
fqn: no visible global function definition for ‘mad’
psdcor: no visible global function definition for ‘posdefify’
psdcor: no visible global function definition for ‘nearcor’
robar: no visible global function definition for ‘frequency’
robcor: no visible global function definition for ‘covMcd’
s_FastQn: no visible global function definition for ‘median’
Undefined global functions or variables:
  as.formula complete.cases covMcd frequency mad median na.omit nearcor
  posdefify residuals toeplitz
Consider adding
  importFrom("stats", "as.formula", "complete.cases", "frequency", "mad",
             "median", "na.omit", "residuals", "toeplitz")
to your NAMESPACE file.
Found the following significant warnings:
  robust.cpp:665:25: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/robfilter.Rcheck/00install.out’ for details.
Running examples in ‘robmed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fortify.test_mediation
> ### Title: Convert (robust) mediation analysis results into a data frame
> ###   for plotting
> ### Aliases: fortify.test_mediation fortify.boot_test_mediation
> ###   fortify.sobel_test_mediation fortify.list
> ### Keywords: utilities
> 
> ### ** Examples
> 
> data("BSG2014")
> 
> # run fast and robust bootstrap test
> test <- test_mediation(BSG2014,
+                        x = "ValueDiversity",
+                        y = "TeamCommitment",
+                        m = "TaskConflict")
> 
> # data for dot plot
> dot <- fortify(test, method = "dot")
> plot_mediation(dot)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
RobRSVD: no visible global function definition for ‘median’
Undefined global functions or variables:
  median
Consider adding
  importFrom("stats", "median")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘fastMcd-kmini.Rnw’ using Sweave
Loading required package: robustbase
--- finished re-building ‘fastMcd-kmini.Rnw’

--- re-building ‘lmrob_simulation.Rnw’ using Sweave
Loading required package: xtable
Loading required package: robustbase
Loading required package: ggplot2
Loading required package: GGally
Loading required package: grid
Loading required package: reshape2

Error: processing vignette 'lmrob_simulation.Rnw' failed with diagnostics:
 chunk 4 (label = fig-psi-functions) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

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

--- re-building ‘psi_functions.Rnw’ using Sweave
Loading required package: robustbase
--- finished re-building ‘psi_functions.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppArmadillo’ ‘mgcv’ ‘robustbase’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Running examples in ‘robustHD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coefPlot
> ### Title: Coefficient plot of a sequence of regression models
> ### Aliases: coefPlot coefPlot.grplars coefPlot.rlars coefPlot.seqModel
> ###   coefPlot.sparseLTS coefPlot.tslars coefPlot.tslarsP
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ## generate data
> # example is not high-dimensional to keep computation time low
> library("mvtnorm")
> set.seed(1234)  # for reproducibility
> n <- 100  # number of observations
> p <- 25   # number of variables
> beta <- rep.int(c(1, 0), c(5, p-5))  # coefficients
> sigma <- 0.5      # controls signal-to-noise ratio
> epsilon <- 0.1    # contamination level
> Sigma <- 0.5^t(sapply(1:p, function(i, j) abs(i-j), 1:p))
> x <- rmvnorm(n, sigma=Sigma)    # predictor matrix
> e <- rnorm(n)                   # error terms
> i <- 1:ceiling(epsilon*n)       # observations to be contaminated
> e[i] <- e[i] + 5                # vertical outliers
> y <- c(x %*% beta + sigma * e)  # response
> x[i,] <- x[i,] + 5              # bad leverage points
> 
> 
> ## robust LARS
> # fit model
> fitRlars <- rlars(x, y, sMax = 10)
> # create plot
> coefPlot(fitRlars)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rlmer.Rnw’ using Sweave
Loading required package: robustlmm
Loading required package: lme4
Loading required package: Matrix
Loading required package: ggplot2

Error: processing vignette 'rlmer.Rnw' failed with diagnostics:
 chunk 7 (label = plotPC1) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘rlmer.Rnw’

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

Error: Vignette re-building failed.
Execution halted
aggregateRanks: no visible binding for global variable ‘median’
aggregateRanks: no visible global function definition for ‘pnorm’
betaScores: no visible global function definition for ‘pbeta’
correctBetaPvaluesExact: no visible binding for global variable ‘qbeta’
thresholdBetaScore: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  median pbeta pnorm qbeta
Consider adding
  importFrom("stats", "median", "pbeta", "pnorm", "qbeta")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘penalized’ ‘splines’ ‘survival’ ‘survivalROC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
boot.ROC: no visible global function definition for ‘qnorm’
boot.ROC: no visible global function definition for ‘penalized’
boot.ROC: no visible global function definition for ‘coefficients’
boot.ROC: no visible global function definition for ‘sd’
boot.ROC: no visible global function definition for ‘optL1’
boot.ROCt: no visible global function definition for ‘qnorm’
boot.ROCt: no visible global function definition for ‘penalized’
boot.ROCt: no visible global function definition for ‘Surv’
boot.ROCt: no visible global function definition for ‘coefficients’
boot.ROCt: no visible global function definition for ‘sd’
boot.ROCt: no visible global function definition for ‘survivalROC’
boot.ROCt: no visible global function definition for ‘optL1’
Undefined global functions or variables:
  Surv coefficients optL1 penalized qnorm sd survivalROC
Consider adding
  importFrom("stats", "coefficients", "qnorm", "sd")
to your NAMESPACE file.
'library' or 'require' call to ‘ROCR’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘ROCR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of ‘level’ to ‘levels’
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of ‘level’ to ‘levels’
o.rocc: no visible global function definition for ‘prediction’
o.rocc: no visible global function definition for ‘performance’
o.rocc: no visible global function definition for ‘binom.test’
tr.rocc: no visible global function definition for ‘prediction’
tr.rocc: no visible global function definition for ‘performance’
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
Running examples in ‘rocTree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotTreeHaz
> ### Title: Plotting the estimated hazard function from an rocTree object
> ### Aliases: plotTreeHaz
> 
> ### ** Examples
> 
> set.seed(1)
> dat <- simu(100, 0, 1.3)
> library(survival)
> system.time(fit <- rocTree(Surv(Time, death) ~ z1 + z2, id = id,
+ data = dat, control = list(prune = TRUE, nflds = 10)))
   user  system elapsed 
  1.992   0.012   2.906 
> plotTreeHaz(fit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
NPROCwoGS: no visible global function definition for ‘quantile’
NPROCwoGS : rdirichlet: no visible global function definition for
  ‘rgamma’
NPROCwoGS: no visible global function definition for ‘rbinom’
NPROCwoGS: no visible global function definition for ‘rbeta’
NPROCwoGS: no visible binding for global variable ‘quantile’
Undefined global functions or variables:
  quantile rbeta rbinom rgamma
Consider adding
  importFrom("stats", "quantile", "rbeta", "rbinom", "rgamma")
to your NAMESPACE file.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘RODBC’
A package should be listed in only one of these fields.
'library' or 'require' call to ‘RODBC’ which was already attached by Depends.
  Please remove these calls from your code.
Running examples in ‘rollply-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rollply
> ### Title: Rollply
> ### Aliases: rollply
> 
> ### ** Examples
> 
> 
> # see also vignette("rollply") for a visual introduction
> library(plyr)
> 
> # 1D example: make a trendline for a time-series
> dat <- data.frame(time     = seq.int(1000),
+                   position = cumsum(rnorm(1000,0,10)))
> 
> rollav <- rollply(dat, ~ time, wdw.size=10,
+                   summarise, position=mean(position))
> 
> plot(position ~ time, data = dat, pch = 20)
> lines(rollav, col = 'red', lwd = 3)
> 
> # 2D example
> 
> # Generate three 2D random walks
> dat <- ddply(data.frame(person = c('francois','nicolas','jacques')), 
+              ~ person,
+              summarise, time = seq.int(1000),
+                         x    = cumsum(rnorm(1000,0,1)),
+                         y    = cumsum(rnorm(1000,0,1)))
> 
> # Smoothed trajectory over ten time-steps
> rollav <- rollply(dat, ~ time | person, wdw.size = 10, grid_res = 1000,
+                   summarise, x = mean(x), y = mean(y))
> 
> if ( require(ggplot2) ) {
+   ggplot(dat, aes(x, y, color = person)) +
+     geom_point(alpha = .5, shape = '+') +
+     geom_path(data = rollav)
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rollply.Rmd’ using rmarkdown
Quitting from lines 51-60 (rollply.Rmd) 
Error: processing vignette 'rollply.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rollply.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotComprehensiveValue
> ### Title: Plot comprehensive values of altarnatives
> ### Aliases: plotComprehensiveValue
> 
> ### ** Examples
> 
> perf <- matrix(c(5, 2, 1, 7, 0.5, 0.9, 0.4, 0.4), ncol = 2)
> problem <- buildProblem(perf, 3, FALSE, c('c', 'g'), c(3, 3))
> problem <- addAssignmentsLB(problem, c(1, 2), c(2, 3))
> 
> representativeFunction <- findRepresentativeFunction(problem, 0)
> plotComprehensiveValue(representativeFunction)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
Running examples in ‘rosetta-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fanova
> ### Title: Flexible anova
> ### Aliases: fanova
> ### Keywords: hplot htest
> 
> ### ** Examples
> 
> 
> ### Oneway anova with a plot
> fanova(dat=mtcars, y='mpg', between='cyl', plot=TRUE);
Flexible Analysis of Variance was called with:

  Dependent variable: mpg
  Factors: cyl

Between-subjects factor 'cyl' does not have class 'factor' in dataframe 'mtcars'. Converting it now.

Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Warning in dotstackGrob(stackaxis = stackaxis, x = tdata$x, y = tdata$y,  :
  Unit type of dotdia should be 'npc'
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rotations-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nickel
> ### Title: Nickel electron backscatter diffraction data set
> ### Aliases: nickel
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(nickel) #Load the dataset
> Rep1 <- subset(nickel, rep == 1) #Subset the data to include only the first scan
> 
> #Get a rough idea of how the grain map looks by plotting the first 
> #element of the rotation matrix at each location
> qplot(xpos, ypos, data = Rep1, colour = V1, size = I(2))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rotations-intro.Rnw’ using knitr
Quitting from lines 294-297 (rotations-intro.Rnw) 
Error: processing vignette 'rotations-intro.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rotations-intro.Rnw’

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

Error: Vignette re-building failed.
Execution halted
bestFM: no visible global function definition for ‘data’
gaRoth: no visible global function definition for ‘data’
ros: no visible global function definition for ‘na.omit’
rosunc: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
mfix : m4m: no visible global function definition for ‘median’
rrfa: no visible global function definition for ‘predict’
rrfb: no visible global function definition for ‘predict’
rrfc1: no visible global function definition for ‘predict’
rrfc2: no visible global function definition for ‘predict’
rrfc3: no visible global function definition for ‘predict’
rrfc4: no visible global function definition for ‘predict’
rrfc5 : regdat: no visible global function definition for ‘predict’
rrfc5 : regdat: no visible global function definition for ‘glm’
rrfc5: no visible global function definition for ‘predict’
rrfc6: no visible global function definition for ‘predict’
rrfc7: no visible global function definition for ‘predict’
rrfd: no visible global function definition for ‘predict’
rrfe : rdms: no visible global function definition for ‘rbinom’
rrfe: no visible global function definition for ‘predict’
Undefined global functions or variables:
  glm median predict rbinom
Consider adding
  importFrom("stats", "glm", "median", "predict", "rbinom")
to your NAMESPACE file.
.computeValueReduct: no visible global function definition for ‘combn’
.findAllReductsFromCore: no visible global function definition for
  ‘combn’
.findFirstReductsFromCore: no visible global function definition for
  ‘combn’
.findSmallestReductFamilyFromCore: no visible global function
  definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
royston.test: no visible global function definition for ‘shapiro.test’
royston.test: no visible global function definition for ‘cor’
royston.test: no visible global function definition for ‘qnorm’
royston.test: no visible global function definition for ‘pnorm’
royston.test: no visible global function definition for ‘cov’
royston.test: no visible global function definition for ‘mahalanobis’
royston.test: no visible global function definition for ‘qqplot’
royston.test: no visible global function definition for ‘qchisq’
royston.test: no visible global function definition for ‘ppoints’
royston.test: no visible global function definition for ‘abline’
royston.test: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline cor cov mahalanobis pchisq pnorm ppoints qchisq qnorm qqplot
  shapiro.test
Consider adding
  importFrom("graphics", "abline")
  importFrom("stats", "cor", "cov", "mahalanobis", "pchisq", "pnorm",
             "ppoints", "qchisq", "qnorm", "qqplot", "shapiro.test")
to your NAMESPACE file.
Running examples in ‘rpact-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AnalysisResults_plot
> ### Title: Analysis Results Plotting - Conditional Power Plot
> ### Aliases: AnalysisResults_plot plot.AnalysisResults
> 
> ### ** Examples
> 
> 
> design <- getDesignGroupSequential(kMax = 2)
> 
> dataExample <- getDataset(
+     n = c(20, 30),
+ 	   means = c(50, 51),
+ 	   stDevs = c(130, 140)
+ )
> 
> result <- getAnalysisResults(design = design, 
+ 	   dataInput = dataExample, thetaH0 = 20, 
+ 	   nPlanned = c(30), thetaH1 = 1.5, stage = 1) 
[PROGRESS] Stage results calculated [0.0294 secs] 
[PROGRESS] Conditional power calculated [0.0025 secs] 
[PROGRESS] Conditional rejection probabilities (CRP) calculated [0.0011 secs] 
[PROGRESS] Repeated confidence interval of stage 1 calculated [1.4588 secs] 
[PROGRESS] Repeated confidence interval calculated [1.46 secs] 
[PROGRESS] Overall repeated p-values of stage 1 calculated [0.5394 secs] 
[PROGRESS] Repeated p-values calculated [0.5407 secs] 
[PROGRESS] Final p-value calculated [0.001 secs] 
[PROGRESS] Final confidence interval calculated [0.0237 secs] 
> 
> if (require(ggplot2)) plot(result, thetaRange = c(0, 100))
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Package in Depends field not imported from: ‘hash’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
P: no visible global function definition for ‘has.key’
get_rand_int: no visible global function definition for ‘runif’
last: no visible global function definition for ‘tail’
rand_partitions: no visible global function definition for ‘hash’
Undefined global functions or variables:
  has.key hash runif tail
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "tail")
to your NAMESPACE file.
evalMedian: no visible global function definition for ‘xtabs’
evalMode: no visible global function definition for ‘xtabs’
rpartScore: no visible global function definition for ‘model.extract’
rpartScore: no visible global function definition for ‘var’
rpartScore: no visible binding for global variable ‘var’
splitAbs: no visible global function definition for ‘xtabs’
Undefined global functions or variables:
  model.extract var xtabs
Consider adding
  importFrom("stats", "model.extract", "var", "xtabs")
to your NAMESPACE file.
'library' or 'require' call to ‘RODBC’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
rpart.rules.push: no visible global function definition for ‘sqlSave’
rpart.rules.table : <anonymous>: no visible global function definition
  for ‘setNames’
rpart.subrules.table : <anonymous>: no visible global function
  definition for ‘setNames’
Undefined global functions or variables:
  setNames sqlSave
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘survival’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenerateData: no visible global function definition for ‘mvrnorm’
GetVarImp : FitPenalizedModel: no visible global function definition
  for ‘clogit’
Undefined global functions or variables:
  clogit mvrnorm
Running examples in ‘rpdo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pdo
> ### Title: Pacific Decadal Oscillation Index
> ### Aliases: pdo
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(rpdo)
> library(ggplot2)
> 
> data(pdo)
> ggplot(data = subset(pdo, pdo$Month == 1), aes(x = Year, y = PDO)) +
+  geom_line() + ylab("January PDO Index")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘RpeakChrom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vanDeemter
> ### Title: Characterization of chromatographic columns using vanDeemter
> ###   equations.
> ### Aliases: vanDeemter
> 
> ### ** Examples
> 
> ggmetoxi <- vanDeemter(col = parameters_col_metoxi, ext = parameters_ext,
+               dead = parameters_dead, length = 150, A = 6, B = 200, C = 0.04,
+               GG = TRUE, Foley = FALSE, do.plot = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: vanDeemter ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘customitem.Rmd’ using knitr
Loading required package: parallel
--- finished re-building ‘customitem.Rmd’

--- re-building ‘diagnostics.Rmd’ using knitr
Quitting from lines 49-78 (diagnostics.Rmd) 
Error: processing vignette 'diagnostics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘diagnostics.Rmd’

--- re-building ‘flexmirt-plots.Rmd’ using knitr
Quitting from lines 37-64 (flexmirt-plots.Rmd) 
Error: processing vignette 'flexmirt-plots.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘flexmirt-plots.Rmd’

SUMMARY: processing the following files failed:
  ‘diagnostics.Rmd’ ‘flexmirt-plots.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rphast.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

--- re-building ‘visualization.Rmd’ using rmarkdown
Quitting from lines 29-33 (visualization.Rmd) 
Error: processing vignette 'visualization.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘visualization.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘diagnostics.Rmd’ using rmarkdown
Loading required package: survival
Quitting from lines 58-59 (diagnostics.Rmd) 
Error: processing vignette 'diagnostics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘diagnostics.Rmd’

--- re-building ‘user_guide.Rmd’ using rmarkdown
Loading required package: survival
Quitting from lines 44-51 (user_guide.Rmd) 
Error: processing vignette 'user_guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘user_guide.Rmd’

SUMMARY: processing the following files failed:
  ‘diagnostics.Rmd’ ‘user_guide.Rmd’

Error: Vignette re-building failed.
Execution halted
but_last: no visible global function definition for ‘head’
first: no visible global function definition for ‘head’
last: no visible global function definition for ‘tail’
preview_frames: no visible global function definition for ‘str’
print.EprimeFrame: no visible global function definition for ‘str’
print.FrameList: no visible global function definition for ‘str’
Undefined global functions or variables:
  head str tail
Consider adding
  importFrom("utils", "head", "str", "tail")
to your NAMESPACE file.
Running examples in ‘Rprofet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: WOE_custom
> ### Title: Custom Binning Numeric Variables
> ### Aliases: WOE_custom
> 
> ### ** Examples
> 
> mydata <- ISLR::Default
> mydata$default <- ifelse(mydata$default=="Yes", 1, 0) ## target coded with 1, 0
> WC_1 <- WOE_custom(dataset=mydata, var="balance", target = "default",
+            breaks=seq(0,3000,1000))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: WOE_custom ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rpsftm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.rpsftm
> ### Title: Plot Method
> ### Aliases: plot.rpsftm
> 
> ### ** Examples
> 
> fit <- rpsftm(Surv(progyrs, prog)~rand(imm,1-xoyrs/progyrs),immdef, censyrs)
> plot(fit)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rpsftm_vignette.Rmd’ using rmarkdown
Quitting from lines 141-143 (rpsftm_vignette.Rmd) 
Error: processing vignette 'rpsftm_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rpsftm_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Non-standard file/directory found at top level:
  ‘rpsychi-Ex.R’
Package which this enhances but not available for checking: ‘rjpod’
Error(s) in re-building vignettes:
  ...
--- re-building ‘CoupledHarmonics.Rmd’ using rmarkdown
Quitting from lines 40-42 (CoupledHarmonics.Rmd) 
Error: processing vignette 'CoupledHarmonics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CoupledHarmonics.Rmd’

--- re-building ‘CoupledHarmonics2.Rmd’ using rmarkdown
Quitting from lines 40-42 (CoupledHarmonics2.Rmd) 
Error: processing vignette 'CoupledHarmonics2.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CoupledHarmonics2.Rmd’

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

SUMMARY: processing the following files failed:
  ‘CoupledHarmonics.Rmd’ ‘CoupledHarmonics2.Rmd’

Error: Vignette re-building failed.
Execution halted
rrBlupM6: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Running examples in ‘rrecsys-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dataChart
> ### Title: Visualization of data characteristics.
> ### Aliases: dataChart
> 
> ### ** Examples
> 
> data(mlLatest100k)
> 
> a <- defineData(mlLatest100k)
There are values smaller that the defined threshold. If you want to keep using them please redefine the "minimum" argument.
> 
> dataChart(a, x = "items", y = "num_of_ratings")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rreg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: regbar
> ### Title: Barplot with explicit data comparison
> ### Aliases: regbar
> 
> ### ** Examples
> 
> # basic usage
> library("rreg")
> regbar(data = hfdata, x = inst, y = case2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Packages in Depends field not imported from:
  ‘glasso’ ‘matrixcalc’ ‘mvoutlier’ ‘pcaPP’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
rrest: no visible binding for global variable ‘glasso’
rrest: no visible global function definition for ‘pcout’
rrest: no visible global function definition for ‘var’
rrest: no visible global function definition for ‘mahalanobis’
rrlda : centerObservations: no visible global function definition for
  ‘l1median_NLM’
rrlda : df.L2glasso: no visible global function definition for
  ‘duplication.matrix’
rrlda : alt.df.L2glasso: no visible global function definition for
  ‘lower.triangle’
Undefined global functions or variables:
  duplication.matrix glasso l1median_NLM lower.triangle mahalanobis
  pcout var
Consider adding
  importFrom("stats", "mahalanobis", "var")
to your NAMESPACE file.
Running examples in ‘rrr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pairwise_plot
> ### Title: Pairwise Plots
> ### Aliases: pairwise_plot
> 
> ### ** Examples
> 
> data(pendigits)
> digits_features <- pendigits[,1:34]
> digits_class <- pendigits[,35]
> pairwise_plot(digits_features, digits_class, type = "pca", pair_x = 1, pair_y = 3)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: pairwise_plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rrr.Rmd’ using rmarkdown
Quitting from lines 89-90 (rrr.Rmd) 
Error: processing vignette 'rrr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rrr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rescaling_data.Rmd’ using rmarkdown
Quitting from lines 36-42 (rescaling_data.Rmd) 
Error: processing vignette 'rescaling_data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rescaling_data.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_2ggplots
> ### Title: Add two ggplots into a document object
> ### Aliases: add_2ggplots
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
> require(magrittr)
Loading required package: magrittr
> require(officer)
Loading required package: officer
> require(rvg)
Loading required package: rvg
> plot1 <- "ggplot(data = iris, aes(Sepal.Length, Petal.Length)) + geom_point()"
> plot2 <- "ggplot(data = iris, aes(Sepal.Length, Petal.Length, color = Species)) + geom_point()"
> read_pptx() %>% add_text(title="Two ggplots") %>% add_2ggplots(plot1=plot1,plot2=plot2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: %>% ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rrtable.Rmd’ using rmarkdown
Loading required package: moonBook
Loading required package: ztable
Welcome to package ztable ver 0.2.0
Loading required package: rrtable

Attaching package: 'rrtable'

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

    roundDf

Loading required package: ggplot2
Quitting from lines 98-99 (rrtable.Rmd) 
Error: processing vignette 'rrtable.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rrtable.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘robustbase’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.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 ‘rsample-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tidy.rsplit
> ### Title: Tidy Resampling Object
> ### Aliases: tidy.rsplit tidy.rset tidy.vfold_cv tidy.nested_cv
> 
> ### ** Examples
> 
> library(ggplot2)
> theme_set(theme_bw())
> 
> set.seed(4121)
> cv <- tidy(vfold_cv(mtcars, v = 5))
> ggplot(cv, aes(x = Fold, y = Row, fill = Data)) + 
+   geom_tile() + scale_fill_brewer()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basics.Rmd’ using rmarkdown
Loading required package: tidyr
--- finished re-building ‘Basics.Rmd’

--- re-building ‘Working_with_rsets.Rmd’ using rmarkdown
Loading required package: tidyr
Quitting from lines 131-134 (Working_with_rsets.Rmd) 
Error: processing vignette 'Working_with_rsets.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Working_with_rsets.Rmd’

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

Error: Vignette re-building failed.
Execution halted
stripslash: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
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.
rsem: no visible global function definition for ‘write.table’
rsem.Ascov: no visible global function definition for ‘qchisq’
rsem.Ascov: no visible global function definition for ‘pchisq’
rsem.emmusig: no visible global function definition for ‘na.omit’
rsem.emmusig: no visible global function definition for ‘qchisq’
rsem.emmusig: no visible global function definition for ‘pchisq’
rsem.fit: no visible global function definition for ‘pchisq’
rsem.fit: no visible global function definition for ‘pf’
rsem.print : print.estimate: no visible global function definition for
  ‘pnorm’
rsem.weight: no visible global function definition for ‘qchisq’
rsem.weight: no visible global function definition for ‘pchisq’
semdiag.call.eqs: no visible global function definition for
  ‘write.table’
semdiag.read.eqs: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  na.omit pchisq pf pnorm qchisq read.fwf write.table
Consider adding
  importFrom("stats", "na.omit", "pchisq", "pf", "pnorm", "qchisq")
  importFrom("utils", "read.fwf", "write.table")
to your NAMESPACE file.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-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.
'library' or 'require' calls to packages already attached by Depends:
  ‘grDevices’ ‘snowfall’
  Please remove these calls from your code.
'library' or 'require' call to ‘ctc’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘biwt’ ‘cairoDevice’ ‘fBasics’ ‘gWidgets’ ‘gWidgetsRGtk2’ ‘gplots’
  ‘minerva’ ‘parmigene’ ‘snowfall’ ‘stringr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘rsgcc/libs/rsgcc.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.multisimsum
> ### Title: autoplot method for multisimsum objects
> ### Aliases: autoplot.multisimsum
> 
> ### ** Examples
> 
> data("frailty", package = "rsimsum")
> ms <- multisimsum(
+   data = frailty,
+   par = "par", true = c(trt = -0.50, fv = 0.75),
+   estvarname = "b", se = "se", methodvar = "model",
+   by = "fv_dist", x = TRUE
+ )
'ref' method was not specified, Cox, Gamma set as the reference
> 
> library(ggplot2)
> autoplot(ms, par = "trt")
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 216-223 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘plotting.Rmd’ using rmarkdown
Quitting from lines 75-76 (plotting.Rmd) 
Error: processing vignette 'plotting.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plotting.Rmd’

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

--- re-building ‘rsimsumtidyverse.Rmd’ using rmarkdown
Quitting from lines 43-53 (rsimsumtidyverse.Rmd) 
Error: processing vignette 'rsimsumtidyverse.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rsimsumtidyverse.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘resource_suitability.Rmd’ using rmarkdown
Loading required package: rsMove
Loading required package: raster
Loading required package: sp
Loading required package: rgdal
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
 Path to GDAL shared files: /usr/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: 1.3-1 
Loading required package: ggplot2
Loading required package: knitr
Loading required package: kableExtra
Loading required package: caret
Loading required package: lattice
Loading required package: igraph

Attaching package: 'igraph'

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

    union

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

    decompose, spectrum

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

    union

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:ggplot2':

    margin

Loading required package: e1071

Attaching package: 'e1071'

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

    interpolate

Quitting from lines 181-183 (resource_suitability.Rmd) 
Error: processing vignette 'resource_suitability.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘resource_suitability.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘benchmark.Rmd’ using rmarkdown
Quitting from lines 176-185 (benchmark.Rmd) 
Error: processing vignette 'benchmark.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘benchmark.Rmd’

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

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

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

Error: Vignette re-building failed.
Execution halted
negbin.pow : negbin.disp: no visible global function definition for
  ‘rpois’
negbin.pow : negbin.disp: no visible global function definition for
  ‘rnbinom’
negbin.pow : inner.fcn: no visible global function definition for
  ‘na.omit’
negbin.pow : inner.fcn: no visible global function definition for
  ‘quantile’
negbin.pow: no visible global function definition for ‘txtProgressBar’
negbin.pow: no visible global function definition for
  ‘setTxtProgressBar’
poiss.pow : inner.fcn: no visible global function definition for
  ‘rpois’
poiss.pow : inner.fcn: no visible global function definition for
  ‘quantile’
poiss.pow: no visible global function definition for ‘txtProgressBar’
poiss.pow: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  na.omit quantile rnbinom rpois setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "quantile", "rnbinom", "rpois")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Running examples in ‘RSSL-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CrossValidationSSL
> ### Title: Cross-validation in semi-supervised setting
> ### Aliases: CrossValidationSSL CrossValidationSSL.list
> ###   CrossValidationSSL.matrix
> 
> ### ** Examples
> 
> X <- model.matrix(Species~.-1,data=iris)
> y <- iris$Species
> 
> classifiers <- list("LS"=function(X,y,X_u,y_u) {
+   LeastSquaresClassifier(X,y,lambda=0)}, 
+   "EM"=function(X,y,X_u,y_u) {
+     SelfLearning(X,y,X_u,
+                  method=LeastSquaresClassifier)}
+ )
> 
> measures <- list("Accuracy" =  measure_accuracy,
+                  "Loss" = measure_losstest,
+                  "Loss labeled" = measure_losslab,
+                  "Loss Lab+Unlab" = measure_losstrain
+ )
> 
> # Cross-validation making sure test folds are non-overlapping
> cvresults1 <- CrossValidationSSL(X,y, 
+                                  classifiers=classifiers, 
+                                  measures=measures,
+                                  leaveout="test", k=10,
+                                  repeats = 2,n_labeled = 10)
> print(cvresults1)
CrossValidation object

Classifiers:
 	 LS
	 EM 
Measures:
 	 Accuracy
	 Loss
	 Loss labeled
	 Loss Lab+Unlab
	 Time 
10  folds
2  repeats
0  missing
> plot(cvresults1)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘aov.Rmd’ using rmarkdown
--- finished re-building ‘aov.Rmd’

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

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

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

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

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

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

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

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

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

--- re-building ‘priors.Rmd’ using rmarkdown
Loading required package: Rcpp
rstanarm (Version 2.18.2, packaged: 2018-11-08 22:19:38 UTC)
- Do not expect the default priors to remain the same in future rstanarm versions.
Thus, R scripts should specify priors explicitly, even if they are just the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())
- Plotting theme set to bayesplot::theme_default().
Quitting from lines 227-236 (priors.Rmd) 
Error: processing vignette 'priors.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘priors.Rmd’

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

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

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

--- re-building ‘rstan.Rmd’ using rmarkdown
Quitting from lines 364-365 (rstan.Rmd) 
Error: processing vignette 'rstan.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rstan.Rmd’

--- re-building ‘stanfit-objects.Rmd’ using rmarkdown
--- finished re-building ‘stanfit-objects.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coregisterImages
> ### Title: Image to Image Co-Registration based on Mutual Information
> ### Aliases: coregisterImages
> 
> ### ** Examples
> 
> library(raster)
Loading required package: sp
> library(ggplot2)
> library(reshape2)
> data(rlogo)
> reference <- rlogo
> ## Shift reference 2 pixels to the right and 3 up
> missreg <- shift(reference, x = 2, y = 3)
> 
> ## Compare shift
> p <- ggR(reference, sat = 1, alpha = .5) 
> p + ggR(missreg, sat = 1, hue = .5, alpha = 0.5, ggLayer=TRUE) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following significant warnings:
  RngStreams.c:332:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rstream.Rcheck/00install.out’ for details.
Running examples in ‘rsvd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rpca
> ### Title: Randomized principal component analysis (rpca).
> ### Aliases: rpca
> 
> ### ** Examples
> 
> 
> library('rsvd')
> #
> # Load Edgar Anderson's Iris Data
> #
> data('iris')
> 
> #
> # log transform
> #
> log.iris <- log( iris[ , 1:4] )
> iris.species <- iris[ , 5]
> 
> #
> # Perform rPCA and compute only the first two PCs
> #
> iris.rpca <- rpca(log.iris, k=2)
> summary(iris.rpca) # Summary
                         PC1   PC2
Explained variance     2.933 0.907
Standard deviations    1.712 0.952
Proportion of variance 0.733 0.227
Cumulative proportion  0.733 0.960
> print(iris.rpca) # Prints the rotations
Standard deviations:
[1] 1.712 0.952

Eigenvalues:
[1] 2.933 0.907

Rotation:
                PC1    PC2
Sepal.Length -0.504 -0.455
Sepal.Width   0.302 -0.889
Petal.Length -0.577 -0.034
Petal.Width  -0.567 -0.035
> 
> #
> # Use rPCA to compute all PCs, similar to \code{prcomp}
> #
> iris.rpca <- rpca(log.iris)
> summary(iris.rpca) # Summary
                         PC1   PC2   PC3   PC4
Explained variance     2.933 0.907 0.133 0.027
Standard deviations    1.712 0.952 0.365 0.166
Proportion of variance 0.733 0.227 0.033 0.007
Cumulative proportion  0.733 0.960 0.993 1.000
> print(iris.rpca) # Prints the rotations
Standard deviations:
[1] 1.712 0.952 0.365 0.166

Eigenvalues:
[1] 2.933 0.907 0.133 0.027

Rotation:
                PC1    PC2    PC3    PC4
Sepal.Length  0.504 -0.455  0.709  0.191
Sepal.Width  -0.302 -0.889 -0.331 -0.091
Petal.Length  0.577 -0.034 -0.219 -0.786
Petal.Width   0.567 -0.035 -0.583  0.580
> plot(iris.rpca) # Produce screeplot, variable and individuls factor maps.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘rsvg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rsvg
> ### Title: Render SVG into Bitmap
> ### Aliases: rsvg rsvg_pdf rsvg_png rsvg_ps rsvg_raw rsvg_svg rsvg_webp
> 
> ### ** Examples
> 
> # create some svg
> options(example.ask=FALSE)
> tmp <- tempfile()
> svglite::svglite(tmp, width = 10, height = 7)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = factor(cyl))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘RSwissMaps-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: can.plot
> ### Title: Plotting canton-level maps of Switzerland
> ### Aliases: can.plot
> 
> ### ** Examples
> 
>  # Generating sample data:
>  dt <- can.template(2016)
>  for(i in 1:nrow(dt)){dt$values[i] <- sample(c(300:700), 1)/1000}
> 
>  # Plotting sample data:
>  can.plot(dt$bfs_nr, dt$values, 2016)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines 33-35 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Math.Sym: no visible binding for global variable ‘transtab’
jythonStart: no visible global function definition for ‘.jinit’
jythonStart: no visible global function definition for ‘.jnew’
jythonStart: no visible binding for global variable ‘.Jython’
sympy: no visible binding for global variable ‘.Jython’
sympy: no visible global function definition for ‘.jstrVal’
sympyStart: no visible binding for global variable ‘.Jython’
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab

Found the following assignments to the global environment:
File ‘rSymPy/R/sympy.R’:
  assign(".Jython", .jnew("org.python.util.PythonInterpreter"), 
    .GlobalEnv)
  assign(".Jython", rJython(modules = system.file("Lib", package = "rSymPy")), 
    .GlobalEnv)
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.
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rtfbs.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rtf.Rnw’ using Sweave

Error: processing vignette 'rtf.Rnw' failed with diagnostics:
 chunk 29 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘rtf.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert_output
> ### Title: Uses output file from MicroPEM to create a 'micropem' object.
> ### Aliases: convert_output
> 
> ### ** Examples
> 
> micropem_example <- convert_output(system.file('extdata', 'CHAI.csv', package = 'rtimicropem'))
> micropem_example$plot()
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘chai_data_cleaning.Rmd’ using rmarkdown
--- finished re-building ‘chai_data_cleaning.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 86-88 (vignette_ammon.Rmd) 
Error: processing vignette 'vignette_ammon.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette_ammon.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘transfer-entropy.Rmd’ using rmarkdown
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
Warning: Removed 1 rows containing non-finite values (stat_smooth).
Warning: Removed 1 rows containing missing values (geom_point).
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
Warning: Removed 1 rows containing non-finite values (stat_smooth).
Warning: Removed 1 rows containing missing values (geom_point).
Quitting from lines 240-241 (transfer-entropy.Rmd) 
Error: processing vignette 'transfer-entropy.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘transfer-entropy.Rmd’

SUMMARY: processing the following file failed:
  ‘transfer-entropy.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rubias-overview.Rmd’ using rmarkdown
Quitting from lines 275-292 (rubias-overview.Rmd) 
Error: processing vignette 'rubias-overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘rubias-overview.Rmd’

--- re-building ‘rubias-underlying-data-structures.Rmd’ using rmarkdown
--- finished re-building ‘rubias-underlying-data-structures.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_path
> ### Title: Plot a path of the simulated ruin process
> ### Aliases: plot_path
> 
> ### ** Examples
> 
> model <- CramerLundberg(initial_capital = 10,
+                         premium_rate = 1,
+                         claim_poisson_arrival_rate = 1,
+                         claim_size_generator = rexp,
+                         claim_size_parameters = list(rate = 1))
> 
> path <- simulate_path(model = model, max_time_horizon = 10)
> 
> plot_path(path)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ruin-intro.Rmd’ using rmarkdown
Set default RNG to L'Ecuyer-CMRG for a safe parallel simulation.
Quitting from lines 77-78 (ruin-intro.Rmd) 
Error: processing vignette 'ruin-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ruin-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-runstats.Rmd’ using rmarkdown
Quitting from lines 176-192 (using-runstats.Rmd) 
Error: processing vignette 'using-runstats.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-runstats.Rmd’

SUMMARY: processing the following file failed:
  ‘using-runstats.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw
> ### Title: Beautiful graphical representation of multiplication tables
> ### Aliases: draw
> 
> ### ** Examples
> 
> draw(table=2,modulo = 10, label=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
HapMendlianCheck: no visible global function definition for
  ‘write.table’
rvPDT.test.sub: no visible global function definition for ‘pnorm’
whap.prehap: no visible global function definition for ‘write.table’
whap.prehap: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  pnorm read.table write.table
Consider adding
  importFrom("stats", "pnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
'library' or 'require' call to ‘pixmap’ which was already attached by Depends.
  Please remove these calls from your code.
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of ‘var’ to ‘variable’
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of ‘var’ to ‘variable’
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Running examples in ‘rvinecopulib-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.vinecop_dist
> ### Title: Plotting 'vinecop_dist' and 'vinecop' objects.
> ### Aliases: plot.vinecop_dist contour.vinecop_dist plot.vinecop
> ###   contour.vinecop plot.vinecop contour.vinecop_dist contour.vinecop
> ### Keywords: plot
> 
> ### ** Examples
> 
> # set up vine copula model
> d <- 20
> n <- 2e2
> u <- matrix(runif(n*d), n, d)
> vc <- vinecop(u, "indep")
> 
> # plot
> plot(vc, tree = c(1,2))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rvinecopulib)
  > 
  > test_check("rvinecopulib")
  ── 1. Error: plot functions work (@test_vinecop_dist.R#78)  ────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_silent(p <- plot(vc, edge_labels = "family", var_names = "legend")) at testthat/test_vinecop_dist.R:78
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: plot(vc, edge_labels = "family", var_names = "legend")
  10: plot.vinecop_dist(vc, edge_labels = "family", var_names = "legend")
  ...
  18: preDraw(x)
  19: preDraw.gTree(x)
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.viewport(X[[i]], ...)
  27: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 227 SKIPPED: 0 FAILED: 1
  1. Error: plot functions work (@test_vinecop_dist.R#78) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
  Output from running autoreconf:
  aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
  configure.in:22: warning: underquoted definition of AC_PROG_R
  configure.in:22:   run info Automake 'Extending aclocal'
  configure.in:22:   or see https://www.gnu.org/software/automake/manual/automake.html#Extending-aclocal
  configure.in:86: warning: the serial number must appear before any macro definition
  configure.in:362: warning: the serial number must appear before any macro definition
lc_TDT: no visible global function definition for ‘pchisq’
rvTDT: no visible global function definition for ‘dbeta’
Undefined global functions or variables:
  dbeta pchisq
Consider adding
  importFrom("stats", "dbeta", "pchisq")
to your NAMESPACE file.
LASSO: no visible global function definition for ‘lm’
LASSO: no visible global function definition for ‘anova’
LASSO: no visible global function definition for ‘glm’
LASSO: no visible global function definition for ‘pchisq’
LASSO : <anonymous>: no visible global function definition for
  ‘extractAIC’
PCR : <anonymous>: no visible global function definition for ‘cor’
PLS : <anonymous>: no visible global function definition for ‘cor’
RR : RRscore: no visible binding for global variable ‘sd’
SPLS: no visible global function definition for ‘lm’
SPLS: no visible global function definition for ‘anova’
SPLS : <anonymous>: no visible global function definition for
  ‘extractAIC’
VTWOD : getScores: no visible global function definition for ‘sd’
VTWOD : getScores: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  anova cor extractAIC glm lm pchisq pnorm sd
Consider adding
  importFrom("stats", "anova", "cor", "extractAIC", "glm", "lm",
             "pchisq", "pnorm", "sd")
to your NAMESPACE file.
check_ISO_code: no visible binding for global variable ‘NoAm_country’
check_ISO_code: no visible binding for global variable ‘SoAm_country’
check_ISO_code: no visible binding for global variable ‘Oceana_country’
check_ISO_code: no visible binding for global variable ‘Africa_country’
check_ISO_code: no visible binding for global variable ‘Asia_country’
check_ISO_code: no visible binding for global variable ‘Eur_country’
climate_map: no visible binding for global variable ‘data’
date_correct: no visible global function definition for ‘tail’
Undefined global functions or variables:
  Africa_country Asia_country Eur_country NoAm_country Oceana_country
  SoAm_country data tail
Consider adding
  importFrom("utils", "data", "tail")
to your NAMESPACE file.
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.
weblogo: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL
Consider adding
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Running examples in ‘RWeka-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Weka_classifier_trees
> ### Title: R/Weka Classifier Trees
> ### Aliases: Weka_classifier_trees J48 LMT M5P DecisionStump plot.Weka_tree
> ###   parse_Weka_digraph
> ### Keywords: models regression classif tree
> 
> ### ** Examples
> 
> m1 <- J48(Species ~ ., data = iris)
> 
> ## print and summary
> m1
J48 pruned tree
------------------

Petal.Width <= 0.6: setosa (50.0)
Petal.Width > 0.6
|   Petal.Width <= 1.7
|   |   Petal.Length <= 4.9: versicolor (48.0/1.0)
|   |   Petal.Length > 4.9
|   |   |   Petal.Width <= 1.5: virginica (3.0)
|   |   |   Petal.Width > 1.5: versicolor (3.0/1.0)
|   Petal.Width > 1.7: virginica (46.0/1.0)

Number of Leaves  : 	5

Size of the tree : 	9

> summary(m1) # calls evaluate_Weka_classifier()

=== Summary ===

Correctly Classified Instances         147               98      %
Incorrectly Classified Instances         3                2      %
Kappa statistic                          0.97  
Mean absolute error                      0.0233
Root mean squared error                  0.108 
Relative absolute error                  5.2482 %
Root relative squared error             22.9089 %
Total Number of Instances              150     

=== Confusion Matrix ===

  a  b  c   <-- classified as
 50  0  0 |  a = setosa
  0 49  1 |  b = versicolor
  0  2 48 |  c = virginica
> table(iris$Species, predict(m1)) # by hand
            
             setosa versicolor virginica
  setosa         50          0         0
  versicolor      0         49         1
  virginica       0          2        48
> 
> ## visualization
> ## use partykit package
> if(require("partykit", quietly = TRUE)) plot(m1)
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit
Calls: plot ... edge_panel -> grid.rect -> rectGrob -> is.unit -> unit
Execution halted
.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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘RxODE-covariates.Rmd’ using rmarkdown
Quitting from lines 73-75 (RxODE-covariates.Rmd) 
Error: processing vignette 'RxODE-covariates.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RxODE-covariates.Rmd’

--- re-building ‘RxODE-data-frame.Rmd’ using rmarkdown
--- finished re-building ‘RxODE-data-frame.Rmd’

--- re-building ‘RxODE-events.Rmd’ using rmarkdown
--- finished re-building ‘RxODE-events.Rmd’

--- re-building ‘RxODE-intro.Rmd’ using rmarkdown
Quitting from lines 134-137 (RxODE-intro.Rmd) 
Error: processing vignette 'RxODE-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RxODE-intro.Rmd’

--- re-building ‘RxODE-mix-lin-ode.Rmd’ using rmarkdown
--- finished re-building ‘RxODE-mix-lin-ode.Rmd’

--- re-building ‘RxODE-shiny.Rmd’ using rmarkdown
--- finished re-building ‘RxODE-shiny.Rmd’

--- re-building ‘RxODE-sim-var.Rmd’ using rmarkdown
Quitting from lines 50-63 (RxODE-sim-var.Rmd) 
Error: processing vignette 'RxODE-sim-var.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RxODE-sim-var.Rmd’

--- re-building ‘RxODE-stiff.Rmd’ using rmarkdown
--- finished re-building ‘RxODE-stiff.Rmd’

--- re-building ‘RxODE-syntax.Rmd’ using rmarkdown
--- finished re-building ‘RxODE-syntax.Rmd’

--- re-building ‘RxODE-transit-compartments.Rmd’ using rmarkdown
Quitting from lines 26-51 (RxODE-transit-compartments.Rmd) 
Error: processing vignette 'RxODE-transit-compartments.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘RxODE-transit-compartments.Rmd’

SUMMARY: processing the following files failed:
  ‘RxODE-covariates.Rmd’ ‘RxODE-intro.Rmd’ ‘RxODE-sim-var.Rmd’
  ‘RxODE-transit-compartments.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: qqnorm_spss
> ### Title: SPSS like QQ-plot
> ### Aliases: qqnorm_spss
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
> 
> set.seed(0)
> x <- sample(0:9, 100, rep=TRUE)
> 
> ### SPSS like
> 
> # Standard QQ-plot
> qq <- qqnorm_spss(x, 1)
> plot(qq)  
> ggplot(qq)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
--- finished re-building ‘introduction.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 90-104 (sentiment.Rmd) 
Error: processing vignette 'sentiment.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sentiment.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  geometry/s2loop.cc:85:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2loop.cc:247:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:52:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:94:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2regioncoverer.cc:119:28: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct S2RegionCoverer::Candidate’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/s2.Rcheck/00install.out’ for details.
calculate.summary: no visible global function definition for ‘sd’
detect.saccades: no visible global function definition for ‘median’
diagnostic.plot: no visible global function definition for ‘dev.new’
diagnostic.plot: no visible global function definition for ‘par’
diagnostic.plot: no visible global function definition for ‘recordPlot’
diagnostic.plot: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.new dev.off median par recordPlot sd
Consider adding
  importFrom("grDevices", "dev.new", "dev.off", "recordPlot")
  importFrom("graphics", "par")
  importFrom("stats", "median", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘sadists.Rnw’ using knitr
Loading required package: ggplot2
Loading required package: grid
Loading required package: polynom
`stat_bin()` using `bins = 30`. Pick better value with
`binwidth`.
Quitting from lines 409-415 (sadists.Rnw) 
Error: processing vignette 'sadists.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sadists.Rnw’

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

Error: Vignette re-building failed.
Execution halted
eblupDyn: no visible global function definition for ‘model.frame’
eblupDyn: no visible global function definition for ‘model.matrix’
eblupDyn: no visible global function definition for ‘pnorm’
eblupRY: no visible global function definition for ‘model.frame’
eblupRY: no visible global function definition for ‘model.matrix’
eblupRY: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  model.frame model.matrix pnorm
Consider adding
  importFrom("stats", "model.frame", "model.matrix", "pnorm")
to your NAMESPACE file.
Running examples in ‘saeRobust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.rfh
> ### Title: Plots
> ### Aliases: plot.rfh plot.prediction.fitrfh plot.mse.fitrfh qqPlot
> ###   blandAltmanPlot
> 
> ### ** Examples
> 
> qqPlot(rnorm(10))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
Package in Depends field not imported from: ‘lpSolveAPI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glm: no visible binding for global variable ‘gaussian’
glm: no visible global function definition for ‘glm.control’
glm: no visible global function definition for ‘model.response’
glm: no visible global function definition for ‘is.empty.model’
glm: no visible global function definition for ‘model.matrix’
glm: no visible global function definition for ‘model.weights’
glm: no visible global function definition for ‘model.offset’
glm: no visible global function definition for ‘model.extract’
glm: no visible global function definition for ‘glm.fit’
glm: no visible global function definition for ‘.getXlevels’
separator: no visible global function definition for ‘make.lp’
separator: no visible global function definition for ‘set.column’
separator: no visible global function definition for ‘set.rhs’
separator: no visible global function definition for ‘set.constr.type’
separator: no visible global function definition for ‘set.objfn’
separator: no visible global function definition for ‘set.bounds’
separator: no visible global function definition for ‘lp.control’
separator: no visible global function definition for ‘get.variables’
separator: no visible global function definition for ‘set.basis’
separator: no visible global function definition for
  ‘get.dual.solution’
Undefined global functions or variables:
  .getXlevels gaussian get.dual.solution get.variables glm.control
  glm.fit is.empty.model lp.control make.lp model.extract model.matrix
  model.offset model.response model.weights set.basis set.bounds
  set.column set.constr.type set.objfn set.rhs
Consider adding
  importFrom("stats", ".getXlevels", "gaussian", "glm.control",
             "glm.fit", "is.empty.model", "model.extract",
             "model.matrix", "model.offset", "model.response",
             "model.weights")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘glue.Rnw’ using Sweave
--- finished re-building ‘glue.Rnw’

--- re-building ‘sc-intro.Rnw’ using Sweave
Simulation started at 2019-03-29 18:12:41.
N2,rho=0.7 Adaptive Metropolis: 557 (156,Inf) evals tuning=0.1; act.y=92.7
Gamma2 Adaptive Metropolis: 649 (155,Inf) evals tuning=0.1; act.y=9.88
N2,rho=0.7 ARMS: 676 (294,9.87e+03) evals tuning=0.1; act.y=5.93
Gamma2 ARMS: 17.8 (11.1,32.3) evals tuning=0.1; act.y=2.01
N2,rho=0.7 Adaptive Metropolis: 13.3 (8.53,21.8) evals tuning=1; act.y=6.6
Gamma2 Adaptive Metropolis: 65.8 (25.6,Inf) evals tuning=1; act.y=9.42
Gamma2 ARMS: 7.01 (5.17,9.83) evals tuning=1; act.y=1.29
N2,rho=0.7 ARMS: 656 (288,4.41e+04) evals tuning=1; act.y=9.88
N2,rho=0.7 Adaptive Metropolis: 250 (69.6,Inf) evals tuning=10; act.y=44.8
N2,rho=0.7 ARMS: 2.73e+03 (893,Inf) evals tuning=10; act.y=28.4
Gamma2 Adaptive Metropolis: 76.2 (35.8,Inf) evals tuning=10; act.y=3.16
Gamma2 ARMS: 12.7 (9.13,16.9) evals tuning=10; act.y=0.999
N2,rho=0.7 Adaptive Metropolis: NA (NA,NA) evals tuning=100; act.y=NA
Gamma2 Adaptive Metropolis: 644 (154,Inf) evals tuning=100; act.y=96.5
Gamma2 ARMS: 12.2 (9.13,16.3) evals tuning=100; act.y=0.94
N2,rho=0.7 ARMS: 1.34e+03 (530,Inf) evals tuning=100; act.y=15
Simulation finished at 2019-03-29 18:12:46.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.

Error: processing vignette 'sc-intro.Rnw' failed with diagnostics:
 chunk 1 
Error in Summary.unit(structure(c(3.2, 3.2), unit = 8L, class = c("margin",  : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

--- failed re-building ‘sc-intro.Rnw’

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

Error: Vignette re-building failed.
Execution halted
propdiff.acc: no visible global function definition for ‘rbeta’
propdiff.acc: no visible global function definition for ‘rbinom’
propdiff.acc: no visible global function definition for ‘pbeta’
propdiff.alc: no visible global function definition for ‘rbeta’
propdiff.alc: no visible global function definition for ‘rbinom’
propdiff.alc: no visible global function definition for ‘qbeta’
propdiff.freq: no visible global function definition for ‘qnorm’
propdiff.mblacc: no visible global function definition for ‘rbeta’
propdiff.mblacc: no visible global function definition for ‘rbinom’
propdiff.mblacc: no visible global function definition for ‘pbeta’
propdiff.mblalc: no visible global function definition for ‘rbeta’
propdiff.mblalc: no visible global function definition for ‘rbinom’
propdiff.mblalc: no visible global function definition for ‘qbeta’
propdiff.mblmodwoc: no visible global function definition for ‘qchisq’
propdiff.mblmodwoc: no visible global function definition for ‘pbeta’
propdiff.mblwoc: no visible global function definition for ‘pbeta’
propdiff.modwoc: no visible global function definition for ‘qchisq’
propdiff.modwoc: no visible global function definition for ‘pbeta’
propdiff.woc: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  pbeta qbeta qchisq qnorm rbeta rbinom
Consider adding
  importFrom("stats", "pbeta", "qbeta", "qchisq", "qnorm", "rbeta",
             "rbinom")
to your NAMESPACE file.
GraphBinaryForestPlot: no visible global function definition for
  ‘abline’
GraphBinaryForestPlot: no visible global function definition for ‘text’
GraphContinuousForestPlot: no visible global function definition for
  ‘abline’
GraphContinuousForestPlot: no visible global function definition for
  ‘text’
ImputeBinaryEvents: no visible global function definition for ‘rbinom’
ImputeSMD: no visible global function definition for ‘rnorm’
funnelplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
generate.sample.core: no visible global function definition for
  ‘predict’
mdh: no visible global function definition for ‘model.frame’
mdh: no visible binding for global variable ‘na.fail’
mdh: no visible global function definition for ‘.getXlevels’
mdh: no visible global function definition for ‘quantile’
mdh: no visible global function definition for ‘hist’
predict.mdh: no visible global function definition for ‘model.frame’
samur: no visible global function definition for ‘predict’
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: ‘mixer’
Running examples in ‘santaR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_eigen_DFoverlay_list
> ### Title: Plot for each eigenSpline the automatically fitted spline,
> ###   splines for all df and a spline at a chosen df
> ### Aliases: get_eigen_DFoverlay_list
> 
> ### ** Examples
> 
> ## 8 subjects, 4 time-points, 3 variables
> inputData  <- acuteInflammation$data[0:32,1:3]
> ind        <- acuteInflammation$meta$ind[0:32]
> time       <- acuteInflammation$meta$time[0:32]
> eigen      <- get_eigen_spline(inputData, ind, time, nPC=NA, scaling="scaling_UV",
+                                method="nipals", verbose=TRUE, centering=TRUE, ncores=0)
nipals calculated PCA
Importance of component(s):
                 PC1     PC2      PC3
R2            0.9272 0.06606 0.006756
Cumulative R2 0.9272 0.99324 1.000000
total time: 0.07 secs
> paramSpace <- get_param_evolution(eigen, step=1)
> plotList   <- get_eigen_DFoverlay_list(eigen,manualDf=3,step=0.5,showPt=TRUE,autofit=TRUE)
> plotList[1]
[[1]]
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced-command-line-functions.Rmd’ using rmarkdown
Quitting from lines 122-132 (advanced-command-line-functions.Rmd) 
Error: processing vignette 'advanced-command-line-functions.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘advanced-command-line-functions.Rmd’

--- re-building ‘automated-command-line.Rmd’ using rmarkdown
--- finished re-building ‘automated-command-line.Rmd’

--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’

--- re-building ‘plotting-options.Rmd’ using rmarkdown
Quitting from lines 38-46 (plotting-options.Rmd) 
Error: processing vignette 'plotting-options.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plotting-options.Rmd’

--- re-building ‘prepare-input-data.Rmd’ using rmarkdown
--- finished re-building ‘prepare-input-data.Rmd’

--- re-building ‘selecting-optimal-df.Rmd’ using rmarkdown
Quitting from lines 124-181 (selecting-optimal-df.Rmd) 
Error: processing vignette 'selecting-optimal-df.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘selecting-optimal-df.Rmd’

--- re-building ‘theoretical-background.Rmd’ using rmarkdown
Quitting from lines 82-133 (theoretical-background.Rmd) 
Error: processing vignette 'theoretical-background.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘theoretical-background.Rmd’

--- re-building ‘santaR-GUI.pdf.asis’ using asis
--- finished re-building ‘santaR-GUI.pdf.asis’

SUMMARY: processing the following files failed:
  ‘advanced-command-line-functions.Rmd’ ‘plotting-options.Rmd’
  ‘selecting-optimal-df.Rmd’ ‘theoretical-background.Rmd’

Error: Vignette re-building failed.
Execution halted
download.sas7bdat.sources : <anonymous>: no visible global function
  definition for ‘download.file’
generate.sas7bdat.source: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
parse.SAScii: no visible binding for global variable ‘end’
parse.SAScii: no visible binding for global variable ‘start’
read.SAScii: no visible global function definition for ‘download.file’
read.SAScii: no visible global function definition for ‘unzip’
read.SAScii: no visible global function definition for ‘read.fwf’
read.SAScii: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
SASPECT: no visible global function definition for ‘dbinom’
my.SOnePro: missing arguments not allowed in calls to ‘c’
my.ttest: no visible global function definition for ‘var’
Undefined global functions or variables:
  dbinom var
Consider adding
  importFrom("stats", "dbinom", "var")
to your NAMESPACE file.
loads: no visible global function definition for ‘untar’
saves: no visible global function definition for ‘tar’
Undefined global functions or variables:
  tar untar
Consider adding
  importFrom("utils", "tar", "untar")
to your NAMESPACE file.
clogistCalc: no visible global function definition for ‘model.matrix’
clogistCalc: no visible global function definition for ‘glm.fit’
clogistCalc: no visible global function definition for ‘binomial’
clogistInfo : all.not.equal: no visible global function definition for
  ‘var’
geeUOmega: no visible global function definition for ‘model.extract’
geeUOmega: no visible global function definition for ‘model.matrix’
geeUOmega: no visible binding for global variable ‘contrasts’
mgee: no visible binding for global variable ‘gaussian’
sawsCalc: no visible global function definition for ‘pf’
sawsCalc: no visible global function definition for ‘qt’
Undefined global functions or variables:
  binomial contrasts gaussian glm.fit model.extract model.matrix pf qt
  var
Consider adding
  importFrom("stats", "binomial", "contrasts", "gaussian", "glm.fit",
             "model.extract", "model.matrix", "pf", "qt", "var")
to your NAMESPACE file.
K: no visible global function definition for ‘dnorm’
sBF: no visible global function definition for ‘density’
sBF: no visible global function definition for ‘txtProgressBar’
sBF: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  density dnorm setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "density", "dnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Running examples in ‘sbpiper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: histogramplot
> ### Title: Plot a generic histogram
> ### Aliases: histogramplot
> 
> ### ** Examples
> 
> a <- as.data.frame(rnorm(100))
> histogramplot(dfCol=a)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
fitSBSA: no visible binding for global variable ‘var’
fitSBSA: no visible global function definition for ‘var’
fitSBSA: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘src-java’
ChooseBest: no visible global function definition for ‘head’
GetScores: no visible global function definition for ‘write.table’
ReportTable: no visible binding for global variable ‘sd’
ReportTable: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  head sd write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head", "write.table")
to your NAMESPACE file.
src/Makevars.win: SHLIB_OPENMP_CXXFLAGS is included in PKG_CXXFLAGS but not in PKG_LIBS
  src/Makevars.win: SHLIB_OPENMP_CFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 90-105 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scat
> ### Title: Scatterplot
> ### Aliases: scat
> 
> ### ** Examples
> 
> set.seed(1337)
> 
> X <- rnorm(100)
> Y <- 0.5*X + rnorm(100)
> dat <- data.frame(X = X, Y = Y)
> 
> scat(dat, x = 'X', y = 'Y', line = 'linear', se = TRUE, marg = 'dens')
Loading required namespace: jmvcore
Loading required namespace: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘scatterpie-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_scatterpie
> ### Title: geom_scatterpie
> ### Aliases: geom_scatterpie
> 
> ### ** Examples
> 
> library(ggplot2)
> d <- data.frame(x=rnorm(5), y=rnorm(5))
> d$A <- abs(rnorm(5, sd=1))
> d$B <- abs(rnorm(5, sd=2))
> d$C <- abs(rnorm(5, sd=3))
> ggplot() + geom_scatterpie(aes(x=x, y=y), data=d, cols=c("A", "B", "C")) + coord_fixed()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘scatterpie.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 49-51 (scatterpie.Rmd) 
Error: processing vignette 'scatterpie.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘scatterpie.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Estimating-effect-sizes.Rmd’ using rmarkdown
Loading required package: nlme
Quitting from lines 147-161 (Estimating-effect-sizes.Rmd) 
Error: processing vignette 'Estimating-effect-sizes.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Estimating-effect-sizes.Rmd’

SUMMARY: processing the following file failed:
  ‘Estimating-effect-sizes.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘scholar.Rmd’ using rmarkdown
Quitting from lines 70-76 (scholar.Rmd) 
Error: processing vignette 'scholar.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘scholar.Rmd’

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

Error: Vignette re-building failed.
Execution halted
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘schoolmath/R/prime.factor.R’:
  data(primlist)
See section ‘Good practice’ in ‘?data’.
Running examples in ‘scico-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot2-scales
> ### Title: Scales to use for ggplot2
> ### Aliases: ggplot2-scales scale_colour_scico scale_color_scico
> ###   scale_fill_scico scale_colour_scico_d scale_color_scico_d
> ###   scale_fill_scico_d
> 
> ### ** Examples
> 
> 
> if (require('ggplot2')) {
+   volcano <- data.frame(
+     x = rep(seq_len(ncol(volcano)), each = nrow(volcano)),
+     y = rep(seq_len(nrow(volcano)), ncol(volcano)),
+     height = as.vector(volcano)
+   )
+   
+   ggplot(volcano, aes(x = x, y = y, fill = height)) + 
+     geom_raster() + 
+     scale_fill_scico(palette = 'tokyo') 
+     
+   ggplot(iris, aes(x=Petal.Width, y=Petal.Length)) +
+     geom_point(aes(color=Species), size=10) + 
+     scale_colour_scico_d() 
+ }
Loading required package: ggplot2
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/scio.Rcheck/00install.out’ for details.
'library' or 'require' call to ‘QUIC’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
scio.cv: no visible global function definition for ‘cov’
scio.refit: no visible global function definition for ‘QUIC’
Undefined global functions or variables:
  QUIC cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Running examples in ‘scmamp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDensities
> ### Title: Kernel based density estimation of the samples
> ### Aliases: plotDensities
> 
> ### ** Examples
> 
> data(data_gh_2010)
> plotDensities(data.gh.2010)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data_loading_and_manipulation.Rmd’ using rmarkdown
--- finished re-building ‘Data_loading_and_manipulation.Rmd’

--- re-building ‘Statistical_assessment_of_the_differences.Rmd’ using rmarkdown
Quitting from lines 47-48 (Statistical_assessment_of_the_differences.Rmd) 
Error: processing vignette 'Statistical_assessment_of_the_differences.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Statistical_assessment_of_the_differences.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: analyzeClones
> ### Title: Clonal assignment analysis
> ### Aliases: analyzeClones
> 
> ### ** Examples
> 
> # Clonal assignment analysis
> results <- analyzeClones(ClonedExampleDb, junction = "JUNCTION", v_call = "V_CALL",
+                           j_call = "J_CALL", clone = "CLONE", first = TRUE)
> # print threshold (a numeric)
> results@threshold
[1] 0.23
> 
> # get inter and intra conal distances (a data.frame)
> df <- results@inter_intra[[1]]
> 
> # density plot of inter versus intra clonal distances  (a ggplot).
> results@plot_inter_intra
[[1]]
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Scoper-Vignette.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 162-175 (Scoper-Vignette.Rmd) 
Error: processing vignette 'Scoper-Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Scoper-Vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: woebin_plot
> ### Title: WOE Binning Visualization
> ### Aliases: woebin_plot
> 
> ### ** Examples
> 
> # Load German credit data
> data(germancredit)
> 
> # Example I
> bins1 = woebin(germancredit, y="creditability", x="credit.amount")
[INFO] creating woe binning ... 
> 
> p1 = woebin_plot(bins1)
> print(p1)
$credit.amount
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
score.GGUM: no visible global function definition for ‘dnorm’
score.GGUM: no visible global function definition for ‘hist’
score.GGUM: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dnorm hist write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CreatePssm: no visible binding for global variable ‘training’
Undefined global functions or variables:
  training
Running examples in ‘SCORPIUS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw_trajectory_plot
> ### Title: Visualise SCORPIUS
> ### Aliases: draw_trajectory_plot
> 
> ### ** Examples
> 
> ## Generate a synthetic dataset
> dataset <- generate_dataset(type="p", num_genes=500, num_samples=300, num_groups=4)
> space <- reduce_dimensionality(dataset$expression, correlation_distance, ndim=2)
> groups <- dataset$sample_info$group_name
> 
> ## Simply plot the samples
> draw_trajectory_plot(space)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ginhoux.Rmd’ using rmarkdown
Quitting from lines 66-67 (ginhoux.Rmd) 
Error: processing vignette 'ginhoux.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ginhoux.Rmd’

--- re-building ‘simulated-data.Rmd’ using rmarkdown
Quitting from lines 68-69 (simulated-data.Rmd) 
Error: processing vignette 'simulated-data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘simulated-data.Rmd’

SUMMARY: processing the following files failed:
  ‘ginhoux.Rmd’ ‘simulated-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Details.Rmd’ using knitr
--- finished re-building ‘Details.Rmd’

--- re-building ‘Tutorial.Rmd’ using knitr
Loading required package: Rcpp
Loading required package: RcppProgress
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Quitting from lines 129-134 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Quitting from lines 43-47 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘my-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘RCurl’ ‘XML’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
scrape: no visible global function definition for ‘getURLAsynchronous’
scrape: no visible global function definition for ‘runif’
scrape: no visible global function definition for ‘capture.output’
scrape: no visible binding for global variable ‘xmlParse’
scrape: no visible binding for global variable ‘htmlParse’
Undefined global functions or variables:
  capture.output getURLAsynchronous htmlParse runif xmlParse
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Found the following calls to attach():
File ‘scriptests/R/source.pkg.R’:
  attach(NULL, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
  attach(envir, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
See section ‘Good practice’ in ‘?attach’.
Running examples in ‘scRNAtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scRNAtools-package
> ### Title: Single Cell RNA Sequencing Data Analysis Tools
> ### Aliases: scRNAtools-package
> 
> ### ** Examples
> 
> ####Here list three main function, cluster, PCA and t-SNE####
> ####cluster####
> data(example1);##Example data in this package.
> k<-6;##set K based on your own requirement.
> scRNAtools_cluster(example1,k)
end fraction
clustered
clustered
clustered
clustered
clustered
> ####PCA####
> data(example1)
> data(types)
> pdf(file=file.path(tempdir(), "PCA_result-R.pdf"))##Save the figures of PCA results.
> scRNAtools_pca(example1,types)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
lahiri.design: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘SDaA_using_survey.Rnw’ using Sweave
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: ‘survey’

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

    dotchart


Attaching package: ‘ggplot2’

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

    seals


Error: processing vignette 'SDaA_using_survey.Rnw' failed with diagnostics:
 chunk 24 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: localSuppression
> ### Title: Local Suppression to obtain k-anonymity
> ### Aliases: localSuppression kAnon
> ### Keywords: manip
> 
> ### ** Examples
> 
> data(francdat)
> ## Local Suppression
> localS <- localSuppression(francdat, keyVar=c(4,5,6))
> localS

-----------------------
Total number of suppressions in the key variables: 4 (new: 4)

Number of suppressions by key variables:
(in parenthesis, the total number suppressions is shown)

   Key2  Key3  Key4
1 1 (1) 0 (0) 3 (3)

2-anonymity == TRUE
-----------------------
> plot(localS)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘flush.console’
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘flush.console’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘quantile’
initialize,sdcTargetMatrixClass: no visible global function definition
  for ‘flush.console’
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
Running examples in ‘sdmpredictors-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_correlation
> ### Title: Plot the correlation matrix for the provided layercodes
> ### Aliases: plot_correlation
> 
> ### ** Examples
> 
> correlation <- layers_correlation(c("BO_calcite", "BO_damin", "MS_bathy_5m"))
> p <- plot_correlation(correlation)
> print(p)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘quickstart.Rmd’ using rmarkdown
Loading required package: raster
Loading required package: sp
Loading required package: rgdal
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
 Path to GDAL shared files: /usr/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: 1.3-1 
trying URL ‘http://www.lifewatch.be/sdmpredictors/BO_ph_lonlat.tif’
Content type 'image/tiff' length 2518560 bytes (2.4 MB)
==================================================
downloaded 2.4 MB

trying URL ‘http://www.lifewatch.be/sdmpredictors/BO_salinity_lonlat.tif’
Content type 'image/tiff' length 5841760 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

trying URL ‘http://www.lifewatch.be/sdmpredictors/BO_ph.tif’
Content type 'image/tiff' length 3201193 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

Quitting from lines 136-163 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘quickstart.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘adehabitat’
'library' or 'require' calls in package code:
  ‘raster’ ‘sp’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘sdmvspecies.Rnw’ using Sweave
Loading required package: sp
[1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio1.bil" 
[2] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio11.bil"
[3] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio12.bil"
[4] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio14.bil"
[5] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio16.bil"
[6] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio5.bil" 
[7] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio7.bil" 
Error: processing vignette 'sdmvspecies.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sdmvspecies.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  catnet_rexport.cpp:221:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:229:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:237:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:240:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:241:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:258:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:257:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sdnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sdwd.Rcheck/00install.out’ for details.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
sealasso: no visible global function definition for ‘lars’
weight.calc: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
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.
Running examples in ‘season-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: third
> ### Title: Third-order Moment
> ### Aliases: third
> 
> ### ** Examples
> 
> data(CVD)
> third(CVD$cvd, n.lag=12)
Maximum at (including symmetries)
0 0 
Minimum at (including symmetries)
-8 8 0 -8 0 8 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: third ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘season-vignette.Rmd’ using rmarkdown
Quitting from lines 32-38 (season-vignette.Rmd) 
Error: processing vignette 'season-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘season-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘NADA’ ‘lubridate’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package in Depends field not imported from: ‘JM’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
fdc2s: no visible global function definition for ‘lm’
fdc3s: no visible global function definition for ‘lm’
fds2s: no visible global function definition for ‘lm’
fds3s: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
Running examples in ‘seedy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: simulateoutbreak
> ### Title: Simulate transmission and evolutionary dynamics
> ### Aliases: simulateoutbreak
> 
> ### ** Examples
> 
> 
> W <- simulateoutbreak(init.sus=10, inf.rate=0.002, rem.rate=0.001, mut.rate=0.0001, 
+                       equi.pop=2000, inoc.size=1, samples.per.time=10, 
+                       samp.schedule="calendar", samp.freq=500, mincases=3) 

Simulating outbreak:
N=2000, b=1, beta=0.002, gamma=0.001, mu=1e-04

Attempt 1
t=500, S=10, I=1, total genotypes=3, next rec time=747
t=1000, S=8, I=1, total genotypes=6, next rec time=1035
t=1035, S=8, I=0, total genotypes=0
Insufficient number of infections! (mincases=3)
Attempt 2
t=500, S=10, I=1, total genotypes=3, next rec time=833
t=1000, S=9, I=1, total genotypes=2, next rec time=5629
Error in strain.log[[newinfect]] <- unique(inoc.samp) : 
  attempt to select more than one element in integerOneIndex
Calls: simulateoutbreak
Execution halted
.read.SeerStatTXT: no visible global function definition for
  ‘read.table’
.write.SeerStatTXT: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Running examples in ‘segclust2d-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: segclust
> ### Title: Segmentation/Clustering of movement data - Generic function
> ### Aliases: segclust segclust.data.frame segclust.Move segclust.ltraj
> 
> ### ** Examples
> 
> #' @examples
> df <-  test_data()$data
> #' # data is a data.frame with column 'x' and 'y'
> # Simple segmentation with automatic subsampling if data has more than 1000 rows:
> res <- segclust(df, Kmax = 15, lmin = 10, ncluster = 2:4, seg.var = c("x","y"))
Rescaling variables - you can disable this with scale.variable = FALSE
Segmenting - 2 class
Smoothing  - 2 class
Segmenting - 3 class
Smoothing  - 3 class
Segmenting - 4 class
Smoothing  - 4 class
>  # Plot results
>  plot(res)
BIC-selected number of class : 3 class.
BIC-selected number of segment : 6
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
get.infectiousness: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
get_statistics_from_file: no visible global function definition for
  ‘read.csv’
glm_anova: no visible global function definition for ‘aov’
glm_anova: no visible global function definition for ‘glm’
glm_anova: no visible global function definition for ‘gaussian’
glm_anova: no visible global function definition for ‘anova’
glm_anova: no visible global function definition for ‘quasipoisson’
glm_anova: no visible global function definition for ‘sd’
glm_anova: no visible global function definition for ‘p.adjust’
ttest_cohens_d: no visible global function definition for ‘t.test’
ttest_cohens_d: no visible global function definition for ‘sd’
Undefined global functions or variables:
  anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test
Consider adding
  importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust",
             "quasipoisson", "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Running examples in ‘selfea-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_statistics_from_dataFrame
> ### Title: get_statistics_from_dataFrame
> ### Aliases: get_statistics_from_dataFrame
> 
> ### ** Examples
> 
> library(selfea)
> 
> ## Test selfea for single protein expression
> values <- c(6,8,10,29,26,22)
> groups <- c("U200","U200","U200","U600","U600","U600")
> experiments <- c("exp1","exp2","exp3","exp4","exp5","exp6")
> 
> df_expr <- data.frame(ID="Protein_1",exp1=6,exp2=8,exp3=10,exp4=29,exp5=26,exp6=22)
> df_group <- data.frame(Col_Name=experiments,Group=groups)
> list_result <- get_statistics_from_dataFrame(df_expr,df_group)
Expression data dimension:	1 IDs x 6 Columns
You chose "fdr" for p-value adjustment.

Group dimension:
				Group U200 has 3 replicates
				Group U600 has 3 replicates
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
Warning in theta.ml(Y, mu, sum(w), w, limit = control$maxit, trace = control$trace >  :
  iteration limit reached
> top_table(list_result)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: top_table ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
Package in Depends field not imported from: ‘sem’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ChiSquaredLRTest: no visible global function definition for ‘na.omit’
ChiSquaredLRTest: no visible global function definition for ‘cov’
ChiSquaredLRTest: no visible global function definition for ‘dmvnorm’
ChiSquaredLRTest: no visible global function definition for ‘pchisq’
NormalTheoryLRTest: no visible global function definition for ‘na.omit’
NormalTheoryLRTest: no visible global function definition for ‘cov’
NormalTheoryLRTest: no visible global function definition for ‘dmvnorm’
NormalTheoryLRTest: no visible global function definition for ‘sd’
NormalTheoryLRTest: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cov dmvnorm na.omit pchisq pnorm sd
Consider adding
  importFrom("stats", "cov", "na.omit", "pchisq", "pnorm", "sd")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘XML’ ‘boot’ ‘sem’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘boot:::const’ ‘stats:::AIC.logLik’ ‘stats:::BIC.logLik’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘addPath.plsm’ ‘endogenous’ ‘predecessors’ ‘qSquared’ ‘reorder’
  ‘resempls’ ‘residuals.sempls’
.plot_attachment: no visible global function definition for ‘dev.off’
.update_list: no visible global function definition for ‘modifyList’
mime_part.data.frame: no visible global function definition for
  ‘write.table’
mime_part.ggplot: no visible binding for global variable ‘pdf’
mime_part.matrix: no visible global function definition for
  ‘write.table’
mime_part.trellis: no visible binding for global variable ‘pdf’
Undefined global functions or variables:
  dev.off modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
'library' or 'require' call to ‘rtiff’ which was already attached by Depends.
  Please remove these calls from your code.
Running examples in ‘sensitivityCalibration-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calibrate_one
> ### Title: Make the calibration plot.
> ### Aliases: calibrate_one
> 
> ### ** Examples
> 
> data(NHANES_blood_lead_small_matched)
> attach(NHANES_blood_lead_small_matched)
> 
> # Prepare the lambda_vec and delta_vec
> lambda_vec = c(seq(0.1,1.9,0.1), 2.2, 2.5, 3, 3.5, 4)
> delta_vec = c(7.31, 5.34, 4.38, 3.76, 3.18, 2.87, 2.55, 2.36, 2.16, 1.99, 1.86,
+ 1.74, 1.63, 1.54, 1.44, 1.40, 1.31, 1.28, 1.22, 1.08, 0.964, 0.877, 0.815, 0.750)
> 
> calibrate_one(lambda_vec, delta_vec, 9, c(1,0), c(0.5,0.5), 1, 0.492,
+ colnames(NHANES_blood_lead_small_matched)[1:8], NHANES_blood_lead_small_matched)
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in eval(family$initialize) :
  non-integer #successes in a binomial glm!
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
gconv: no visible global function definition for ‘convolve’
sens.analysis.aberrant.rank: no visible global function definition for
  ‘pnorm’
sens.analysis.mh: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  convolve pnorm
Consider adding
  importFrom("stats", "convolve", "pnorm")
to your NAMESPACE file.
mscorev: no visible global function definition for ‘quantile’
senmwCI : funcCI: no visible global function definition for ‘qnorm’
senmwCI : funcCI2: no visible global function definition for ‘qnorm’
separable1k: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm quantile
Consider adding
  importFrom("stats", "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
plot.sensitivity.2.0d: no visible global function definition for ‘gray’
sensitivitySGD: no visible global function definition for ‘tail’
sensitivitySGL: no visible global function definition for ‘tail’
Undefined global functions or variables:
  gray tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in ‘sensitivity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: support
> ### Title: Support index functions: Measuring the effect of input variables
> ###   over their support
> ### Aliases: support
> 
> ### ** Examples
> 
> 
> # -----------------
> # ishigami function
> # -----------------
> n <- 5000
> n.points <- 1000
> d <- 3
> 
> set.seed(0)
> X <- matrix(runif(d*n, min = -pi, max = pi), n, d)
> Xnew <- matrix(seq(from = -pi, to = pi, length=n.points), n.points, d)
> 
> b <- support(model = ishigami.fun, X, Xnew)
> 
> # plot method (x-axis in probability scale), of the normalized support index functions
> plot(b, col = c("lightskyblue4", "lightskyblue1", "black"), 
+      xprob = TRUE, p = 'punif', p.arg = list(min = -pi, max = pi), ylim = c(0, 2))
> 
> # below : diagonal scatterplots of the gradient, 
> # on which are based the estimation by smoothing
> scatterplot(b, xprob = TRUE) 
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: scatterplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘SensMixed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot
> ### Title: function creates plots for the sensmixed object
> ### Aliases: plot.sensmixed
> 
> ### ** Examples
> 
> res <- sensmixed(c("Coloursaturation", "Colourbalance", "Noise"),
+                   prod_effects=c("TVset", "Picture"), 
+                   assessor="Assessor", data=TVbo, MAM=TRUE, 
+                   control=list(reduce.random=FALSE))

  |                                                                            
  |                                                                      |   0%fixed-effect model matrix is rank deficient so dropping 1 column / coefficient

  |                                                                            
  |=======================                                               |  33%fixed-effect model matrix is rank deficient so dropping 1 column / coefficient

  |                                                                            
  |===============================================                       |  67%Warning: 
 Random term (1 | TVset:Assessor) was eliminated because of standard deviation being equal to 0 

Warning: 
 Random term (1 | TVset:Picture:Assessor) was eliminated because of standard deviation being equal to 0 

fixed-effect model matrix is rank deficient so dropping 1 column / coefficient

  |                                                                            
  |======================================================================| 100%
> plot(res, isRand = TRUE)
Using effs, effs_short, abbreffs as id variables
Using effs as id variables
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘sensobol-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_scatter
> ### Title: Scatterplots of the model output against the model inputs
> ### Aliases: plot_scatter
> 
> ### ** Examples
> 
> # Define settings:
> n <- 100; k <- 8; R <- 10
> # Design the sample matrix:
> A <- sobol_matrices(n = n, k = k, second = TRUE, third = TRUE)
> # Compute the model output:
> Y <- sobol_Fun(A)
> # Plot scatterplots:
> plot_scatter(x = A, Y = Y, n = n, params = colnames(data.frame(A)))
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sensobol.Rmd’ using rmarkdown
Quitting from lines 53-57 (sensobol.Rmd) 
Error: processing vignette 'sensobol.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sensobol.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generateDictionary
> ### Title: Generates dictionary of decisive terms
> ### Aliases: generateDictionary generateDictionary.Corpus
> ###   generateDictionary.character generateDictionary.data.frame
> ###   generateDictionary.TermDocumentMatrix
> ###   generateDictionary.DocumentTermMatrix
> ### Keywords: dictionary evaluation sentiment
> 
> ### ** Examples
> 
> # Create a vector of strings
> documents <- c("This is a good thing!",
+                "This is a very good thing!",
+                "This is okay.",
+                "This is a bad thing.",
+                "This is a very bad thing.")
> response <- c(1, 0.5, 0, -0.5, -1)
> 
> # Generate dictionary with LASSO regularization
> dictionary <- generateDictionary(documents, response)
> 
> # Show dictionary
> dictionary
Type: weighted (words with individual scores)
Intercept: 5.55333e-05
-0.51 bad
 0.51 good
> summary(dictionary)
Dictionary type:  weighted (words with individual scores)
Total entries:    2
Positive entries: 1 (50%)
Negative entries: 1 (50%)
Neutral entries:  0 (0%)

Details
Average score:      -5.251165e-05
Median:             -5.251165e-05
Min:                -0.5119851
Max:                0.5118801
Standard deviation: 0.7239821
Skewness:           0
> plot(dictionary)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SentimentAnalysis.Rmd’ using rmarkdown
Quitting from lines 67-91 (SentimentAnalysis.Rmd) 
Error: processing vignette 'SentimentAnalysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘SentimentAnalysis.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.sentomeasures
> ### Title: Plot sentiment measures
> ### Aliases: plot.sentomeasures
> 
> ### ** Examples
> 
> data("usnews", package = "sentometrics")
> data("list_lexicons", package = "sentometrics")
> data("list_valence_shifters", package = "sentometrics")
> 
> # construct a sentomeasures object to start with
> corpus <- sento_corpus(corpusdf = usnews)
> corpusSample <- quanteda::corpus_sample(corpus, size = 500)
> l <- sento_lexicons(list_lexicons[c("LM_en")], list_valence_shifters[["en"]])
> ctr <- ctr_agg(howTime = c("equal_weight", "linear"), by = "year", lag = 3)
> sentomeasures <- sento_measures(corpusSample, l, ctr)
> 
> # plot sentiment measures
> plot(sentomeasures, group = "features")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
separationplot: no visible global function definition for ‘dev.new’
separationplot: no visible global function definition for ‘pdf’
separationplot: no visible global function definition for ‘par’
separationplot: no visible global function definition for ‘plot’
separationplot: no visible global function definition for ‘title’
separationplot: no visible global function definition for ‘segments’
separationplot: no visible global function definition for ‘rect’
separationplot: no visible global function definition for ‘points’
separationplot: no visible global function definition for ‘lines’
separationplot: no visible global function definition for
  ‘colorRampPalette’
separationplot: no visible global function definition for ‘layout’
separationplot: no visible global function definition for ‘plot.new’
separationplot: no visible global function definition for ‘legend’
separationplot: no visible global function definition for ‘dev.off’
separationplot: no visible global function definition for ‘locator’
sp.categorical: no visible global function definition for ‘dev.new’
sp.categorical: no visible global function definition for ‘pdf’
sp.categorical: no visible global function definition for ‘par’
sp.categorical: no visible global function definition for ‘layout’
sp.categorical: no visible global function definition for ‘plot’
sp.categorical: no visible global function definition for ‘text’
sp.categorical: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  colorRampPalette dev.new dev.off layout legend lines locator par pdf
  plot plot.new points rect segments text title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "pdf")
  importFrom("graphics", "layout", "legend", "lines", "locator", "par",
             "plot", "plot.new", "points", "rect", "segments", "text",
             "title")
to your NAMESPACE file.
GammaDist: no visible binding for global variable ‘rgamma’
VEpowerPP: no visible global function definition for ‘qnorm’
applyStopRules: no visible global function definition for ‘qnorm’
finalLogRankTest: no visible global function definition for ‘qnorm’
finalLogRankTest: no visible global function definition for ‘pchisq’
generateDropout: no visible global function definition for ‘rexp’
generateEnrollment: no visible global function definition for ‘rpois’
generateEnrollment: no visible global function definition for ‘runif’
generateInfection: no visible global function definition for ‘rexp’
generateInfection : <anonymous>: no visible global function definition
  for ‘rexp’
getAlphaPerTest: no visible global function definition for ‘uniroot’
getHarmBound: no visible global function definition for ‘dbinom’
getHarmBound: no visible global function definition for ‘write.csv’
getTreatmentAssignment : <anonymous>: no visible global function
  definition for ‘runif’
getTreatmentAssignment: no visible global function definition for
  ‘runif’
simTrial: no visible global function definition for ‘runif’
sumTrialOneTrtArm: no visible global function definition for ‘quantile’
testVE: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  dbinom pchisq qnorm quantile rexp rgamma rpois runif uniroot
  write.csv
Consider adding
  importFrom("stats", "dbinom", "pchisq", "qnorm", "quantile", "rexp",
             "rgamma", "rpois", "runif", "uniroot")
  importFrom("utils", "write.csv")
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.
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.

Found the following calls to attach():
File ‘session/R/session.R’:
  attach(sub("file:", "", i))
See section ‘Good practice’ in ‘?attach’.
Running examples in ‘SetMethods-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pimplot
> ### Title: Prime implicants, truth table rows, and necessity plots.
> ### Aliases: pimplot
> ### Keywords: QCA
> 
> ### ** Examples
> 
> # Import your data. For example:
> 
> data(SCHF)
> 
> # Get the parsimonious solution:
> 
> 
> sol_yp <- minimize(SCHF, outcome = "EXPORT",
+                 conditions = c("EMP","BARGAIN","UNI","OCCUP","STOCK", "MA"),
+                 incl.cut = .9, 
+                 include = "?", 					   
+                 details = TRUE, show.cases = TRUE)
> 
> # Plot the prime implicants of the parsimonious solution:
> 
> pimplot(data = SCHF, results = sol_yp, outcome = "EXPORT")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: pimplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
setpath: no visible global function definition for ‘cov’
setpath: no visible global function definition for ‘median’
setpath: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
random.number.test: no visible global function definition for ‘runif’
random.number.test: no visible global function definition for ‘rnorm’
setRNG: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Package suggested but not available for checking: ‘loomR’
Running examples in ‘Seurat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ColorTSNESplit
> ### Title: Color tSNE Plot Based on Split
> ### Aliases: ColorTSNESplit
> 
> ### ** Examples
> 
> pbmc_small
An object of class seurat in project SeuratProject 
 230 genes across 80 samples.
> PlotClusterTree(pbmc_small)
> ColorTSNESplit(pbmc_small, node = 6)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ColorTSNESplit ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
'library' or 'require' call to ‘graphics’ which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for ‘qnorm’
severity: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
L_exp: no visible global function definition for ‘pnorm’
L_hNV: no visible global function definition for ‘pnorm’
L_trunc: no visible global function definition for ‘pnorm’
L_trunc_mufest: no visible global function definition for ‘pnorm’
dgp: no visible global function definition for ‘runif’
dgp: no visible global function definition for ‘rnorm’
eff.sfa: no visible global function definition for ‘predict’
fitted.sfa: no visible global function definition for ‘predict’
predict.sfa: no visible global function definition for ‘coef’
print.sfa: no visible global function definition for ‘coef’
residuals.sfa: no visible global function definition for ‘fitted’
sfa: no visible global function definition for ‘model.frame’
sfa: no visible global function definition for ‘model.response’
sfa.fit: no visible global function definition for ‘lm’
sfa.fit: no visible global function definition for ‘resid’
sfa.fit: no visible global function definition for ‘var’
sfa.fit: no visible global function definition for ‘optim’
summary.sfa: no visible global function definition for ‘logLik’
summary.sfa: no visible global function definition for ‘pchisq’
te.eff.sfa: no visible global function definition for ‘residuals’
te.eff.sfa: no visible global function definition for ‘pnorm’
u.sfa: no visible global function definition for ‘residuals’
u.sfa: no visible global function definition for ‘dnorm’
u.sfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘sf1.Rmd’ using rmarkdown
--- finished re-building ‘sf1.Rmd’

--- re-building ‘sf2.Rmd’ using rmarkdown
--- finished re-building ‘sf2.Rmd’

--- re-building ‘sf3.Rmd’ using rmarkdown
--- finished re-building ‘sf3.Rmd’

--- re-building ‘sf4.Rmd’ using rmarkdown
--- finished re-building ‘sf4.Rmd’

--- re-building ‘sf5.Rmd’ using rmarkdown
Quitting from lines 172-175 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sf5.Rmd’

--- re-building ‘sf6.Rmd’ using rmarkdown
--- finished re-building ‘sf6.Rmd’

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

Error: Vignette re-building failed.
Execution halted
.computePStar: no visible global function definition for ‘uniroot’
plotBoundary: no visible global function definition for
  ‘scale_y_continuous’
Undefined global functions or variables:
  scale_y_continuous uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.
Running examples in ‘sglr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotBoundary
> ### Title: A function to plot the boundary of the decision region
> ### Aliases: plotBoundary
> ### Keywords: design
> 
> ### ** Examples
> 
> plotBoundary(b1=2.8, b0=3.3, p=c(.5, .75))
Warning: Removed 2 rows containing missing values (geom_path).
Warning: Removed 4 rows containing missing values (geom_path).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘sgmodel-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_sgmod
> ### Title: plot_sgmod
> ### Aliases: plot_sgmod
> 
> ### ** Examples
> 
> model <- sgmodel( grid = 100, rho = 0.2, sigma = 0.02)
> plot_sgmod(model)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘sGMRFmix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_multivariate_data
> ### Title: Plot multivariate data
> ### Aliases: plot_multivariate_data
> 
> ### ** Examples
> 
> library(sGMRFmix)
> 
> test_data <- generate_test_data()
> test_label <- generate_test_labels()
> 
> plot_multivariate_data(test_data)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sGMRFmix.Rmd’ using rmarkdown
Quitting from lines 37-41 (sGMRFmix.Rmd) 
Error: processing vignette 'sGMRFmix.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sGMRFmix.Rmd’

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

Error: Vignette re-building failed.
Execution halted
amse: no visible global function definition for ‘na.omit’
arb: no visible global function definition for ‘na.omit’
rdatagen: no visible global function definition for ‘qnorm’
rdatagen: no visible global function definition for ‘pbinom’
rdatagen: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  na.omit pbinom pnorm qnorm
Consider adding
  importFrom("stats", "na.omit", "pbinom", "pnorm", "qnorm")
to your NAMESPACE file.
UQnormalize.count: no visible binding for global variable ‘quantile’
plotNScores: no visible global function definition for ‘par’
plotNScores: no visible global function definition for ‘hist’
plotNScores: no visible global function definition for ‘title’
plotScores: no visible global function definition for ‘par’
plotScores: no visible global function definition for ‘hist’
plotScores: no visible global function definition for ‘title’
sgRSEA: no visible binding for global variable ‘sd’
sgRSEA: no visible global function definition for ‘p.adjust’
sgRSEA.mean: no visible binding for global variable ‘sd’
sgRSEA.mean: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  hist p.adjust par quantile sd title
Consider adding
  importFrom("graphics", "hist", "par", "title")
  importFrom("stats", "p.adjust", "quantile", "sd")
to your NAMESPACE file.
Running examples in ‘shadowtext-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_shadowtext
> ### Title: geom_shadowtext
> ### Aliases: geom_shadowtext
> 
> ### ** Examples
> 
> library(ggplot2)
> d <- data.frame(x = rnorm(3), y=rnorm(3), label = c('hello', 'world', '!!!'))
> ggplot(d, aes(x,y)) + geom_shadowtext(aes(label=label, color=label), bg.colour='firebrick')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘shadowtext.Rmd’ using rmarkdown
Quitting from lines 52-75 (shadowtext.Rmd) 
Error: processing vignette 'shadowtext.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘shadowtext.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘foreign’ which was already attached by Depends.
  Please remove these calls from your code.
Running examples in ‘shazam-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: distToNearest
> ### Title: Distance to nearest neighbor
> ### Aliases: distToNearest
> 
> ### ** Examples
> 
> # Subset example data to one sample as a demo
> data(ExampleDb, package="alakazam")
> db <- subset(ExampleDb, SAMPLE == "-1h")
> 
> # Use genotyped V assignments, Hamming distance, and normalize by junction length
> dist <- distToNearest(db, vCallColumn="V_CALL_GENOTYPED", model="ham", 
+                       first=FALSE, normalize="len")
>                            
> # Plot histogram of non-NA distances
> p1 <- ggplot(data=subset(dist, !is.na(DIST_NEAREST))) + 
+       theme_bw() + 
+       ggtitle("Distance to nearest: Hamming") + 
+       xlab("distance") +
+       geom_histogram(aes(x=DIST_NEAREST), binwidth=0.025, 
+                      fill="steelblue", color="white")
> plot(p1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Dirichlet-elicitation.Rmd’ using rmarkdown
Quitting from lines 69-72 (Dirichlet-elicitation.Rmd) 
Error: processing vignette 'Dirichlet-elicitation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Dirichlet-elicitation.Rmd’

--- re-building ‘Multivariate-normal-copula.Rmd’ using rmarkdown
Quitting from lines 50-53 (Multivariate-normal-copula.Rmd) 
Error: processing vignette 'Multivariate-normal-copula.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Multivariate-normal-copula.Rmd’

--- re-building ‘SHELF-overview.Rmd’ using rmarkdown
Quitting from lines 70-71 (SHELF-overview.Rmd) 
Error: processing vignette 'SHELF-overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘SHELF-overview.Rmd’

SUMMARY: processing the following files failed:
  ‘Dirichlet-elicitation.Rmd’ ‘Multivariate-normal-copula.Rmd’
  ‘SHELF-overview.Rmd’

Error: Vignette re-building failed.
Execution halted
popify: no visible global function definition for ‘runif’
tipify: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘shinyrecap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: simulateEstimates
> ### Title: Simulates capture re-capture estimates
> ### Aliases: simulateEstimates
> 
> ### ** Examples
> 
> library(ggplot2)
> # Simulate estimates from the Mt model with no population heterogeneity
> ests <- simulateEstimates(15,500,c(.1,.1,.1))
> 
> # Simulate estimates from the Mth (Normal) model with no population heterogeneity.
> ests2 <- simulateEstimates(20,500,c(.1,.1,.1), htype="Normal")
> 
> df <- data.frame(est = ests[[1]],type="Mt")
> df <- rbind(df, data.frame(est = ests2[[1]],type="Mth (Normal)"))
> qplot(x=est, color=type, data=df, geom="density") +
+   geom_vline(xintercept=500,color="purple")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
shrink.estim: no visible global function definition for ‘cov’
shrink.estim: no visible global function definition for ‘cor’
shrink.estim: no visible global function definition for ‘cov2cor’
targetCor: no visible global function definition for ‘cor.test’
targetCor: no visible global function definition for ‘cor’
targetCor: no visible global function definition for ‘sd’
targetCor: no visible global function definition for ‘cov’
targetD: no visible binding for global variable ‘var’
targetF: no visible global function definition for ‘cov’
targetF: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘sd’
targetG: no visible global function definition for ‘cov’
targetGpos: no visible global function definition for ‘cor’
targetGpos: no visible global function definition for ‘sd’
targetGpos: no visible global function definition for ‘cov’
targetGstar: no visible global function definition for ‘cor’
targetGstar: no visible global function definition for ‘sd’
targetGstar: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cor cor.test cov cov2cor sd var
Consider adding
  importFrom("stats", "cor", "cor.test", "cov", "cov2cor", "sd", "var")
to your NAMESPACE file.
.params: no visible binding for global variable ‘URLencode’
.params: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘bayesm’ ‘coda’ ‘hdrcde’ ‘mnormt’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Centroid-Vectors.Rmd’ using rmarkdown
Quitting from lines 135-165 (Centroid-Vectors.Rmd) 
Error: processing vignette 'Centroid-Vectors.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Centroid-Vectors.Rmd’

--- re-building ‘Customising-Plots-Manually.Rmd’ using rmarkdown
--- finished re-building ‘Customising-Plots-Manually.Rmd’

--- re-building ‘Ellipse-Overlap.Rmd’ using rmarkdown
--- finished re-building ‘Ellipse-Overlap.Rmd’

--- re-building ‘Introduction-to-SIBER.Rmd’ using rmarkdown
--- finished re-building ‘Introduction-to-SIBER.Rmd’

--- re-building ‘Plot-posterior-ellipses.Rmd’ using rmarkdown
Quitting from lines 143-150 (Plot-posterior-ellipses.Rmd) 
Error: processing vignette 'Plot-posterior-ellipses.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Plot-posterior-ellipses.Rmd’

--- re-building ‘Points-Inside-Outside-Ellipse.Rmd’ using rmarkdown
--- finished re-building ‘Points-Inside-Outside-Ellipse.Rmd’

--- re-building ‘Test-convergence.Rmd’ using rmarkdown
--- finished re-building ‘Test-convergence.Rmd’

SUMMARY: processing the following files failed:
  ‘Centroid-Vectors.Rmd’ ‘Plot-posterior-ellipses.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages in Depends field not imported from:
  ‘ade4’ ‘corpcor’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
dSepAdji: no visible global function definition for ‘as’
dag2cpdagAdj: no visible global function definition for ‘as’
randomDAG: no visible global function definition for ‘rbinom’
structIntervDist: no visible global function definition for ‘as’
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.cluster: no visible global function definition for ‘kmeans’
.plot.sigclust: no visible global function definition for ‘par’
.plot.sigclust: no visible global function definition for ‘density’
.plot.sigclust: no visible global function definition for ‘runif’
.plot.sigclust: no visible global function definition for ‘dnorm’
.plot.sigclust: no visible global function definition for ‘lines’
.plot.sigclust: no visible global function definition for ‘points’
.plot.sigclust: no visible global function definition for ‘title’
.plot.sigclust: no visible global function definition for ‘text’
.plot.sigclust: no visible global function definition for ‘qnorm’
.plot.sigclust: no visible global function definition for ‘abline’
.plot.sigclust: no visible global function definition for ‘quantile’
.plot.sigclust: no visible global function definition for ‘legend’
.simnull: no visible global function definition for ‘rnorm’
.vareigen: no visible global function definition for ‘mad’
.vareigen: no visible global function definition for ‘cov’
sigclust: no visible global function definition for ‘sd’
sigclust: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline cov density dnorm kmeans legend lines mad par pnorm points
  qnorm quantile rnorm runif sd text title
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "points",
             "text", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "mad",
             "pnorm", "qnorm", "quantile", "rnorm", "runif", "sd")
to your NAMESPACE file.
Sight.Est: no visible global function definition for ‘glm’
Sight.Est: no visible global function definition for ‘binomial’
Sight.Est: no visible global function definition for ‘coef’
Sight.Est: no visible global function definition for ‘terms’
Sight.Est: no visible binding for global variable ‘binomial’
covtheta: no visible global function definition for ‘cov’
print.sightest: no visible global function definition for ‘qnorm’
summary.sightest: no visible global function definition for ‘qnorm’
vardiff: no visible global function definition for ‘vcov’
vardiff: no visible global function definition for ‘coef’
vardiff: no visible global function definition for ‘terms’
varlog.lam: no visible global function definition for ‘vcov’
varlog.lam: no visible global function definition for ‘coef’
varlog.lam: no visible global function definition for ‘terms’
Undefined global functions or variables:
  binomial coef cov glm qnorm terms vcov
Consider adding
  importFrom("stats", "binomial", "coef", "cov", "glm", "qnorm", "terms",
             "vcov")
to your NAMESPACE file.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sigmajs)
  Welcome to sigmajs
  
  Docs: sigmajs.john-coene.com
  > 
  > test_check("sigmajs")
  Found # 2 clusters
  ── 1. Failure: delay (@test-graph.R#50)  ───────────────────────────────────────
  unlist(unname(sg$x$addNodesDelay[[1]][5])) not equal to " 566.004".
  1/1 mismatches
  x[1]: " 548.9736"
  y[1]: " 566.004"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 65 SKIPPED: 0 FAILED: 1
  1. Failure: delay (@test-graph.R#50) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sigmoid.Rmd’ using rmarkdown
Quitting from lines 59-67 (sigmoid.Rmd) 
Error: processing vignette 'sigmoid.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sigmoid.Rmd’

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

Error: Vignette re-building failed.
Execution halted
signmedian.test: no visible global function definition for ‘median’
signmedian.test: no visible global function definition for ‘binom.test’
signmedian.test: no visible global function definition for ‘pbinom’
signmedian.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binom.test median pbinom pnorm
Consider adding
  importFrom("stats", "binom.test", "median", "pbinom", "pnorm")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘gdata’ ‘splines’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
Running examples in ‘SimCorrMix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_simpdf_theory
> ### Title: Plot Simulated Probability Density Function and Target PDF by
> ###   Distribution Name or Function for Continuous or Count Variables
> ### Aliases: plot_simpdf_theory
> ### Keywords: plot
> 
> ### ** Examples
> 
> # Using normal mixture variable from contmixvar1 example
> Nmix <- contmixvar1(n = 1000, "Polynomial", means = 0, vars = 1,
+   mix_pis = c(0.4, 0.6), mix_mus = c(-2, 2), mix_sigmas = c(1, 1),
+   mix_skews = c(0, 0), mix_skurts = c(0, 0), mix_fifths = c(0, 0),
+   mix_sixths = c(0, 0))
Total Simulation time: 0 minutes 
> plot_simpdf_theory(Nmix$Y_mix[, 1],
+   title = "Mixture of Normal Distributions",
+   fx = function(x) 0.4 * dnorm(x, -2, 1) + 0.6 * dnorm(x, 2, 1),
+   lower = -5, upper = 5)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cont_mixture.Rmd’ using rmarkdown
Quitting from lines 129-132 (cont_mixture.Rmd) 
Error: processing vignette 'cont_mixture.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cont_mixture.Rmd’

--- re-building ‘corr_mixture.Rmd’ using rmarkdown
Loading required package: SimMultiCorrData

Attaching package: 'SimMultiCorrData'

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

    poly

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

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

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

--- re-building ‘workflow.Rmd’ using rmarkdown
Loading required package: SimMultiCorrData

Attaching package: 'SimMultiCorrData'

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

    poly

Quitting from lines 294-308 (workflow.Rmd) 
Error: processing vignette 'workflow.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘cont_mixture.Rmd’ ‘workflow.Rmd’

Error: Vignette re-building failed.
Execution halted
getFormula: no visible global function definition for ‘as.formula’
internalSimXyplot : f: no visible global function definition for
  ‘median’
runSimulation: no visible global function definition for ‘runif’
setup: no visible global function definition for ‘runif’
clusterSetup,ANY-data.frame-SampleControl: no visible binding for
  global variable ‘cnam’
clusterSetup,ANY-data.frame-TwoStageControl: no visible binding for
  global variable ‘cnam’
initialize,DCARContControl: no visible binding for global variable
  ‘rnorm’
initialize,DataControl: no visible binding for global variable ‘rnorm’
Undefined global functions or variables:
  as.formula cnam median rnorm runif
Consider adding
  importFrom("stats", "as.formula", "median", "rnorm", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘GeneralizedModels_legacy.Rmd’ using rmarkdown
--- finished re-building ‘GeneralizedModels_legacy.Rmd’

--- re-building ‘Intro_legacy.Rmd’ using rmarkdown
Quitting from lines 171-174 (Intro_legacy.Rmd) 
Error: processing vignette 'Intro_legacy.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Intro_legacy.Rmd’

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

--- re-building ‘simulation_arguments.Rmd’ using rmarkdown
Quitting from lines 111-116 (simulation_arguments.Rmd) 
Error: processing vignette 'simulation_arguments.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘simulation_arguments.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘Intro_legacy.Rmd’ ‘simulation_arguments.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mon
> ### Title: Plot Methods for 'simmer' Monitoring Statistics
> ### Aliases: plot.mon plot.arrivals plot.attributes plot.resources
> 
> ### ** Examples
> 
> t0 <- trajectory("my trajectory") %>%
+   ## add an intake activity
+   seize("nurse", 1) %>%
+   timeout(function() rnorm(1, 15)) %>%
+   release("nurse", 1) %>%
+   ## add a consultation activity
+   seize("doctor", 1) %>%
+   timeout(function() rnorm(1, 20)) %>%
+   release("doctor", 1) %>%
+   ## add a planning activity
+   seize("administration", 1) %>%
+   timeout(function() rnorm(1, 5)) %>%
+   release("administration", 1)
> 
> env <- simmer("SuperDuperSim") %>%
+   add_resource("nurse", 1) %>%
+   add_resource("doctor", 2) %>%
+   add_resource("administration", 1) %>%
+   add_generator("patient", t0, function() rnorm(1, 10, 2)) %>%
+   run(until=80)
> 
> resources <- get_mon_resources(env)
> arrivals <- get_mon_arrivals(env)
> 
> plot(resources, metric="usage", "doctor", items = "server", steps = TRUE)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plot.simmer.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'simmer.plot'

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

    get_mon_arrivals, get_mon_attributes, get_mon_resources

Quitting from lines 72-76 (plot.simmer.Rmd) 
Error: processing vignette 'plot.simmer.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘plot.simmer.Rmd’

--- re-building ‘plot.trajectory.Rmd’ using rmarkdown
--- finished re-building ‘plot.trajectory.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.simmr_input
> ### Title: Plot the 'simmr_input' data created from 'simmr_load'
> ### Aliases: plot.simmr_input
> 
> ### ** Examples
> 
> # A simple example with 10 observations, 4 food sources and 2 tracers
> mix = matrix(c(-10.13, -10.72, -11.39, -11.18, -10.81, -10.7, -10.54, 
+ -10.48, -9.93, -9.37, 11.59, 11.01, 10.59, 10.97, 11.52, 11.89, 
+ 11.73, 10.89, 11.05, 12.3), ncol=2, nrow=10)
> colnames(mix) = c('d13C','d15N')
> s_names=c('Source A','Source B','Source C','Source D')
> s_means = matrix(c(-14, -15.1, -11.03, -14.44, 3.06, 7.05, 13.72, 5.96), ncol=2, nrow=4)
> s_sds = matrix(c(0.48, 0.38, 0.48, 0.43, 0.46, 0.39, 0.42, 0.48), ncol=2, nrow=4)
> c_means = matrix(c(2.63, 1.59, 3.41, 3.04, 3.28, 2.34, 2.14, 2.36), ncol=2, nrow=4)
> c_sds = matrix(c(0.41, 0.44, 0.34, 0.46, 0.46, 0.48, 0.46, 0.66), ncol=2, nrow=4)
> conc = matrix(c(0.02, 0.1, 0.12, 0.04, 0.02, 0.1, 0.09, 0.05), ncol=2, nrow=4)
> 
> simmr_1 = simmr_load(mixtures=mix,
+                      source_names=s_names,
+                      source_means=s_means,
+                      source_sds=s_sds,
+                      correction_means=c_means,
+                      correction_sds=c_sds,
+                      concentration_means = conc)
> 
> # Plot
> plot(simmr_1)
Warning: Ignoring unknown aesthetics: height
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simmr.Rmd’ using rmarkdown
Quitting from lines 122-123 (simmr.Rmd) 
Error: processing vignette 'simmr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘simmr.Rmd’

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

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

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

Attaching package: 'SimMultiCorrData'

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

    poly

Quitting from lines 107-109 (dist_comp.Rmd) 
Error: processing vignette 'dist_comp.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dist_comp.Rmd’

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

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

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

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

Attaching package: 'SimMultiCorrData'

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

    poly

Quitting from lines 208-214 (sixth_validpdf.Rmd) 
Error: processing vignette 'sixth_validpdf.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sixth_validpdf.Rmd’

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

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

Attaching package: 'SimMultiCorrData'

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

    poly

Quitting from lines 293-294 (workflow.Rmd) 
Error: processing vignette 'workflow.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘workflow.Rmd’

SUMMARY: processing the following files failed:
  ‘dist_comp.Rmd’ ‘sixth_validpdf.Rmd’ ‘workflow.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggfitStrata
> ### Title: Graph fitted stratified survival curves from Cox Proportional
> ###   Hazards models
> ### Aliases: ggfitStrata
> 
> ### ** Examples
> 
> # Load packages
> library(survival)
> library(simPH)
> 
> # Subset data
> bladder1 <- bladder[bladder$enum < 5, ]
> 
> # Estimate coxph model (note that this model is for code illustration only)
> M1 <- coxph(Surv(stop, event) ~ (rx + size + number) + strata(enum) +
+                 cluster(id), bladder1)
> 
> # Find predicted values
> M1Fit <- survfit(M1)
> 
> # Plot strata in a grid
> ggfitStrata(M1Fit, byStrata = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ggfitStrata ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simPH-overview.Rnw’ using knitr
All Xl set to 0.
`geom_smooth()` using method = 'gam' and formula 'y ~ s(x, bs = "cs")'
Quitting from lines 309-319 (simPH-overview.Rnw) 
Error: processing vignette 'simPH-overview.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘simPH-overview.Rnw’

SUMMARY: processing the following file failed:
  ‘simPH-overview.Rnw’

Error: Vignette re-building failed.
Execution halted
randInitializeWeights: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘HISTORY’
Package in Depends field not imported from: ‘mclust’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
simrel: no visible global function definition for ‘runif’
simrel: no visible global function definition for ‘rnorm’
simrelplot: no visible global function definition for ‘par’
simrelplot: no visible global function definition for ‘layout’
simrelplot: no visible global function definition for ‘devAskNewPage’
simrelplot: no visible global function definition for ‘dev.hold’
simrelplot: no visible global function definition for ‘plot’
simrelplot: no visible global function definition for ‘abline’
simrelplot: no visible global function definition for ‘dev.flush’
simrelplot: no visible global function definition for ‘points’
simrelplot: no visible global function definition for ‘axis’
simrelplot: no visible global function definition for ‘mtext’
simrelplot: no visible global function definition for ‘box’
simrelplot: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cov dev.flush dev.hold devAskNewPage layout mtext par
  plot points rnorm runif
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "box", "layout", "mtext",
             "par", "plot", "points")
  importFrom("stats", "cov", "rnorm", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Corr_Cont_System.Rmd’ using rmarkdown
Loading required package: SimMultiCorrData

Attaching package: 'SimMultiCorrData'

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

    poly

Loading required package: SimCorrMix
Quitting from lines 378-386 (Corr_Cont_System.Rmd) 
Error: processing vignette 'Corr_Cont_System.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Corr_Cont_System.Rmd’

--- re-building ‘Corr_MultiVarType_System.Rmd’ using rmarkdown
Loading required package: SimMultiCorrData

Attaching package: 'SimMultiCorrData'

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

    poly

Loading required package: SimCorrMix
Quitting from lines 331-339 (Corr_MultiVarType_System.Rmd) 
Error: processing vignette 'Corr_MultiVarType_System.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Corr_MultiVarType_System.Rmd’

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

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

SUMMARY: processing the following files failed:
  ‘Corr_Cont_System.Rmd’ ‘Corr_MultiVarType_System.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘simstandard_tutorial.Rmd’ using rmarkdown
Quitting from lines 122-124 (simstandard_tutorial.Rmd) 
Error: processing vignette 'simstandard_tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘simstandard_tutorial.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addCondition
> ### Title: Add a single column to existing data set based on a condition
> ### Aliases: addCondition
> 
> ### ** Examples
> 
> 
> # New data set
> 
> def <- defData(varname = "x", dist = "categorical", formula = ".33;.33")
> def <- defData(def, varname="y", dist="uniform", formula="-5;5")
> 
> dt <- genData(1000, def)
> 
> # Define conditions
> 
> defC <- defCondition(condition = "x == 1", formula = "5 + 2*y-.5*y^2",
+                      variance = 1,dist = "normal")
> defC <- defCondition(defC, condition = "x == 2",
+                      formula = "3 - 3*y + y^2", variance = 2, dist="normal")
> defC <- defCondition(defC, condition = "x == 3",
+                      formula = "abs(y)", dist="poisson")
> 
> # Add column
> 
> dt <- addCondition(defC, dt, "NewVar")
> 
> # Plot data
> 
> library(ggplot2)
> 
> ggplot(data = dt, aes(x=y, y=NewVar, group = x)) +
+   geom_point(aes(color = factor(x)))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Found the following hidden files and directories:
  vignettes/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘abind’ ‘svUnit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
simSummary: no visible global function definition for ‘abind’
simSummary_unitTests: no visible global function definition for
  ‘clearLog’
simSummary_unitTests: no visible global function definition for
  ‘runTest’
simSummary_unitTests: no visible global function definition for
  ‘svSuite’
simSummary_unitTests: no visible global function definition for ‘Log’
simSummary_unitTests: no visible global function definition for ‘stats’
simSummary_unitTests: no visible global function definition for
  ‘metadata’
simSummary_unitTests: no visible global function definition for
  ‘errorLog’
Undefined global functions or variables:
  Log abind clearLog errorLog metadata runTest stats svSuite
Running ‘testthat.R’ [52s/81s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Got this Sys.setenv line from https://github.com/luckyrandom/cmaker/blob/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0/tests/testthat.R
  > # so that devtools:check() won't hang.
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(simulator)
  
  Attaching package: 'simulator'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("simulator")
  ── 1. Failure: create makes a template that can be run without error (@test-crea
  any(grepl("error", readLines(a), ignore.case = TRUE)) isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 125 SKIPPED: 3 FAILED: 1
  1. Failure: create makes a template that can be run without error (@test-create.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘big_crush_test.Rmd’ using rmarkdown
--- finished re-building ‘big_crush_test.Rmd’

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

--- re-building ‘uniform_rng_with_sitmo.Rmd’ using rmarkdown
Quitting from lines 159-163 (uniform_rng_with_sitmo.Rmd) 
Error: processing vignette 'uniform_rng_with_sitmo.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘uniform_rng_with_sitmo.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ss.cc
> ### Title: Control Charts
> ### Aliases: ss.cc
> 
> ### ** Examples
> 
> ss.cc("mr", ss.data.pb1, CTQ = "pb.humidity")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ss.cc ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘SiZer-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Arkansas
> ### Title: Time Series of Macroinvertabrates Abundance in the Arkansas
> ###   River.
> ### Aliases: Arkansas
> ### Keywords: datasets
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
> 
> data(Arkansas)
> ggplot(Arkansas, aes(x=year, y=sqrt.mayflies)) + 
+    geom_point()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘sjPlot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dist_chisq
> ### Title: Plot chi-squared distributions
> ### Aliases: dist_chisq
> 
> ### ** Examples
> 
> # a simple chi-squared distribution
> # for 6 degrees of freedom
> dist_chisq(deg.f = 6)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: dist_chisq ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
cvskda: no visible global function definition for ‘detectCores’
cvskda: no visible global function definition for ‘makeCluster’
cvskda: no visible global function definition for ‘clusterApplyLB’
cvskda: no visible global function definition for ‘mclapply’
cvskda: no visible global function definition for ‘stopCluster’
Undefined global functions or variables:
  clusterApplyLB detectCores makeCluster mclapply stopCluster
dskt: no visible global function definition for ‘dt’
pskt: no visible global function definition for ‘pt’
qskt: no visible global function definition for ‘qt’
rskt: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
Error(s) in re-building vignettes:
  ...
--- re-building ‘skynet.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'kableExtra'

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

    group_rows

Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(x) == "unit") { :
  the condition has length > 1 and only the first element will be used
Quitting from lines 97-101 (skynet.Rmd) 
Error: processing vignette 'skynet.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘skynet.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘slim.Rmd’ using rmarkdown
Quitting from lines 65-69 (slim.Rmd) 
Error: processing vignette 'slim.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘slim.Rmd’

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

Error: Vignette re-building failed.
Execution halted
cvsmac: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Running examples in ‘SmartEDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ExpCatViz
> ### Title: Distributions of categorical variables
> ### Aliases: ExpCatViz
> 
> ### ** Examples
> 
> ExpCatViz(data=mtcars,gp=NULL,fname=file.path(tempdir(),"Cat_1"),clim=10,margin=1,Page = c(2,2))
Warning in matrix(data = seq(1, pn), nrow = nr, ncol = nc) :
  data length [5] is not a sub-multiple or multiple of the number of rows [2]
$`0`
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ExpCatViz ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(SmartEDA)
  > 
  > 
  > context("Summary statistics")
  > 
  > test_that("ExpKurtosis and ExpSkew are measures of shapes value", {
  +   expect_equal(ExpKurtosis(c(1:4),type="moment"), 1.64)
  +   set.seed(1234)
  +   expect_equal(ExpSkew(sample(1:100,10),type="moment"),-0.2131082)
  + })
  Error: Test failed: 'ExpKurtosis and ExpSkew are measures of shapes value'
  * ExpSkew(sample(1:100, 10), type = "moment") not equal to -0.2131082.
  1/1 mismatches
  [1] 0.618 - -0.213 == 0.831
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CustomTable.Rmd’ using rmarkdown
--- finished re-building ‘CustomTable.Rmd’

--- re-building ‘SmartEDA.Rmd’ using rmarkdown
Quitting from lines 134-137 (SmartEDA.Rmd) 
Error: processing vignette 'SmartEDA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘SmartEDA.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SmartProject
> ### Title: SmartProject Class
> ### Aliases: SmartProject
> ### Keywords: data
> 
> ### ** Examples
> 
> # Initialize SmartProject
> yourSmartRstudy <- SmartProject$new()
> 
> # Initialize fleet object
> yourSmartRstudy$createFleet()
> 
> 
> ######################
> ## Environment Data ##
> ######################
> 
> # Locate the example environment asset' file
> envAssetPath <- system.file("extdata/mapAsset.RDS", package = "smartR")
> 
> # Load environment asset' data
> yourSmartRstudy$importEnv(readRDS(envAssetPath))
> 
> # Setup case study' map
> yourSmartRstudy$sampMap$getGooMap()
> yourSmartRstudy$sampMap$setGooGrid()
> yourSmartRstudy$sampMap$setGooBbox()
> yourSmartRstudy$sampMap$setGgDepth()
> yourSmartRstudy$sampMap$setGgBioDF()
> # View case study' grid
> print(yourSmartRstudy$sampMap$gooGrid)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
File ‘smco/R/smco.R’:
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

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

smco: no visible global function definition for ‘runif’
smco: no visible global function definition for ‘rnorm’
smco: no visible global function definition for ‘qnorm’
smco: no visible global function definition for ‘pnorm’
smco: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "optim", "pnorm", "qnorm", "rnorm", "runif")
to your NAMESPACE file.
SMCP : fun: no visible global function definition for ‘cor’
manipulate : fun: no visible global function definition for ‘sd’
sp: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cor sd
Consider adding
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
File ‘SMC/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("##\n", "## Sequential Monte Carlo Package (SMC)\n",     "##\n", "## Functionality: sequential Monte Carlo (SMC) or sequential importance\n",     "## sampling (SIS) or hidden Markov models (HMM), particle filter (PF)\n",     "## and auxiliary particle filter (APF)\n", "##\n", "## Use: \"help(package = SMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

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

.MHUpdateFuncGen.PF : MHUpdateFunc: no visible global function
  definition for ‘runif’
MarkovSwitchingFuncGenerator : generateNextStreamsFunc: no visible
  global function definition for ‘runif’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘rnorm’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘runif’
MarkovSwitchingFuncGenerator : logObsDensFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘runif’
Undefined global functions or variables:
  dnorm rnorm runif
Consider adding
  importFrom("stats", "dnorm", "rnorm", "runif")
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.
'library' or 'require' call to ‘proxy’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘proxy’ ‘tm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
normalize: no visible binding for global variable ‘sd’
simDic: no visible global function definition for ‘simil’
simDoc: no visible global function definition for ‘simil’
Undefined global functions or variables:
  sd simil
Consider adding
  importFrom("stats", "sd")
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.
'library' or 'require' calls to packages already attached by Depends:
  ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘corpcor’ ‘ggplot2’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error(s) in re-building vignettes:
  ...
--- re-building ‘readme.Rmd’ using rmarkdown
Quitting from lines 119-130 (readme.Rmd) 
Error: processing vignette 'readme.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘readme.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [3s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(Smisc)
  > 
  > # There shouldn't be any files in the tmp folder
  > unlink("testthat/tmp", recursive = TRUE, force = TRUE)
  > dir.create("testthat/tmp")
  > 
  > test_check("Smisc")
  ── 1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJ
  `xout` not equal to `xin`.
  Component "x2": Component 1: Mean relative difference: 0.8461538
  Component "x2": Component 2: Mean relative difference: 0.7532468
  Component "x2": Component 3: Mean relative difference: 0.5416667
  Component "x2": Component 4: Mean relative difference: 0.34375
  Component "x2": Component 5: Mean relative difference: 0.5441176
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 275 SKIPPED: 0 FAILED: 1
  1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJob.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Running examples in ‘smoof-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.smoof_function
> ### Title: Generate ggplot2 object.
> ### Aliases: autoplot.smoof_function
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> # Simple 2D contour plot with activated heatmap for the Himmelblau function
> fn = makeHimmelblauFunction()
> print(autoplot(fn))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Fourier2d: no visible global function definition for ‘fft’
kernel2dsmooth: no visible global function definition for ‘fft’
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
Running examples in ‘smpic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: smpic_save
> ### Title: Save a social media sized ggplot
> ### Aliases: smpic_save
> 
> ### ** 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(ggplot2)
> library(smpic)
> 
> p <- ggplot(iris) +
+      geom_point(aes(Petal.Length, Petal.Width, color = Species), show.legend = FALSE) +
+        geom_label(data = summarise_if(group_by(iris, Species), is.numeric, mean),
+                   aes(Petal.Length, Petal.Width, label = Species, color = Species),
+                   show.legend = FALSE) +
+        labs(x = "Petal Length", y = "Petal Width",
+             title = "Look mom, a flower plot!",
+             subtitle = "Yet another iris data set visualization.",
+             caption = "Source: iris") +
+        theme_minimal()
> 
>   smpic_view(p, sm = "facebook_shared_images", text_factor = 2.2)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: smpic_view ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(smpic)
  > 
  > test_check("smpic")
  ── 1. Error: (unknown) (@test-functions.R#20)  ─────────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_silent({
         smpic_view(p, sm = "facebook_shared_images", text_factor = 2.2)
     }) at testthat/test-functions.R:20
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: smpic_view(p, sm = "facebook_shared_images", text_factor = 2.2) at testthat/test-functions.R:21
  10: ggplot2::ggsave(filename = filename, dpi = dpi, width = width.calc, height = height.calc, 
         units = "in", plot = p)
  ...
  19: preDraw(x)
  20: preDraw.gTree(x)
  21: pushvpgp(x)
  22: pushgrobvp(x$vp)
  23: pushgrobvp.viewport(x$vp)
  24: pushViewport(vp, recording = FALSE)
  25: lapply(vps, push.vp, recording)
  26: FUN(X[[i]], ...)
  27: push.vp.viewport(X[[i]], ...)
  28: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-functions.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘make_a_social_media_plot.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 41-42 (make_a_social_media_plot.Rmd) 
Error: processing vignette 'make_a_social_media_plot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘make_a_social_media_plot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
dNMR: no visible global function definition for ‘pnorm’
dNMR: no visible global function definition for ‘dnorm’
pNMR: no visible global function definition for ‘pnorm’
pNMR: no visible global function definition for ‘dnorm’
rMR: no visible global function definition for ‘rnorm’
rMR: no visible global function definition for ‘rchisq’
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
SMVar.paired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.paired: no visible global function definition for ‘var’
SMVar.paired: no visible global function definition for ‘pt’
SMVar.paired: no visible global function definition for ‘p.adjust’
SMVar.paired: no visible global function definition for ‘write.table’
SMVar.unpaired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.unpaired: no visible global function definition for ‘var’
SMVar.unpaired: no visible global function definition for ‘pt’
SMVar.unpaired: no visible global function definition for ‘p.adjust’
SMVar.unpaired: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  p.adjust pt var write.table
Consider adding
  importFrom("stats", "p.adjust", "pt", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running examples in ‘snfa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: allocative.efficiency
> ### Title: Allocative efficiency estimation
> ### Aliases: allocative.efficiency
> 
> ### ** Examples
> 
> data(USMacro)
> 
> USMacro <- USMacro[complete.cases(USMacro),]
> 
> #Extract data
> X <- as.matrix(USMacro[,c("K", "L")])
> y <- USMacro$Y
> 
> X.price <- as.matrix(USMacro[,c("K.price", "L.price")])
> y.price <- rep(1e9, nrow(USMacro)) #Price of $1 billion of output is $1 billion
> 
> #Run model
> efficiency.model <- allocative.efficiency(X, y,
+                                          X.price, y.price,
+                                          X.constrained = X,
+                                          model = "br",
+                                          method = "mc")
> 
> #Plot technical/allocative efficiency over time
> library(ggplot2)
> 
> technical.df <- data.frame(Year = USMacro$Year,
+                           Efficiency = efficiency.model$technical.efficiency)
> 
> ggplot(technical.df, aes(Year, Efficiency)) +
+   geom_line()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pairwiseSNHT.Rnw’ using knitr
Quitting from lines 114-121 (pairwiseSNHT.Rnw) 
Error: processing vignette 'pairwiseSNHT.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pairwiseSNHT.Rnw’

--- re-building ‘snht.Rnw’ using knitr
Quitting from lines 93-105 (snht.Rnw) 
Error: processing vignette 'snht.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘snht.Rnw’

SUMMARY: processing the following files failed:
  ‘pairwiseSNHT.Rnw’ ‘snht.Rnw’

Error: Vignette re-building failed.
Execution halted
sclust: no visible global function definition for ‘var’
snipEM: no visible global function definition for ‘cov’
stEM: no visible global function definition for ‘cov’
stEM: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov quantile var
Consider adding
  importFrom("stats", "cov", "quantile", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘snow’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
KS.test: no visible global function definition for ‘quantile’
KS.test : Fgaus: no visible global function definition for ‘pnorm’
KS.test: no visible global function definition for ‘setNames’
cs.test: no visible global function definition for ‘pbinom’
cs.test: no visible global function definition for ‘pnorm’
cs.test: no visible global function definition for ‘setNames’
kde: no visible global function definition for ‘quantile’
kde : Fgaus: no visible global function definition for ‘pnorm’
kde: no visible global function definition for ‘par’
kre: no visible global function definition for ‘quantile’
kre: no visible global function definition for ‘lines’
ns.test: no visible global function definition for ‘complete.cases’
ns.test: no visible global function definition for ‘qnorm’
ns.test: no visible global function definition for ‘pnorm’
ns.test: no visible global function definition for ‘pchisq’
ns.test: no visible global function definition for ‘setNames’
ns.test: no visible global function definition for ‘qt’
quant.test: no visible global function definition for ‘complete.cases’
quant.test: no visible global function definition for ‘pbinom’
quant.test: no visible global function definition for ‘pnorm’
quant.test: no visible global function definition for ‘setNames’
quant.test: no visible global function definition for ‘quantile’
quant.test: no visible global function definition for ‘phyper’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘setNames’
runs.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘mvtnorm’ ‘combinat’
A package should be listed in only one of these fields.
chisq.test.a: no visible global function definition for ‘chisq.test’
maxsel: no visible global function definition for ‘complete.cases’
maxsel.asymp.test: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  chisq.test complete.cases
Consider adding
  importFrom("stats", "chisq.test", "complete.cases")
to your NAMESPACE file.
MDSplot: no visible global function definition for ‘par’
MDSplot: no visible global function definition for ‘rainbow’
MDSplot: no visible global function definition for ‘plot’
MDSplot: no visible global function definition for ‘pairs’
classCenter : <anonymous>: no visible binding for global variable
  ‘median’
grow.snpRF: no visible global function definition for ‘update’
na.roughfix.data.frame : roughfix: no visible global function
  definition for ‘median’
na.roughfix.default: no visible global function definition for ‘median’
outlier.default: no visible global function definition for ‘median’
outlier.default: no visible global function definition for ‘mad’
plot.margin: no visible global function definition for
  ‘installed.packages’
plot.margin: no visible global function definition for ‘rainbow’
plot.margin: no visible global function definition for ‘plot.default’
plot.snpRF: no visible global function definition for ‘matplot’
tuneSnpRF: no visible global function definition for ‘axis’
varImpPlot: no visible global function definition for ‘par’
varImpPlot: no visible global function definition for ‘dotchart’
varImpPlot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis dotchart installed.packages mad matplot median mtext pairs par
  plot plot.default rainbow update
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "dotchart", "matplot", "mtext", "pairs",
             "par", "plot", "plot.default")
  importFrom("stats", "mad", "median", "update")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘colorspace’ ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.args: no visible global function definition for ‘is’
write.sbams: no visible global function definition for ‘as’
write.sbams: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  as is write.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 163-167 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
calculate.areas: no visible global function definition for ‘runif’
calculate.gradedareas: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘SoDA’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘base::WHAT’
Packages in Depends field not imported from:
  ‘MASS’ ‘magic’ ‘ppls’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.hnx.B.initialW: no visible global function definition for
  ‘normalize.vector’
get.hnx.B.initialW: no visible global function definition for ‘adiag’
hclust.wrap: no visible global function definition for ‘hclust’
hclust.wrap: no visible global function definition for ‘dist’
hclust.wrap: no visible global function definition for ‘cutree’
my.normdata.gen: no visible global function definition for ‘mvrnorm’
my.normdata.gen: no visible global function definition for ‘rnorm’
odc.clust: no visible binding for global variable ‘kmeans’
odc.cv: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible global function definition for ‘tr’
odc.optimallambda2: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible binding for global variable ‘sd’
sodc.clust: no visible binding for global variable ‘kmeans’
Undefined global functions or variables:
  adiag cutree dist ginv hclust kmeans mvrnorm normalize.vector rnorm
  sd tr
Consider adding
  importFrom("stats", "cutree", "dist", "hclust", "kmeans", "rnorm",
             "sd")
to your NAMESPACE file.
Ssimpute.als: no visible global function definition for ‘rnorm’
Ssvd.als: no visible global function definition for ‘rnorm’
cs.default: no visible binding for global variable ‘weighted.mean’
simpute.als: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm weighted.mean
Consider adding
  importFrom("stats", "rnorm", "weighted.mean")
to your NAMESPACE file.
Running examples in ‘solarius-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotKinship2
> ### Title: Plot the double kinship matrix
> ### Aliases: histKinship2 imageKinship2 plotKinship2
> 
> ### ** Examples
> 
> # load `kin` kinship matrix from `dat50` data set
> data(dat50)
> kin2 <- 2* kin # double kinship matrix
> 
> plotKinship2(kin2) # equivalent to `imageKinship2(kin2)`
> 
> plotKinship2(kin2, "hist") # equivalent to `histKinship2(kin2)`
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
bm: no visible global function definition for ‘rnorm’
bm: no visible global function definition for ‘ts’
fbm: no visible global function definition for ‘fft’
fbm: no visible global function definition for ‘rnorm’
fbm: no visible global function definition for ‘ts’
gbm: no visible global function definition for ‘rnorm’
gbm: no visible global function definition for ‘ts’
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for ‘pbinom’
kfweOrd: no visible global function definition for ‘qnbinom’
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘someMTP’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to ‘hexbin’ which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for ‘quantile’
hexbinpie: no visible global function definition for ‘polygon’
hexbinpie: no visible global function definition for ‘text’
makehexbinplot: no visible global function definition for ‘rainbow’
makehexbinplot: no visible global function definition for ‘col2rgb’
makehexbinplot: no visible global function definition for ‘edit’
makehexbinplot: no visible global function definition for ‘dev.new’
makehexbinplot: no visible global function definition for ‘plot.new’
makehexbinplot: no visible global function definition for ‘plot.window’
makehexbinplot: no visible global function definition for ‘box’
makehexbinplot: no visible global function definition for ‘axis’
makehexbinplot: no visible global function definition for ‘legend’
som.plot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
plot.soo_function: no visible global function definition for
  ‘terrain.colors’
plot.soo_function: no visible binding for global variable ‘image’
plot.soo_function: no visible binding for global variable ‘contour’
plot3d: no visible global function definition for ‘persp3d’
plot3d: no visible global function definition for ‘terrain.colors’
random_parameters.soo_function: no visible global function definition
  for ‘runif’
random_rotation_matrix: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  contour image persp3d runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "contour", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘sophisthse_intro.Rmd’ using rmarkdown
Quitting from lines 42-44 (sophisthse_intro.Rmd) 
Error: processing vignette 'sophisthse_intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sophisthse_intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Non-standard files/directories found at top level:
  ‘README.markdown’ ‘build_package.sh’ ‘upload.sh’
simdata_contaminated : <anonymous>: no visible global function
  definition for ‘rbinom’
simdata_uniform : multivariate_uniform : <anonymous>: no visible global
  function definition for ‘runif’
which_min: no visible global function definition for ‘head’
which_min: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head rbinom runif tail
Consider adding
  importFrom("stats", "rbinom", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
convert_municipality_names: no visible global function definition for
  ‘read.csv’
regression_plot: no visible binding for global variable ‘loess’
regression_plot: no visible global function definition for
  ‘colorRampPalette’
regression_plot: no visible global function definition for
  ‘loess.control’
regression_plot: no visible global function definition for ‘predict’
regression_plot : <anonymous>: no visible global function definition
  for ‘quantile’
regression_plot : <anonymous>: no visible global function definition
  for ‘pnorm’
regression_plot: no visible global function definition for
  ‘flush.console’
regression_plot: no visible global function definition for ‘density’
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘sorvi_tutorial.Rmd’ using rmarkdown
sorvi - Tools for Finnish Open Data.
Copyright (C) 2010-2015 Leo Lahti, Juuso Parkkinen, Juuso Haapanen, Einari Happonen, Jussi Paananen, Joona Lehtomaki ym.

http://github.com/ropengov/sorvi 

 Hard sciences are successful because they deal with soft problems; 
 soft sciences are struggling because they deal with hard problems.
-                        Von Foerster

Computing boostrapped smoothers ...
convert bootstrapped spaghettis to long format
Computing density estimates for each vertical cut ...
vertical cross-sectional density estimate
Tile approach
Build ggplot figure ...
Quitting from lines 241-245 (sorvi_tutorial.Rmd) 
Error: processing vignette 'sorvi_tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sorvi_tutorial.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tutorial.Rmd’ using knitr
Sotkanet R tools (C) 2013-2017 rOpenGov
https://github.com/ropengov/sotkanet
Retrieving indicator 10013
Quitting from lines 99-114 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘SciencesPo’
Package suggested but not available for checking: ‘r2cytoscape’
Running examples in ‘SourceSet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: easyLookSource
> ### Title: Easy look results
> ### Aliases: easyLookSource
> 
> ### ** Examples
> 
> ## Load the SourceSetObj obtained from the source set analysis of ALL dataset
> 
> # see vignette for more details
> print(load(file=system.file("extdata","ALLsourceresult.RData",package = "SourceSet")))
[1] "results.all"
> class(results.all)
[1] "sourceSetList"
> n.primary<-length(lapply(results.all,function(x) x$primarySet))
> 
> # show only genes that appear in at least one of the source sets of the investigated pathways
> easyLookSource(sourceObj=results.all, maxnum.variable = n.primary,
+                label.variable = "Genes",label.graph = "Pathways")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown
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, colMeans, colSums, 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, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Identifing all possible orderings..
Total run time: 1.52 secs
Quitting from lines 311-312 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.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.
SPA: no visible global function definition for ‘var’
Score.Test.Interact: no visible global function definition for ‘pchisq’
Score.Test.Overall: no visible global function definition for ‘var’
Score.Test.Overall: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq var
Consider adding
  importFrom("stats", "pchisq", "var")
to your NAMESPACE file.
'library' or 'require' call to ‘Matrix’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Matrix’ ‘igraph’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GenPar: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘colorspace’ ‘picante’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
hausman: no visible global function definition for ‘pchisq’
span.formula: no visible global function definition for ‘model.frame’
span.formula: no visible global function definition for ‘model.matrix’
span.formula: no visible global function definition for
  ‘model.response’
spbe: no visible global function definition for ‘cor’
spbe: no visible global function definition for ‘pt’
spfe: no visible global function definition for ‘cor’
spfe: no visible global function definition for ‘pt’
sprandom: no visible global function definition for ‘cor’
sprandom: no visible global function definition for ‘pt’
summary.span: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
plot.spa: no visible global function definition for ‘plot’
plot.spa: no visible global function definition for ‘lines’
plot.spa: no visible global function definition for ‘points’
plot.spa: no visible global function definition for ‘gray’
plot.spa: no visible global function definition for ‘box’
predict.spa: no visible global function definition for ‘fitted’
predict.spa: no visible global function definition for ‘coef’
spa.gcv: no visible global function definition for ‘density’
spa.gcv: no visible global function definition for ‘quantile’
spa.sim: no visible global function definition for ‘runif’
spa.sim: no visible global function definition for ‘rnorm’
spa.sim: no visible global function definition for ‘rbinom’
update.spa: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  box coef density fitted gray lines plot points quantile rbinom rnorm
  runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "box", "lines", "plot", "points")
  importFrom("stats", "coef", "density", "fitted", "quantile", "rbinom",
             "rnorm", "runif")
to your NAMESPACE file.
Running examples in ‘spa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict.spa
> ### Title: Inductive Predict Procedure For SPA
> ### Aliases: predict.spa
> ### Keywords: classes models methods
> 
> ### ** Examples
> 
> ## Use simulated example (two moon) and generate a contour plot of the border
> set.seed(100)
> dat=spa.sim(type="moon") 
> 
> L=which(!is.na(dat$y))
> U=which(is.na(dat$y))
> Dij=as.matrix(daisy(dat[,-1]))
> 
> ##Use spa to train with a supervised/transductive kernel smoother
> gsup<-spa(dat$y[L],graph=Dij[L,L],control=spa.control(gcv="lGCV"))
Error in if (g1 < g2) { : missing value where TRUE/FALSE needed
Calls: spa -> spa.gcv
Execution halted
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPARQL : <anonymous>: no visible global function definition for
  ‘URLencode’
SPARQL: no visible binding for global variable ‘getURL’
SPARQL: no visible global function definition for ‘URLencode’
SPARQL: no visible binding for global variable ‘xmlParse’
SPARQL: no visible global function definition for ‘getNodeSet’
SPARQL: no visible global function definition for ‘xpathApply’
SPARQL: no visible binding for global variable ‘postForm’
get_attr: no visible global function definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xpathSApply’
get_value: no visible binding for global variable ‘xmlValue’
get_value: no visible global function definition for ‘xpathApply’
get_value: no visible binding for global variable ‘xmlGetAttr’
readCSVstring: no visible global function definition for ‘read.csv’
readTSVstring: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  URLencode getNodeSet getURL postForm read.csv read.delim xmlDoc
  xmlGetAttr xmlParse xmlValue xpathApply xpathSApply
Consider adding
  importFrom("utils", "URLencode", "read.csv", "read.delim")
to your NAMESPACE file.
f.I2.cont: no visible global function definition for ‘combn’
f.I2.dich: no visible global function definition for ‘combn’
f.pstar.cont: no visible global function definition for ‘combn’
f.pstar.dich: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
Missing or unexported object: ‘RCy3::displayGraph’
Error(s) in re-building vignettes:
  ...
--- re-building ‘sparseMVN.Rnw’ using knitr
Quitting from lines 627-643 (sparseMVN.Rnw) 
Error: processing vignette 'sparseMVN.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sparseMVN.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using.Rmd’ using rmarkdown
Quitting from lines 54-55 (using.Rmd) 
Error: processing vignette 'using.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generate_emulators_and_ensemble
> ### Title: Generate a set of emulators and combine into an ensemble
> ### Aliases: generate_emulators_and_ensemble
> 
> ### ** Examples
> 
> sampleMaxes <- cbind(100,0.9,0.5,0.08,1,5)
> sampleMins <-cbind(0,0.1,0.1,0.015,0.1,0.25)
> modelList <- c("RF","GLM")
> measures<-c("Velocity")
> parameters<-c("stableBindProbability","chemokineExpressionThreshold",
+ "initialChemokineExpressionValue","maxChemokineExpressionValue",
+ "maxProbabilityOfAdhesion","adhesionFactorExpressionSlope")
> data("sim_data_for_emulation")
> partitionedData <- partition_dataset(sim_data_for_emulation[,1:7], parameters,
+ measures, percent_train=75, percent_test=15, percent_validation=10, normalise=TRUE,
+ sample_mins = sampleMins, sample_maxes = sampleMaxes)
> generated_ensemble<-generate_emulators_and_ensemble(modelList, parameters,
+ measures, partitionedData, normalised=TRUE)
[1] "RF"
Velocity ~ stableBindProbability + chemokineExpressionThreshold + 
    initialChemokineExpressionValue + maxChemokineExpressionValue + 
    maxProbabilityOfAdhesion + adhesionFactorExpressionSlope
<environment: 0x555ec3ace380>
Saving 7 x 7 in image
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: generate_emulators_and_ensemble ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘SpatialBall-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DefShotSeasonGraphTeam
> ### Title: Generates an defensive shot chart for a given team
> ### Aliases: DefShotSeasonGraphTeam
> 
> ### ** Examples
> 
> data("season2017")
> #Examples with several teams
> DefShotSeasonGraphTeam(season2017, team = "Sas")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Starting.Rmd’ using rmarkdown
Quitting from lines 52-54 (Starting.Rmd) 
Error: processing vignette 'Starting.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Starting.Rmd’

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

Error: Vignette re-building failed.
Execution halted
gev.impute: no visible global function definition for ‘rnorm’
gev.init: no visible global function definition for ‘rbinom’
gev.init: no visible global function definition for ‘var’
gev.init: no visible global function definition for ‘optimize’
gev.logscore: no visible global function definition for ‘density’
gev.logscore: no visible global function definition for ‘splinefun’
gev.update.M: no visible global function definition for ‘runif’
gev.update.hyper: no visible global function definition for ‘rgamma’
gev.update.lambda: no visible global function definition for ‘rnorm’
gev.update.lambda: no visible global function definition for ‘dgamma’
gev.update.lambda: no visible global function definition for ‘dnorm’
gev.update.lambda: no visible global function definition for ‘runif’
gev.update.tau.kappa: no visible global function definition for ‘rnorm’
gev.update.tau.kappa: no visible global function definition for ‘dnorm’
gev.update.tau.kappa: no visible global function definition for ‘runif’
gev.update.tau.mu: no visible global function definition for ‘rnorm’
gev.update.tau.mu: no visible global function definition for ‘dnorm’
gev.update.tau.mu: no visible global function definition for ‘runif’
gev.update.tau.xi: no visible global function definition for ‘rnorm’
gev.update.tau.xi: no visible global function definition for ‘dnorm’
gev.update.tau.xi: no visible global function definition for ‘runif’
gev.update.theta: no visible global function definition for ‘rnorm’
gp.like.lambda: no visible global function definition for ‘dgamma’
Undefined global functions or variables:
  density dgamma dnorm optimize rbinom rgamma rnorm runif splinefun var
Consider adding
  importFrom("stats", "density", "dgamma", "dnorm", "optimize", "rbinom",
             "rgamma", "rnorm", "runif", "splinefun", "var")
to your NAMESPACE file.
I2BR: no visible global function definition for ‘pnorm’
I2SmD2: no visible global function definition for ‘pnorm’
IBR: no visible global function definition for ‘pnorm’
ISmD2: no visible global function definition for ‘pnorm’
MestimatorBR: no visible global function definition for ‘optim’
MestimatorSmith: no visible global function definition for ‘optim’
psidotBR: no visible global function definition for ‘dnorm’
psidotBR: no visible global function definition for ‘pnorm’
psidotSmD2: no visible global function definition for ‘dnorm’
psidotSmD2: no visible global function definition for ‘pnorm’
tailBRInt: no visible global function definition for ‘pnorm’
tailSmithInt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm optim pnorm
Consider adding
  importFrom("stats", "dnorm", "optim", "pnorm")
to your NAMESPACE file.
Running examples in ‘spatialwarnings-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_indicator
> ### Title: Custom Spatial Early-Warning signals
> ### Aliases: create_indicator custom_indicator
> 
> ### ** Examples
> 
> 
> # Use the maximum patch size as indicator of degradation
> maxpatchsize <- function(mat) { 
+   max(patchsizes(mat))
+ }
> 
> # Create the indicator function
> maxpatch_sews <- create_indicator(maxpatchsize)
> 
> # Then work with this function as if it were a function from the *_sews 
> # family. 
> mp_indic <- maxpatch_sews(forestgap)
> summary(mp_indic)
Spatial Early-Warning: maxpatchsize 

 9 matrices (size: 400x400)

 Mat. # maxpatchsize
      1       146796
      2       128553
      3       107995
      4        48320
      5          322
      6           70
      7           26
      8           10
      9            6

Use as.data.frame() to retrieve values in a convenient form
> 
> ## Not run: 
> ##D  
> ##D # Assess significance and display trends
> ##D mp_test <- indictest(mp_indic, nperm = 49)
> ##D plot(mp_test)
> ## End(Not run)
> 
> 
> 
> # Try spatial coefficient of variation as a spatial EWS. This function can 
> # have arguments. 
> spatial_cv <- function(mat, subsize) { 
+   matc <- coarse_grain(mat, subsize)
+   return( sd(matc) / mean(matc) )
+ }
> 
> # Create indicator function
> cv_sews <- create_indicator(spatial_cv)
> 
> # Compute and display trends
> cv_indic <- cv_sews(serengeti, subsize = 3)
> plot(cv_indic, along = serengeti.rain)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sfbabel.Rmd’ using rmarkdown
--- finished re-building ‘sfbabel.Rmd’

--- re-building ‘spbabel.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

Loading required package: sp
Checking rgeos availability: TRUE
Quitting from lines 116-122 (spbabel.Rmd) 
Error: processing vignette 'spbabel.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘spbabel.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘spcosa.Rmd’ using rmarkdown
Loading required package: sp
rgdal: version: 1.4-3, (SVN revision 828)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.0, released 2018/12/14
 Path to GDAL shared files: /usr/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: 1.3-1 
Quitting from lines 184-185 (spcosa.Rmd) 
Error: processing vignette 'spcosa.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘spcosa.Rmd’

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

Error: Vignette re-building failed.
Execution halted
GenerateCliquesCovariance: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Package suggested but not available for checking: ‘spDataLarge’
Error(s) in re-building vignettes:
  ...
--- re-building ‘classic_speaq_vignette.Rmd’ using rmarkdown
--- finished re-building ‘classic_speaq_vignette.Rmd’

--- re-building ‘speaq2_illustrations.Rmd’ using rmarkdown
Quitting from lines 93-105 (speaq2_illustrations.Rmd) 
Error: processing vignette 'speaq2_illustrations.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘speaq2_illustrations.Rmd’

SUMMARY: processing the following file failed:
  ‘speaq2_illustrations.Rmd’

Error: Vignette re-building failed.
Execution halted
bartlett: no visible global function definition for ‘pchisq’
local.rbfdot: no visible binding for global variable ‘sd’
local.rbfdot: no visible global function definition for ‘dist’
local.rbfdot : <anonymous>: no visible global function definition for
  ‘median’
speccalt: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
ChaoBunge: no visible global function definition for ‘qnorm’
ChaoLee1992: no visible global function definition for ‘qnorm’
Pmix: no visible global function definition for ‘dpois’
PmixSCon: no visible global function definition for ‘dbeta’
bootPCG: no visible global function definition for ‘flush.console’
bootPCG: no visible global function definition for ‘quantile’
bootPnpmle: no visible global function definition for ‘flush.console’
bootPnpmle: no visible global function definition for ‘quantile’
bootUnpmle: no visible global function definition for ‘flush.console’
bootUnpmle: no visible global function definition for ‘quantile’
chao1984: no visible global function definition for ‘qnorm’
jackknife: no visible global function definition for ‘dbinom’
jackknife: no visible global function definition for ‘qnorm’
pcg: no visible global function definition for ‘flush.console’
unpmle: no visible global function definition for ‘flush.console’
untrunPmix: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dbeta dbinom dpois flush.console qnorm quantile
Consider adding
  importFrom("stats", "dbeta", "dbinom", "dpois", "qnorm", "quantile")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Package suggested but not available for checking: ‘rcytoscapejs’
Running examples in ‘specmine-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dendrogram_plot
> ### Title: Plot dendrogram
> ### Aliases: dendrogram_plot
> ### Keywords: clustering dendrogram hclust
> 
> ### ** Examples
> 
>   ## Example of a dendrogram
>   data(cachexia)
>   hc.result = hierarchical_clustering(cachexia)
>   dendrogram_plot(cachexia, hc.result)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘spectacles-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot-Spectra
> ### Title: Plots an object inheriting from the Spectra class
> ### Aliases: plot-Spectra plot plot.Spectra plot,Spectra,ANY-method
> ###   plot.Spectra
> 
> ### ** Examples
> 
> 
> # Loading example data
> data(australia)
> spectra(australia) <- sr_no ~ ... ~ 350:2500
Wavelength range: 350 to 2500 nm
Spectral resolution: 1 nm
> 
> # Default plotting method
> plot(australia[1:5,])
> 
> # Default plot using ggplot2
> plot(australia[1:5,], gg = TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘Spectrum-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Spectrum
> ### Title: Spectrum: Fast Adaptive Spectral Clustering for Single and
> ###   Multi-view Data
> ### Aliases: Spectrum
> 
> ### ** Examples
> 
> res <- Spectrum(brain[[1]][,1:50])
***Spectrum***
detected views: 1
method: 1
kernel: density
calculating kernel 1
done.
combining kernels if > 1 and making KNN graph...
done.
diffusing on tensor graph...
done.
calculating graph laplacian...
getting eigendecomposition of L...
done.
examining eigenvalues to select K...
optimal K: 3
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: Spectrum ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Spectrum_vignette.Rmd’ using rmarkdown
Quitting from lines 49-51 (Spectrum_vignette.Rmd) 
Error: processing vignette 'Spectrum_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Spectrum_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘leaps’ which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for ‘glm’
modSearch: no visible binding for global variable ‘binomial’
modSearch: no visible global function definition for ‘na.omit’
modSearch: no visible global function definition for ‘as.formula’
speff: no visible binding for global variable ‘na.pass’
speff: no visible global function definition for ‘model.matrix’
speff: no visible global function definition for ‘terms’
speff: no visible global function definition for ‘model.response’
speff: no visible global function definition for ‘as.formula’
speff: no visible global function definition for ‘predict’
speff: no visible global function definition for ‘na.omit’
speff: no visible global function definition for ‘glm’
speff: no visible binding for global variable ‘na.omit’
speffSurv: no visible global function definition for ‘model.matrix’
speffSurv: no visible global function definition for ‘terms’
speffSurv: no visible global function definition for ‘model.response’
speffSurv: no visible global function definition for ‘as.formula’
speffSurv: no visible global function definition for ‘uniroot’
summary.speff: no visible global function definition for ‘qnorm’
summary.speff: no visible global function definition for ‘pnorm’
summary.speffSurv: no visible global function definition for ‘qnorm’
summary.speffSurv: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
Running examples in ‘spef-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PanelSurv
> ### Title: Create a PanelSurv Object
> ### Aliases: PanelSurv PanelSurv is.PanelSurv
> 
> ### ** Examples
> 
> data(blaTum)
> response <- with(blaTum, PanelSurv(id, time, count))
> is.PanelSurv(response)
[1] TRUE
> plot(response)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of ‘nr’ to ‘nrow’
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of ‘nc’ to ‘ncol’
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘spFSR.Rmd’ using rmarkdown
Quitting from lines 299-301 (spFSR.Rmd) 
Error: processing vignette 'spFSR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘spFSR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package in Depends field not imported from: ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pointsphere: no visible global function definition for ‘runif’
rgl.sphMW: no visible global function definition for ‘plot3d’
rgl.sphcirc: no visible global function definition for ‘rotate3d’
rgl.sphcirc: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘open3d’
rgl.sphgrid: no visible global function definition for ‘plot3d’
rgl.sphgrid: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘text3d’
rgl.sphpoints: no visible global function definition for ‘points3d’
rgl.sphsun: no visible global function definition for ‘plot3d’
rgl.sphtext: no visible global function definition for ‘text3d’
Undefined global functions or variables:
  lines3d open3d plot3d points3d rotate3d runif text3d
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘lars’ ‘parallel’ ‘randomForest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘spind-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: covar.plot
> ### Title: Plot wavelet variance/covariance
> ### Aliases: covar.plot
> 
> ### ** Examples
> 
> data(carlinadata)
> coords <- carlinadata[,4:5]
> 
> covariance <- covar.plot(carlina.horrida ~ aridity + land.use - 1,
+                          data = carlinadata,
+                          coord = coords,
+                          wavelet = "d4",
+                          wtrafo = 'modwt',
+                          plot = 'covar')
> 
> covariance$plot
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘spind_vignette.Rmd’ using rmarkdown
Quitting from lines 51-76 (spind_vignette.Rmd) 
Error: processing vignette 'spind_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘spind_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘quadprog’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPIn: no visible global function definition for ‘density’
SPIn: no visible global function definition for ‘quantile’
SPIn: no visible global function definition for ‘solve.QP’
bootSPIn: no visible global function definition for ‘runif’
plot.SPIn: no visible global function definition for ‘hist’
plot.SPIn: no visible global function definition for ‘lines’
plot.SPIn: no visible global function definition for ‘text’
plot.SPIn: no visible global function definition for ‘quantile’
plot.SPIn: no visible global function definition for ‘legend’
Undefined global functions or variables:
  density hist legend lines quantile runif solve.QP text
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "text")
  importFrom("stats", "density", "quantile", "runif")
to your NAMESPACE file.
spi: no visible global function definition for ‘read.table’
spi: no visible global function definition for ‘ecdf’
spi: no visible global function definition for ‘qnorm’
spi: no visible global function definition for ‘colorRampPalette’
spi: no visible global function definition for ‘filled.contour’
spi: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis colorRampPalette ecdf filled.contour qnorm read.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "filled.contour")
  importFrom("stats", "ecdf", "qnorm")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in ‘splinetree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotNode
> ### Title: Plot the predicted trajectory for a single node
> ### Aliases: plotNode
> 
> ### ** Examples
> 
> plotNode(tree, 6, includeData=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DPsplithalf-vignette.Rmd’ using rmarkdown
Quitting from lines 207-213 (DPsplithalf-vignette.Rmd) 
Error: processing vignette 'DPsplithalf-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DPsplithalf-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(splitstackshape)
  > 
  > test_check("splitstackshape")
  ── 1. Failure: stratified returns the expected number of rows (@test_stratified.
  nrow(stratified(DF, "A", 0.1, select = list(A = c("AA", "BB")))) not equal to 3.
  1/1 mismatches
  [1] 4 - 3 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 51 SKIPPED: 0 FAILED: 1
  1. Failure: stratified returns the expected number of rows (@test_stratified.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
R2.global: no visible global function definition for ‘var’
calculer.var.exp: no visible global function definition for ‘var’
creer.noeud: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘cov’
spodt: no visible global function definition for ‘model.frame’
spodt.tree: no visible global function definition for ‘plot.new’
spodt.tree: no visible global function definition for ‘par’
spodt.tree: no visible global function definition for ‘plot.window’
spodt.tree: no visible global function definition for ‘text’
spodt.tree: no visible global function definition for ‘segments’
test.spodt: no visible global function definition for ‘model.frame’
test.spodt: no visible global function definition for ‘hist’
test.spodt: no visible global function definition for ‘abline’
tracer.noeud: no visible global function definition for ‘text’
tracer.noeud: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘sport_in_r.Rmd’ using rmarkdown
r is missing and will set to default=1500
rd is missing and will set to default=350
r is missing and will set to default=1500
rd is missing and will set to default=350
sigma is missing and will set to default=0.05
r is missing and will set to default=25
rd is missing and will set to default=8.33333333333333
Quitting from lines 133-135 (sport_in_r.Rmd) 
Error: processing vignette 'sport_in_r.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘sport_in_r.Rmd’

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

Error: Vignette re-building failed.
Execution halted
fetch_NBAPlayerStatistics: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  points.within
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'points.within':
  ‘points.within’

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 ‘spreadr_vignette.Rmd’ using rmarkdown
Quitting from lines 79-88 (spreadr_vignette.Rmd) 
Error: processing vignette 'spreadr_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘spreadr_vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biplot.prm
> ### Title: Biplot for prm objects
> ### Aliases: biplot.prm
> 
> ### ** Examples
> 
> set.seed(5023)
> U <- c(rep(3,20), rep(4,30))
> X <- replicate(6, U+rnorm(50))
> beta <- c(rep(1, 3), rep(-1,3))
> e <- c(rnorm(45,0,1.5),rnorm(5,-20,1))
> y <- X%*%beta + e
> d <- as.data.frame(X)
> d$y <- y
> mod <- prms(y~., data=d, a=2, fun="Hampel")
> biplot(mod, comps = c(1, 2))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: biplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
plotThin: no visible global function definition for ‘par’
plotThin: no visible global function definition for ‘dev.interactive’
plotThin: no visible global function definition for ‘plot’
plotThin: no visible global function definition for ‘hist’
thin: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  dev.interactive hist par plot write.csv
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "hist", "par", "plot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Running examples in ‘SPUTNIK-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binKmeans,msi.dataset-method
> ### Title: Return a binary mask generated applying k-means clustering on
> ###   peaks intensities.
> ### Aliases: binKmeans,msi.dataset-method binKmeans
> 
> ### ** Examples
> 
> ## Load package
> library("SPUTNIK")
> 
> ## Create the msi.dataset-class object
> sz <- c(5, 4)
> x <- matrix(rnorm(sz[1] * sz[2] * 20), sz[1]*sz[2], 20)
> mz <- sort(sample(100, ncol(x)))
> msiX <- msiDataset(x, mz, sz[1], sz[2])
> 
> ## Binarize the reference image
> refBin <- binKmeans(msiX)
> 
> ## Plot the binarized reference
> plot(refBin)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
sGda : <anonymous>: no visible global function definition for ‘cov’
sortgene: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘RJDBC’ ‘RMySQL’ ‘RODBC’ ‘RPostgreSQL’ ‘RSQLite’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for ‘read.csv’
cacheQuery: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable ‘median’
SQN: no visible global function definition for ‘quantile’
SQN.demo.data: no visible global function definition for ‘rnorm’
mix.qn: no visible global function definition for ‘ecdf’
mix.qn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
plot.srafit: no visible global function definition for ‘layout’
plot.srafit: no visible global function definition for ‘par’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘dnorm’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘pnorm’
sraData : vartruncGauss: no visible global function definition for
  ‘uniroot’
sraPlotMean: no visible global function definition for ‘axis’
sraPlotMean: no visible global function definition for ‘points’
sraPlotMean: no visible global function definition for ‘lines’
sraPlotMeanResid: no visible global function definition for ‘axis’
sraPlotMeanResid: no visible global function definition for ‘abline’
sraPlotMeanResid: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘axis’
sraPlotVar: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘lines’
sraPlotVarResid: no visible global function definition for ‘axis’
sraPlotVarResid: no visible global function definition for ‘abline’
sraPlotVarResid: no visible global function definition for ‘points’
sraPlotlegend: no visible global function definition for ‘legend’
sraStartingvalues : sraStartingvalues.mu0: no visible global function
  definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarA0: no visible global
  function definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarE0: no visible global
  function definition for ‘rnorm’
sraStartingvalues: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis dnorm layout legend lines par pnorm points rnorm uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "legend", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "pnorm", "rnorm", "uniroot")
to your NAMESPACE file.
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
File ‘sROC/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

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

AUC : TrapezInt: no visible global function definition for ‘approx’
AUC : SimpsonInt: no visible global function definition for ‘approx’
CI.CDF: no visible global function definition for ‘qnorm’
bw.CDF: no visible global function definition for ‘sd’
bw.CDF: no visible global function definition for ‘IQR’
bw.CDF.pi: no visible global function definition for ‘sd’
bw.CDF.pi: no visible global function definition for ‘bw.nrd0’
bw.CDF.pi: no visible global function definition for ‘bw.nrd’
bw.CDF.pi: no visible global function definition for ‘bw.ucv’
bw.CDF.pi: no visible global function definition for ‘bw.bcv’
bw.CDF.pi: no visible global function definition for ‘bw.SJ’
bw.CDF.pi: no visible global function definition for ‘IQR’
plot.CDF: no visible global function definition for ‘plot.default’
plot.CDF: no visible global function definition for ‘lines’
plot.CDF: no visible global function definition for ‘polygon’
plot.ROC: no visible global function definition for ‘plot.default’
plot.ROC: no visible global function definition for ‘abline’
Undefined global functions or variables:
  IQR abline approx bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv lines
  plot.default polygon qnorm sd
Consider adding
  importFrom("graphics", "abline", "lines", "plot.default", "polygon")
  importFrom("stats", "IQR", "approx", "bw.SJ", "bw.bcv", "bw.nrd",
             "bw.nrd0", "bw.ucv", "qnorm", "sd")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending-srvyr.Rmd’ using rmarkdown
--- finished re-building ‘extending-srvyr.Rmd’

--- re-building ‘srvyr-database.Rmd’ using rmarkdown
--- finished re-building ‘srvyr-database.Rmd’

--- re-building ‘srvyr-vs-survey.Rmd’ using rmarkdown
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

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

    dotchart


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 31-47 (srvyr-vs-survey.Rmd) 
Error: processing vignette 'srvyr-vs-survey.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘srvyr-vs-survey.Rmd’

SUMMARY: processing the following file failed:
  ‘srvyr-vs-survey.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ss3sim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_scalar_boxplot
> ### Title: Print scalar values as boxplots.
> ### Aliases: plot_scalar_boxplot
> 
> ### ** Examples
> 
> scalar_dat$depletion <- with(scalar_dat,
+   (depletion_om - depletion_em) / depletion_om)
> plot_scalar_boxplot(scalar_dat, x = "E", y = "depletion", horiz = "D",
+   relative.error = TRUE)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_scalar_boxplot ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 680-688 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘making-functions.Rmd’ using rmarkdown
--- finished re-building ‘making-functions.Rmd’

--- re-building ‘making-models.Rmd’ using rmarkdown
--- finished re-building ‘making-models.Rmd’

--- re-building ‘modifying-models.Rmd’ using rmarkdown
--- finished re-building ‘modifying-models.Rmd’

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

Error: Vignette re-building failed.
Execution halted
ssd : correction_method_D: no visible global function definition for
  ‘rnorm’
ssd : generate_bootstrap: no visible global function definition for
  ‘rmultinom’
ssd : bootstrap_method: no visible global function definition for
  ‘median’
ssd : bootstrap_method: no visible global function definition for
  ‘quantile’
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for ‘rmultinom’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘median’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘quantile’
ssd: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
Running examples in ‘ssdtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.fitdist
> ### Title: Autoplot
> ### Aliases: autoplot.fitdist
> 
> ### ** Examples
> 
> ggplot2::autoplot(boron_lnorm)
Warning: Removed 98 rows containing missing values (geom_path).
geom_path: Each group consists of only one observation. Do you need to adjust
the group aesthetic?
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ssdtools-manual.Rmd’ using rmarkdown
Quitting from lines 115-119 (ssdtools-manual.Rmd) 
Error: processing vignette 'ssdtools-manual.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ssdtools-manual.Rmd’

SUMMARY: processing the following file failed:
  ‘ssdtools-manual.Rmd’

Error: Vignette re-building failed.
Execution halted
L_hNV: no visible global function definition for ‘pnorm’
L_hNV_rho: no visible global function definition for ‘pnorm’
eff.ssfa: no visible global function definition for ‘pnorm’
plot_fitted: no visible global function definition for ‘lines’
plot_moran: no visible global function definition for ‘residuals’
print.summary.ssfa: no visible global function definition for
  ‘printCoefmat’
ssfa: no visible global function definition for ‘model.frame’
ssfa: no visible global function definition for ‘model.response’
ssfa.fit: no visible global function definition for ‘lm’
ssfa.fit: no visible global function definition for ‘var’
ssfa.fit: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pnorm’
summary.ssfa: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pchisq’
summary.ssfa: no visible binding for global variable ‘df’
u.ssfa: no visible global function definition for ‘dnorm’
u.ssfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘survey’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for ‘hadamard’
Undefined global functions or variables:
  hadamard
mem.usage: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
sslCoTrain: no visible global function definition for ‘predict’
sslSelfTrain: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  dbfopenSSN.c:1119:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/SSN.Rcheck/00install.out’ for details.
map.world: no visible global function definition for ‘par’
map.world: no visible global function definition for ‘plot.new’
map.world: no visible global function definition for ‘plot.window’
map.world: no visible global function definition for ‘lines’
map.world: no visible global function definition for ‘title’
map.world: no visible global function definition for ‘axis’
map.world: no visible global function definition for ‘box’
plot.smooth.sspline: no visible global function definition for
  ‘predict’
plot.smooth.sspline: no visible global function definition for
  ‘filled.contour’
plot.smooth.sspline: no visible binding for global variable
  ‘terrain.colors’
plot.smooth.sspline: no visible global function definition for ‘title’
plot.smooth.sspline: no visible global function definition for ‘axis’
station: no visible binding for global variable ‘WTdiff’
station: no visible global function definition for ‘points’
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
Running examples in ‘sssc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary_vcf
> ### Title: VCF Data Summary
> ### Aliases: summary_vcf
> 
> ### ** Examples
> 
> data("vcf_example")
> tmp <- summary_vcf(vcf = vcf_example, ZG = 'het', CHR = c(1,2))
> plot(tmp$scatter)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
SS.ID: no visible global function definition for ‘var’
SS.sim.chol: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm var
Consider adding
  importFrom("stats", "rnorm", "var")
to your NAMESPACE file.
error.est : <anonymous>: no visible global function definition for
  ‘median’
holm.robust: no visible global function definition for ‘pnorm’
holm.robust: no visible global function definition for ‘median’
holm.robust: no visible global function definition for ‘mad’
huberize: no visible global function definition for ‘quantile’
ssvd.initial: no visible global function definition for ‘mad’
ssvd.iter.thresh: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
Running examples in ‘stability-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ammi_biplot
> ### Title: Additive Main Effects and Multiplicative Interaction (AMMI)
> ###   Biplot
> ### Aliases: ammi_biplot ammi_biplot.default
> 
> ### ** Examples
> 
> 
> data(ge_data)
>      ammi_biplot(
+             .data = ge_data
+           , .y    = Yield
+           , .rep  = Rep
+           , .gen  = Gen
+           , .env  = Env
+       )
$aami.biplot
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘stabm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotFeatures
> ### Title: Plot Selected Features
> ### Aliases: plotFeatures
> 
> ### ** Examples
> 
> feats = list(1:3, 1:4, 1:5)
> mat = 0.92 ^ abs(outer(1:10, 1:10, "-"))
> plotFeatures(features = feats)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotFeatures ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
.expandLevels: no visible global function definition for ‘na.omit’
.ffStack: no visible global function definition for ‘na.omit’
.ffffStack: no visible global function definition for ‘na.omit’
Stack : <anonymous>: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-data.frame: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-ffdf: no visible global function definition for ‘na.omit’
ffStack,ffdf-list: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Running examples in ‘stacomiR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: report_df-class
> ### Title: Report on fishway operation
> ### Aliases: report_df-class report_df
> ### Keywords: classes
> 
> ### ** Examples
> 
> require(stacomiR)
> stacomi(gr_interface=FALSE,
+ 	login_window=FALSE,
+ 	database_expected=FALSE)
> ## An example that will work with the database installed only
> ## Not run: 
> ##D   r_df=new("report_df")
> ##D   r_df<-choice_c(r_df,
> ##D 	  1,
> ##D 	  horodatedebut="2015-01-01",
> ##D 	  horodatefin="2015-12-31",
> ##D 	  silent=TRUE)
> ##D   Sys.setenv(TZ='GMT')
> ##D   # the times at Arzal are recorded continuously
> ##D   # they are converted to date when a time appears while the hour is changing
> ##D   # hence the following
> ##D   r_df<-connect(r_df)
> ## End(Not run)
> 
> data("r_df")
> plot(r_df,plot.type="4")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘stacomir.Rmd’ using rmarkdown
Quitting from lines 308-310 (stacomir.Rmd) 
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘stacomir.Rmd’

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

Error: Vignette re-building 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.
Non-standard file/directory found at top level:
  ‘Licence’
'library' or 'require' calls to packages already attached by Depends:
  ‘np’ ‘sp’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘np’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.

Found the following calls to attach():
File ‘stam/R/stkde.sig.r’:
  attach(samdata)
See section ‘Good practice’ in ‘?attach’.
find.names: no visible global function definition for ‘na.omit’
generate.names: no visible global function definition for ‘na.omit’
standardize.countrynames: no visible global function definition for
  ‘data’
standardize.names: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Running examples in ‘staRdom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: eem_extend2largest
> ### Title: EEM sample data is extended to include all wavelengths in all
> ###   samples
> ### Aliases: eem_extend2largest
> 
> ### ** 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

> data(eem_list)
> eem_list <- eem_exclude(eem_list[1:5] %>%
+ `class<-`("eemlist"), exclude = list(em = c(318,322,326,550,438), ex = c(270,275))) %>%
+ eem_bind(eem_list[6:15] %>% `class<-`("eemlist"))
> ggeem(eem_list)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_analysis_of_DOM_samples.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

Writing 21 Bibtex entries ... OK
Results written to file 'references.bib'
--- finished re-building ‘Basic_analysis_of_DOM_samples.Rmd’

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

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 151-152 (PARAFAC_analysis_of_EEM.Rmd) 
Error: processing vignette 'PARAFAC_analysis_of_EEM.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘PARAFAC_analysis_of_EEM.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘mnlogit’
Running examples in ‘starma-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stacf
> ### Title: Space-time autocorrelation functions
> ### Aliases: stacf stpacf
> ### Keywords: starma identification diagnostic acf stacf pacf stpacf
> 
> ### ** Examples
> 
> data(nb_mat)	# Get neighbourhood matrices
> 
> # Simulate a STARMA model
> eps <- matrix(rnorm(94*200), 200, 94)
> sim <- eps
> for (t in 3:200) {
+ 	sim[t,] <- (.4*blist[[1]] + .25*blist[[2]]) %*% sim[t-1,] +
+ 		(.25*blist[[1]]                ) %*% sim[t-2,] +
+ 		(            - .3*blist[[2]]) %*% eps[t-1,] +
+ 		eps[t, ]
+ }
> 
> sim <- sim[101:200,]
> sim <- stcenter(sim)	# Center and scale the dataset
> 
> # Plot stacf and stpacf
> stacf(sim, blist)
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: stacf ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘starmie-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bestK
> ### Title: Determine a suitable K value from multiple Structure runs
> ### Aliases: bestK
> 
> ### ** Examples
> 
> multi_K <- exampleStructure("multiple_runs")
> # Run the evanno method and display diagnostic plots.
> evanno_results <- bestK(multi_K, method = "evanno")
Creating diagnostic plots for structure runs.
Error in Summary.unit(c(4.4, 4.4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: bestK -> bestK.structList -> bestK_evanno
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using-starmie-admixture.Rmd’ using rmarkdown
Quitting from lines 71-72 (using-starmie-admixture.Rmd) 
Error: processing vignette 'using-starmie-admixture.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-starmie-admixture.Rmd’

--- re-building ‘using-starmie.Rmd’ using rmarkdown
Quitting from lines 112-113 (using-starmie.Rmd) 
Error: processing vignette 'using-starmie.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-starmie.Rmd’

SUMMARY: processing the following files failed:
  ‘using-starmie-admixture.Rmd’ ‘using-starmie.Rmd’

Error: Vignette re-building failed.
Execution halted
'library' or 'require' call to ‘codetools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘codetools’ ‘gss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘starsdata’
Running examples in ‘stars-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_stars
> ### Title: ggplot geom for stars objects
> ### Aliases: geom_stars
> 
> ### ** Examples
> 
> system.file("tif/L7_ETMs.tif", package = "stars") %>% read_stars() -> x
> library(ggplot2)
> ggplot() + geom_stars(data = x) +
+     coord_equal() +
+     facet_wrap(~band) +
+     theme_void() +
+     scale_x_discrete(expand=c(0,0))+
+     scale_y_discrete(expand=c(0,0))
Error in Summary.unit(c(0, 0), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘stars1.Rmd’ using rmarkdown
--- finished re-building ‘stars1.Rmd’

--- re-building ‘stars2.Rmd’ using rmarkdown
--- finished re-building ‘stars2.Rmd’

--- re-building ‘stars3.Rmd’ using rmarkdown
Quitting from lines 105-115 (stars3.Rmd) 
Error: processing vignette 'stars3.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘stars3.Rmd’

--- re-building ‘stars4.Rmd’ using rmarkdown
--- finished re-building ‘stars4.Rmd’

--- re-building ‘stars5.Rmd’ using rmarkdown
--- finished re-building ‘stars5.Rmd’

SUMMARY: processing the following file failed:
  ‘stars3.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following hidden files and directories:
  inst/.Renviron.d
  inst/.Rprofile.d
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Running examples in ‘statar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_binmean
> ### Title: Plot the mean of y over the mean of x within bins of x.
> ### Aliases: stat_binmean
> 
> ### ** Examples
> 
> library(ggplot2)
> g <- ggplot(iris, aes(x = Sepal.Width , y = Sepal.Length)) 
> g + stat_binmean(n = 10)
Warning: Computation failed in `stat_binmean()`:
could not find function "ntile"
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘states-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: id_date_sequence
> ### Title: Identify date sequences
> ### Aliases: id_date_sequence
> 
> ### ** Examples
> 
> library("ggplot2")
> d1 <- as.Date("2018-01-01")
> d2 <- as.Date("2025-01-01")
> seq1 <- seq(d1, d2, by = "year")
> data.frame(seq1, id=id_date_sequence(seq1, "year"))
        seq1 id
1 2018-01-01  1
2 2019-01-01  1
3 2020-01-01  1
4 2021-01-01  1
5 2022-01-01  1
6 2023-01-01  1
7 2024-01-01  1
8 2025-01-01  1
> # With a gap, should be two ids
> df <- data.frame(date = seq1[-4], id=id_date_sequence(seq1[-4], "year"), cowcode = 999)
> df
        date id cowcode
1 2018-01-01  1     999
2 2019-01-01  1     999
3 2020-01-01  1     999
4 2022-01-01  2     999
5 2023-01-01  2     999
6 2024-01-01  2     999
7 2025-01-01  2     999
> 
> # The point is to plot countries with interrupted independence correctly:
> df$y <- c(rep(1, 3), rep(2, 4))
> df$id <- paste0(df$cowcode, df$id)
> df
        date   id cowcode y
1 2018-01-01 9991     999 1
2 2019-01-01 9991     999 1
3 2020-01-01 9991     999 1
4 2022-01-01 9992     999 2
5 2023-01-01 9992     999 2
6 2024-01-01 9992     999 2
7 2025-01-01 9992     999 2
> ggplot(df, aes(x = date, y = y, group = cowcode)) + geom_line()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
inspect: no visible global function definition for ‘par’
inspect: no visible global function definition for ‘abline’
inspect: no visible global function definition for ‘lines’
inspect: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘dev.off’
plotfit: no visible global function definition for ‘par’
plotfit: no visible global function definition for ‘lines’
plotfit: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘legend’
plothill: no visible global function definition for ‘par’
plothill: no visible global function definition for ‘abline’
plothill: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘par’
plotmultifit: no visible global function definition for ‘lines’
plotmultifit: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘pexp’
plotmultifit: no visible global function definition for ‘plnorm’
plotmultifit: no visible global function definition for ‘ppois’
plotmultifit: no visible global function definition for ‘legend’
plotols: no visible global function definition for ‘dev.off’
plotols: no visible global function definition for ‘lm’
plotols: no visible global function definition for ‘par’
plotols: no visible global function definition for ‘abline’
plotols: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
Running examples in ‘StatRank-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Visualization.Empirical
> ### Title: RPD Visualization
> ### Aliases: Visualization.Empirical
> 
> ### ** Examples
> 
> library(ggplot2)
> library(gridExtra)
> data(Data.Test)
> Visualization.Empirical(Data.Test, 0.5)
Warning: Removed 1 rows containing missing values (position_stack).
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: Visualization.Empirical ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Get_started_with_statsDK.Rmd’ using rmarkdown

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'lubridate'

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

    date

Tables collected succesfully
Quitting from lines 109-120 (Get_started_with_statsDK.Rmd) 
Error: processing vignette 'Get_started_with_statsDK.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Get_started_with_statsDK.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bandit_posterior
> ### Title: bandit posterior
> ### Aliases: bandit_posterior
> 
> ### ** Examples
> 
> data = data.frame(machine = c(1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L), 
+                   outcome = c("W", "L", "W", "L", "L", "W", "L", "L", "L", "W"))
> bandit_posterior(data)
m1_good m2_good 
    0.5     0.5 
> plot_bandit_posterior(data)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
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.
Stem.Bootstrap: no visible global function definition for ‘runif’
filtering: no visible global function definition for ‘is.ts’
filtering: no visible global function definition for ‘ts’
filtering: no visible global function definition for ‘start’
filtering: no visible global function definition for ‘end’
filtering: no visible global function definition for ‘frequency’
kalman: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘is.ts’
smoothing: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘start’
smoothing: no visible global function definition for ‘end’
smoothing: no visible global function definition for ‘frequency’
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
d1spectrum: no visible global function definition for ‘fft’
d2spectrum: no visible global function definition for ‘fft’
plot.d1nat: no visible global function definition for ‘plot’
plot.d1nat: no visible global function definition for ‘lines’
plot.d1nat: no visible global function definition for ‘legend’
plot.d1nat: no visible global function definition for ‘title’
plot.d1spec: no visible global function definition for ‘plot’
plot.d1spec: no visible global function definition for ‘lines’
plot.d1spec: no visible global function definition for ‘legend’
plot.d1spec: no visible global function definition for ‘title’
plot.d2spec: no visible global function definition for ‘plot’
plot.d2spec: no visible global function definition for ‘lines’
plot.d2spec: no visible global function definition for ‘legend’
plot.d2spec: no visible global function definition for ‘title’
plot.pvalign: no visible global function definition for ‘plot’
plot.pvalign: no visible global function definition for ‘lines’
plot.pvalign: no visible global function definition for ‘legend’
plot.pvalign: no visible global function definition for ‘title’
print.d1nat: no visible global function definition for ‘plot’
print.d1spec: no visible global function definition for ‘plot’
print.d2spec: no visible global function definition for ‘plot’
print.pvalign: no visible global function definition for ‘plot’
utild1bin: no visible global function definition for ‘median’
utild1bin: no visible global function definition for ‘sd’
utild1clean: no visible global function definition for ‘sd’
utild1filt: no visible global function definition for ‘convolve’
Undefined global functions or variables:
  convolve fft legend lines median plot sd title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "title")
  importFrom("stats", "convolve", "fft", "median", "sd")
to your NAMESPACE file.
Running examples in ‘stminsights-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_effects
> ### Title: extract stm effect estimates
> ### Aliases: get_effects
> 
> ### ** Examples
> 
> 
> library(stm)
stm v1.3.3 (2018-1-26) successfully loaded. See ?stm for help. 
 Papers, resources, and other materials at structuraltopicmodel.com
> 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(ggplot2)
> 
> # store effects
> prep <- estimateEffect(1:3 ~ treatment + pid_rep, gadarianFit, gadarian)
> 
> effects <- get_effects(estimates = prep,
+                       variable = 'treatment',
+                       type = 'pointestimate')
> 
> 
> # plot effects
> effects %>% filter(topic == 3) %>%
+ ggplot(aes(x = value, y = proportion)) +
+  geom_errorbar(aes(ymin = lower, ymax = upper), width = 0.1, size = 1) +
+  coord_flip() + theme_light() + labs(x = 'Treatment', y = 'Topic Proportion')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘STMotif-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: displayPlotSeries
> ### Title: Plot spatial series by selected columns
> ### Aliases: displayPlotSeries
> 
> ### ** Examples
> 
> #Launch all the workflow
> #Plot the result
> D  <- STMotif::example_dataset
> DS <- NormSAX(STMotif::example_dataset,7)
> stmotifs <- SearchSTMotifs(D,DS,3,7,10,10,3,7)
> rstmotifs <- RankSTMotifs(stmotifs)
> displayPlotSeries(dataset = D, rmotifs = rstmotifs ,position = 1 ,space = c(1,2,5:7))
Error in Summary.unit(c(4, 4), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘discovery-motifs.Rmd’ using rmarkdown
--- finished re-building ‘discovery-motifs.Rmd’

--- re-building ‘examples.Rmd’ using rmarkdown
Quitting from lines 84-86 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘examples.Rmd’

--- re-building ‘normalization-and-sax.Rmd’ using rmarkdown
--- finished re-building ‘normalization-and-sax.Rmd’

--- re-building ‘search-stmotifs.Rmd’ using rmarkdown
--- finished re-building ‘search-stmotifs.Rmd’

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

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Linking to GEOS 3.7.1, GDAL 2.4.0, PROJ 5.2.0
Quitting from lines 237-261 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Details.Rmd’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 77-78 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Overview.Rmd’

SUMMARY: processing the following files failed:
  ‘Details.Rmd’ ‘Overview.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rinfec
> ### Title: Generate infection point patterns
> ### Aliases: rinfec
> 
> ### ** Examples
> 
> # inhibition; spatial distribution: uniform
> inf1 = rinfec(npoints=100, alpha=0.2, beta=0.6, gamma=0.5,
+ maxrad=c(0.075,0.5), t.region=c(0,50), s.distr="uniform", 
+ t.distr="uniform", h="gaussian", p="min", recent="all", t0=0.02, 
+ inhibition=TRUE)
> plot(inf1$xyt, style="elegant")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
StratPhyloCongruence: no visible global function definition for ‘runif’
StratPhyloCongruence: no visible global function definition for
  ‘txtProgressBar’
StratPhyloCongruence: no visible global function definition for
  ‘setTxtProgressBar’
StratPhyloCongruence: no visible global function definition for ‘pnorm’
StratPhyloCongruence: no visible global function definition for ‘sd’
geoscalePhylo: no visible global function definition for ‘data’
geoscalePhylo: no visible global function definition for ‘par’
geoscalePhylo: no visible global function definition for ‘text’
geoscalePhylo: no visible global function definition for ‘segments’
geoscalePhylo: no visible global function definition for ‘rect’
geoscalePhylo: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  data par pnorm rect rgb runif sd segments setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "rect", "segments", "text")
  importFrom("stats", "pnorm", "runif", "sd")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Running examples in ‘strataG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sequenceLikelihoods
> ### Title: Sequence Likelihoods
> ### Aliases: sequenceLikelihoods
> 
> ### ** Examples
> 
> library(ape)
> data(dolph.haps)
> 
> sequenceLikelihoods(as.DNAbin(dolph.haps))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: sequenceLikelihoods ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘StratigrapheR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fastPairs
> ### Title: Scatterplot Matrices for large dataset
> ### Aliases: fastPairs
> 
> ### ** Examples
> 
> fastPairs(iris[1:4],bins=10)
Error in Summary.unit(c(4.8, 4.8), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘STraTUS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: draw.fully.sampled
> ### Title: For a sample with no unsampled hosts, draw the annotated
> ###   phylogeny using 'ggtree'
> ### Aliases: draw.fully.sampled
> 
> ### ** Examples
> 
> generator <- tt.generator(stratus.example.tree)
> samples <- sample.tt(generator, 1)
> draw.fully.sampled(generator, samples[[1]])
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Missing or unexported object: ‘limma::ebayes’
Running examples in ‘stripless-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: print.structured
> ### Title: Methods for structured objects.
> ### Aliases: plot.structured print.structured print.summary.structured
> ###   summary.structured
> 
> ### ** Examples
> 
> require(datasets)
> # quakes data
> #
> # Create and save plot
> out <- strucplot(lat ~ long|cut(mag,5)*cut(depth,4), data = quakes,
+   col="blue", main = "Earthquake locations, by magnitude and depth")
> 
> # Summary:
> summary(out)

  xyplot call:
xyplot(lat ~ long | cut(mag, 5) * cut(depth, 4), data = quakes, 
    col = "blue", main = "Earthquake locations, by magnitude and depth")

 Actual formula:
NULL

PLOT STRUCTURE

_Horizontal_
cut(mag, 5):  (4,4.48]  (4.48,4.96]  (4.96,5.44]  (5.44,5.92]  (5.92,6.4]

_Vertical_
cut(depth, 4):  (39.4,200]  (200,360]  (360,520]  (520,681]

> 
> # Default output -- structure legend on console only
>    print(out)

PLOT STRUCTURE

_Horizontal_
cut(mag, 5):  (4,4.48]  (4.48,4.96]  (4.96,5.44]  (5.44,5.92]  (5.92,6.4]

_Vertical_
cut(depth, 4):  (39.4,200]  (200,360]  (360,520]  (520,681]

> 
> # Add legends to the plot on either right or bottom (note partial matching)
>    print(out, legendLoc = "right")

PLOT STRUCTURE

_Horizontal_
cut(mag, 5):  (4,4.48]  (4.48,4.96]  (4.96,5.44]  (5.44,5.92]  (5.92,6.4]

_Vertical_
cut(depth, 4):  (39.4,200]  (200,360]  (360,520]  (520,681]

Error in matchData[[i]] * amount[i] : 
  non-numeric argument to binary operator
Calls: print ... <Anonymous> -> widthDetails -> widthDetails.frame -> Summary.unit
Execution halted
Package suggested but not available for checking: ‘STRaitRazoR’
breakpoints.formula: no visible global function definition for
  ‘%dopar%’
breakpoints.formula: no visible binding for global variable ‘i’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
sctest.default: no visible global function definition for ‘tail’
Undefined global functions or variables:
  %dopar% i tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘StructFDR.Rmd’ using rmarkdown
Loading required package: StructFDR
Loading required package: nlme
Loading required package: ape
Loading required package: cluster
Loading required package: dirmult
Loading required package: matrixStats
Loading required package: ggplot2
Loading required package: reshape
Quitting from lines 172-187 (StructFDR.Rmd) 
Error: processing vignette 'StructFDR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘StructFDR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
PlotHypTree: no visible global function definition for ‘browseURL’
treePValues: no visible global function definition for ‘lm’
treePValues: no visible global function definition for ‘pf’
plot,GBH-ANY: no visible binding for global variable ‘sorted.hyp’
plot,GBH-ANY: no visible binding for global variable ‘pval’
plot,GBH-ANY: no visible binding for global variable ‘group’
plot,GBH-ANY: no visible binding for global variable ‘type’
Undefined global functions or variables:
  browseURL group lm pf pval sorted.hyp type
Consider adding
  importFrom("stats", "lm", "pf")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Found the following significant warnings:
  computeQ.cpp:75:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/strum.Rcheck/00install.out’ for details.
Warning: no function found corresponding to methods exports from ‘stsm.class’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
stsm.model: no visible global function definition for ‘is.ts’
stsm.model: no visible global function definition for ‘var’
stsm.model: no visible global function definition for ‘frequency’
stsm.model: no visible global function definition for ‘na.omit’
stsm.model: no visible global function definition for ‘fft’
stsm.model: no visible global function definition for ‘new’
stsm.sgf: no visible global function definition for ‘frequency’
char2numeric,stsm: no visible global function definition for
  ‘frequency’
set.cpar,stsm: no visible global function definition for ‘validObject’
set.nopars,stsm: no visible global function definition for
  ‘validObject’
set.pars,stsm: no visible global function definition for ‘validObject’
transPars,stsm: no visible global function definition for ‘var’
Undefined global functions or variables:
  fft frequency is.ts na.omit new validObject var
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "fft", "frequency", "is.ts", "na.omit", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.