File ‘fastcmh/libs/fastcmh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastdigest/libs/fastdigest.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.9Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Namespace in Imports field not imported from: ‘RobustGaSP’
  All declared Imports should be used.
installed size is 39.4Mb
  sub-directories of 1Mb or more:
    libs  39.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
File ‘FastGP/libs/FastGP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.0Mb
File ‘fastmatch/libs/fastmatch.so’:
  Found non-API call to R: ‘match5’
File ‘fastmatch/libs/fastmatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-clang/FastRWeb.Rcheck/00install.out’ for details.
Output from running autoreconf:
  configure.ac:36: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/c.m4:1444: AC_C_BIGENDIAN is expanded from...
  configure.ac:36: the top level
  configure.ac:36: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/c.m4:1444: AC_C_BIGENDIAN is expanded from...
  configure.ac:36: the top level
  configure.ac:36: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/c.m4:1444: AC_C_BIGENDIAN is expanded from...
  configure.ac:36: the top level
  configure.ac:36: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2590: _AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2606: AC_COMPILE_IFELSE is expanded from...
  ../../lib/autoconf/c.m4:1444: AC_C_BIGENDIAN is expanded from...
  configure.ac:36: the top level
Note: information on .o files is not available
File ‘FastRWeb/libs/null.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fastSOM/libs/fastSOM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fasttime/libs/fasttime.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘whisker’
  All declared Imports should be used.
File ‘fBasics/libs/fBasics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
File ‘FBFsearch/libs/FBFsearch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 43.7Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
File ‘fdaPDE/libs/fdaPDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.6Mb
File ‘FDGcopulas/libs/FDGcopulas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FD/libs/FD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FDRreg/libs/FDRreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fdrtool/libs/fdrtool.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fechner/libs/fechner.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rvest’ ‘stringi’
  All declared Imports should be used.
File ‘FFD/libs/FFD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ff/libs/ff.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Namespace in Imports field not imported from: ‘pROC’
  All declared Imports should be used.
File ‘fGarch/libs/fGarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FGSG/libs/FGSG.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FIACH/libs/FIACH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rappdirs’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘mapproj’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.0Mb
File ‘FisHiCal/libs/FisHiCal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fishMod/libs/fishMod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FitARMA/libs/FitARMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FitAR/libs/FitAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rstudioapi’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
File ‘flars/libs/flars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘flashClust/libs/flashClust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
File ‘flock/libs/flock.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
File ‘FME/libs/FME.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fmri/libs/fmri.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
File ‘fmrs/libs/fmrs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FMStable/libs/FMStable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fNonlinear/libs/fNonlinear.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
File ‘fOptions/libs/fOptions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘forensim/libs/forensim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rgeos’ ‘viridis’
  All declared Imports should be used.
File ‘fpow/libs/fpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fractional/libs/fractional.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘base’ ‘pbapply’ ‘stringr’
  All declared Imports should be used.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.4Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Found the following significant warnings:
  c_hd_mf.cpp:157:12: warning: explicitly assigning value of variable of type 'Eigen::VectorXd' (aka 'Matrix<double, Dynamic, 1>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/FRegSigCom.Rcheck/00install.out’ for details.
installed size is 64.3Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs  62.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   6.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package suggested but not available for checking: ‘dggrids’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
installed size is 40.1Mb
  sub-directories of 1Mb or more:
    libs  39.7Mb
File ‘frontiles/libs/frontiles.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
File ‘fssemR/libs/fssemR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
File ‘ftnonpar/libs/ftnonpar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘FTRLProximal/libs/FTRLProximal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fts/libs/fts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘fugeR/libs/fugeR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
File ‘FunctionalNetworks/libs/FunctionalNetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: predict.funHDDC
> ### Title: Predict new results from a funHDDC model
> ### Aliases: predict.funHDDC
> 
> ### ** Examples
> 
> ##Univariate example
>     data("trigo")
>     basis<- create.bspline.basis(c(0,1), nbasis=25)
>     z<-sample(1:100,0.8*100,replace=FALSE)
>     var1_train<-smooth.basis(argvals=seq(0,1,length.out = 100),y=t(trigo[z,1:100]),
+                              fdParobj=basis)$fd
>     var1_test<-smooth.basis(argvals=seq(0,1,length.out = 100),y=t(trigo[-z,1:100]),
+                             fdParobj=basis)$fd
> 
>     model<-funHDDC(var1_train,K=2)
      model K threshold complexity         BIC
1 AKJBKQKDK 2       0.2        103 -373,867.94

SELECTED: model  AKJBKQKDK  with  2  clusters.
Selection Criterion: BIC.
>     pred<-predict(model,var1_test)
> 
> ##Multivariate example
>     data("triangle")
>     basis<- create.bspline.basis(c(1,21), nbasis=25)
>     z<-sample(1:100,0.8*100,replace=FALSE)
>     var1_train<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[z,1:101]),
+                               fdParobj=basis)$fd
>     var1_test<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[-z,1:101]),
+                             fdParobj=basis)$fd
>     var2_train<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[z,102:202]),
+                             fdParobj=basis)$fd
>     var2_test<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[-z,102:202]),
+                             fdParobj=basis)$fd
> 
>     model<-funHDDC(list(var1_train,var2_train),K=3)
Warning in funHDDC(list(var1_train, var2_train), K = 3) :
  All models diverged.
>     pred<-predict(model,list(var1_test,var2_test))
Error in UseMethod("predict") : 
  no applicable method for 'predict' applied to an object of class "list"
Calls: predict
Execution halted
File ‘fUnitRoots/libs/fUnitRoots.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘futureheatwaves/libs/futureheatwaves.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable ‘nn’
Undefined global functions or variables:
  nn
Namespaces in Imports field not imported from:
  ‘future’ ‘utils’
  All declared Imports should be used.
File ‘gafit/libs/gafit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
File ‘GAMBoost/libs/GAMBoost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.3Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   8.4Mb
installed size is 101.2Mb
  sub-directories of 1Mb or more:
    libs  100.7Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘rstantools’
  All declared Imports should be used.
installed size is 73.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     69.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  15.6Mb
File ‘gbp/libs/gbp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gCat/libs/gCat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

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

Error: Vignette re-building failed.
Execution halted
File ‘gconcord/libs/gconcord.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GCPM/libs/GCPM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
File ‘gdmp/libs/gdmp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GEEaSPU/libs/GEEaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘geepack/libs/geepack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
File ‘gelnet/libs/gelnet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gemtc/libs/gemtc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘NMF’ ‘RColorBrewer’ ‘VennDiagram’ ‘clValid’ ‘data.table’ ‘grid’
  ‘gtools’ ‘pca3d’ ‘rmarkdown’ ‘scales’ ‘shinydashboard’ ‘shinyjs’
  ‘statmod’ ‘stringr’
  All declared Imports should be used.
Running examples in ‘geneHummus-Ex.R’ failed
The error most likely occurred in:

> ### Name: getAccessions
> ### Title: Get the acessions ids and the organism for each protein
> ###   identifier
> ### Aliases: getAccessions
> 
> ### ** Examples
> 
> prot_ids <- c("593705262", "1379669790", "357520645",  "1150156484")
> getAccessions(prot_ids)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Error in the HTTP2 framing layer
Calls: getAccessions ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
File ‘genepi/libs/genepi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
File ‘GenKern/libs/GenKern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    exdata   5.1Mb
File ‘genMOSSplus/libs/genMOSSplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘genMOSS/libs/genMOSS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘genSurv/libs/genSurv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.4Mb
File ‘geoCount/libs/geoCount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘maptools’ ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
File ‘GeoGenetix/libs/GeoGenetix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   5.7Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R         6.1Mb
    extdata   1.4Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  10.3Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Found the following assignments to the global environment:
File ‘geoR/R/auxiliar.R’:
  assign(".objfuncQQ", objfunc, pos = 1)
  assign(".bounds.list", .bounds.list, pos = 1)
  assign("madtonormalQQ", madtonormalQQ, pos = 1)
File ‘geoR/R/likGRF.R’:
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords), 
    realisations), vecdist), pos = 1)
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords), 
    realisations), vecdist), pos = 1)
  assign(".likGRF.dists.vec", lapply(split(as.data.frame(coords.c), 
    temp.list$realisations), vecdist), pos = 1)
  assign(".temp.lower.lambda", -2, pos = 1)
  assign(".temp.upper.lambda", 2, pos = 1)
File ‘geoR/R/profiles.R’:
  assign(".temp.list", list(n = n, z = data, beta.size = dim(trend)[2], 
    kappa = obj.likfit$kappa, xmat = trend, method.lik = obj.likfit$method.lik, 
    dists.lowertri = dists.vec, cov.model = obj.likfit$cov.model, 
    fix.lambda = obj.likfit$transform.info$fix.lambda, lambda = obj.likfit$lambda, 
    lower.phi = lower.phi, upper.phi = upper.phi, lower.sigmasq = lower.sigmasq, 
    phi.est = phi, tausq.rel.est = tausq.rel, tausq.est = tausq, 
    sigmasq.est = sigmasq), pos = 1)
  assign(".temp.temp.list", get(".temp.list", pos = 1), pos = 1)
  assign(".temp.list", .temp.temp.list, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
  assign(".temp.lambda", lambda, pos = 1)
File ‘geoR/R/simul.R’:
  assign("setRF", geoR2RF(cov.model = cov.model, cov.pars = cov.pars, 
    nugget = nugget, kappa = kappa, aniso.pars = aniso.pars), 
    pos = 1)
File ‘geoR/R/variofit.R’:
  assign(".temp.theta", NULL, pos = 1)
  assign(".temp.theta", theta, pos = 1)
  assign(".IND.geoR.variog.model.env", TRUE, pos = 1)
File ‘geoR/R/variogram.R’:
  assign(".variog4.nomessage", TRUE, pos = 1)
File ‘geoR/libs/geoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘utils’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bitops’ ‘data.table’ ‘dplyr’ ‘httr’
  All declared Imports should be used.
File ‘gettz/libs/gettz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  FORCE_certify.c:116:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/GFORCE.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggforce’ ‘plyr’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘GGEBiplotGUI’ ‘gge’ ‘utils’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  17.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘lazyeval’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggforce’ ‘webshot’ ‘ztable’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/gglasso.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grid’ ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘reshape2’ ‘viridisLite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘grDevices’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Formula’ ‘Hmisc’ ‘colourpicker’ ‘dplyr’ ‘ggpmisc’ ‘ggrepel’
  ‘grDevices’ ‘gridExtra’ ‘lazyeval’ ‘markdown’ ‘plotly’ ‘quantreg’
  ‘rlang’ ‘shinyjs’ ‘table1’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.0Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
Namespaces in Imports field not imported from:
  ‘reshape2’ ‘rosm’
  All declared Imports should be used.
File ‘ghyp/libs/ghyp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘GiRaF/libs/GiRaF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
File ‘GLDEX/libs/GLDEX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gld/libs/gld.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GLIDE/libs/GLIDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gllm/libs/gllm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
File ‘GLMaSPU/libs/GLMaSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
File ‘glmgraph/libs/glmgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    libs  36.0Mb
installed size is 45.3Mb
  sub-directories of 1Mb or more:
    libs  44.4Mb
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  42.0Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/glmulti.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘cplexAPI’
File ‘globalOptTests/libs/globalOptTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rworldmap’ ‘shape’
  All declared Imports should be used.
File ‘gMWT/libs/gMWT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/gnmf.Rcheck/00install.out’ for details.
File ‘gnmf/libs/gnmf.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’
File ‘gnmf/libs/gnmf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cluster’
  All declared Imports should be used.
File ‘gof/libs/gof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GPB/libs/GPB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gpclib/libs/gpclib.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gplm/libs/gplm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    4.0Mb
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    R  27.6Mb
File ‘gRain/libs/gRain.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GrammR/libs/GrammR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
File ‘graphscan/libs/graphscan.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.5Mb
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Running examples in ‘gremlin-Ex.R’ failed
The error most likely occurred in:

> ### Name: gremlin-package
> ### Title: Mixed-Effects REML Incorporating Generalized Inverses
> ### Aliases: gremlin-package _PACKAGE
> 
> ### ** Examples
> 
>   require(nadiv)
Loading required package: nadiv
>   Ainv <- makeAinv(Mrode3[-c(1:2), 1:3])$Ainv
>   mod11 <- gremlinR(WWG11 ~ sex - 1,
+ random = ~ calf,
+ data = Mrode11,
+ ginverse = list(calf = Ainv),
+ Gstart = matrix(0.2), Rstart = matrix(0.4),
+ maxit = 10, v = 2)
gremlin started:		 21:12:07 
   1 of max 10 			 21:12:07 
	EM to find next theta
Element 0.2124631 must be a symmetric matrix or a number
Error in FUN(X[[i]], ...) : 
Calls: gremlinR -> sapply -> lapply -> FUN
Execution halted
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
File ‘groupRemMap/libs/groupRemMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
File ‘growcurves/libs/growcurves.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
File ‘grr/libs/grr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gsDesign/libs/gsDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespace in Imports field not imported from: ‘rrcov’
  All declared Imports should be used.
Missing or unexported object: ‘cellWise::DetectDeviatingCells’
File ‘GSE/libs/GSE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: TSGS
> ### Title: Two-Step Generalized S-Estimator for cell- and case-wise
> ###   outliers
> ### Aliases: TSGS
> 
> ### ** Examples
> 
> set.seed(12345)
> 
> # Generate 5% cell-wise contaminated normal data
> # using a random correlation matrix with condition number 100
> x <- generate.cellcontam(n=100, p=10, cond=100, contam.size=5, contam.prop=0.05)
> 
> ## Using MLE
> slrt( cov(x$x), x$A)
[1] 69.01395
> 
> ## Using Fast-S
> slrt( rrcov:::CovSest(x$x)@cov, x$A)
[1] 44.9836
> 
> ## Using 2SGS
> slrt( TSGS(x$x)@S, x$A)
Error: 'DetectDeviatingCells' is not an exported object from 'namespace:cellWise'
Execution halted
File ‘gsmoothr/libs/gsmoothr.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gsscopu/libs/gsscopu.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gte/libs/gte.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.5Mb
File ‘GUILDS/libs/GUILDS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘urca’
  All declared Imports should be used.
File ‘GWASExactHW/libs/GWASExactHW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘GWEX/libs/GWEX.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘gwfa/libs/gwfa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘spgwr’
  All declared Imports should be used.
File ‘gyriq/libs/gyriq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 125.2Mb
  sub-directories of 1Mb or more:
    java  123.3Mb
File ‘hapassoc/libs/hapassoc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HapEstXXR/libs/HapEstXXR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Found the following significant warnings:
  HARDataCreationC.cpp:19:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/HARModel.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [28s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(harvestr)
  > foreach::registerDoSEQ()
  > test_check("harvestr")
  ── 1. Failure: caching in reap with long sample (@test-caching.R#76)  ──────────
  all(t2[1] <= t1[1]) isn't true.
  
  ── 2. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42)  
  RNGkind() not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  ── 3. Failure: gather replaces seed. (@test-gather.R#57)  ──────────────────────
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ── 4. Failure: get.seed retrieves properly (@test-seeds.R#14)  ─────────────────
  `seed` not identical to `eseed`.
  Mean relative difference: 0.9608917
  
  ── 5. Failure: replace.seed (@test-seeds.R#29)  ────────────────────────────────
  `k` not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ── 6. Failure: replace.seed (@test-seeds.R#30)  ────────────────────────────────
  `l` not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  ── 7. Failure: withseed replaces previous seed. (@test-seeds.R#56)  ────────────
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 118 SKIPPED: 5 FAILED: 7
  1. Failure: caching in reap with long sample (@test-caching.R#76) 
  2. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42) 
  3. Failure: gather replaces seed. (@test-gather.R#57) 
  4. Failure: get.seed retrieves properly (@test-seeds.R#14) 
  5. Failure: replace.seed (@test-seeds.R#29) 
  6. Failure: replace.seed (@test-seeds.R#30) 
  7. Failure: withseed replaces previous seed. (@test-seeds.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘hashFunction/libs/hashFunction.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
File ‘hashr/libs/hashr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hawkes/libs/hawkes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data  10.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   1.3Mb
File ‘HDGLM/libs/HDGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hdlm/libs/hdlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
File ‘HDtweedie/libs/HDtweedie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Found the following significant warnings:
  indiv-ctstm.cpp:35:15: warning: explicitly assigning value of variable of type 'std::vector<int>' to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/hesim.Rcheck/00install.out’ for details.
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs  19.7Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘purrr’ ‘tidyverse’
  All declared Imports should be used.
File ‘HiCseg/libs/HiCseg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HiDimDA/libs/HiDimDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hierarchicalSets/libs/hierarchicalSets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hierband/libs/hierband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hier.part/libs/hier.part.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.0Mb
File ‘highD2pop/libs/highD2pop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        7.4Mb
File ‘hillmakeR/libs/hillmakeR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hint/libs/hint.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘HI/libs/HI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.2Mb
File ‘hit/libs/hit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hkevp/libs/hkevp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HKprocess/libs/HKprocess.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HLMdiag/libs/HLMdiag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   3.7Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’
  All declared Imports should be used.
File ‘HotDeckImputation/libs/HotDeckImputation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
Found the following significant warnings:
  sar.cpp:210:32: warning: explicitly assigning value of variable of type 'arma::sp_mat' (aka 'SpMat<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/HSAR.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   2.5Mb
File ‘hSDM/libs/hSDM.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.o’
File ‘hSDM/libs/hSDM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hsmm/libs/hsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘hsphase/libs/hsphase.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘htdp/libs/htdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  language.c:41:5: warning: flexible array initialization is a GNU extension [-Wgnu-flexible-array-initializer]
See ‘/data/gannet/ripley/R/packages/tests-clang/htmltidy.Rcheck/00install.out’ for details.
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data  12.1Mb
    doc    2.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
File ‘humaniformat/libs/humaniformat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
File ‘HUM/libs/HUM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   4.9Mb
File ‘HWxtest/libs/HWxtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘HybridMC/libs/HybridMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
File ‘hyphenatr/libs/hyphenatr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘ggplot2’ ‘pander’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.0Mb
File ‘iBATCGH/libs/iBATCGH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ibdreg/libs/ibdreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  IBDsim.c:27:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:39:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:54:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:61:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/IBDsim.Rcheck/00install.out’ for details.
Running examples in ‘IBDsim-Ex.R’ failed
The error most likely occurred in:

> ### Name: oneLocusIBD
> ### Title: Estimating pairwise IBD coefficients
> ### Aliases: oneLocusIBD
> ### Keywords: math
> 
> ### ** Examples
> 
> ### Example 1: Full siblings
> x <- nuclearPed(2) 
> Nsim <- 100 # Should be increased substantially
> 
> # Autosomal kappa: Estimate vs exact 
> k_est = oneLocusIBD(x, ind1=3, ind2=4, Nsim=Nsim, seed=123)
---------------
Performing unconditional simulation
Mode: autosomal 
Recombination model: haldane (poisson process) 
Number of simulations: 100 
Simulation finished. Time used: 0.041 seconds
---------------
IBD analysis finished. Total time used: 0.044 seconds.
> k_exact = c(0.25, 0.5, 0.25)
> stopifnot(all(round(k_est - k_exact, 1) == 0))
Error: all(round(k_est - k_exact, 1) == 0) is not TRUE
Execution halted
File ‘ibmcraftr/libs/ibmcraftr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ibm/libs/ibm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Iboot/libs/Iboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Registration problems:
  symbol ‘nom1’ in the local frame:
   .C(nom1, as.double(xord), as.integer(length(xord)), as.double(yord), 
       as.double(gridbw), as.integer(length(gridbw)), as.integer(effold), 
       as.integer(neffold), double(length(gridbw)), double(length(gridbw)))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1))
  symbol ‘nom2’ in the local frame:
   .C(nom2, as.double(x), as.integer(n), as.double(y), as.double(bandwidth), 
       as.double(x), as.integer(n), double(n), double(1), double(n))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1))
  symbol ‘nom’ in the local frame:
   .C(nom, as.double(x), as.integer(length(x)), as.double(y), as.double(object$bandwidth), 
       as.double(newdata), as.integer(length(newdata)), double(length(newdata)), 
       double(1), double(length(newdata)))
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
File ‘iBST/libs/iBST.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
File ‘icapca/libs/icapca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    R     14.5Mb
    doc    4.8Mb
    libs   9.8Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
File ‘icensmis/libs/icensmis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ICE/libs/ICE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  RccpSource_.cpp:978:54: warning: explicitly assigning value of variable of type 'Rcpp::NumericVector' (aka 'Vector<14>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/icosa.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.4Mb
installed size is 64.8Mb
  sub-directories of 1Mb or more:
    libs  63.7Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gtools’ ‘maxLik’
  All declared Imports should be used.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  24.3Mb
File ‘identity/libs/identity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
File ‘ieeeround/libs/ieeeround.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ifa/libs/ifa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ifctools/libs/ifctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘IFP/libs/IFP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ifs/libs/ifs.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.1Mb
File ‘IHSEP/libs/IHSEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 43.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.3Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     31.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Found the following significant warnings:
  IM4ECpp.cpp:24:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:22:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:32:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/Immigrate.Rcheck/00install.out’ for details.
File ‘imputeMDR/libs/imputeMDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
File ‘imputeMulti/libs/imputeMulti.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘IM/libs/IM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘V8’ ‘assertive’ ‘shinydashboard’
  All declared Imports should be used.
File ‘inarmix/libs/inarmix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
File ‘IndependenceTests/libs/IndependenceTests.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Running ‘testthat.R’ [14s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(infer)
  > 
  > test_check("infer")
  Setting `type = "permute"` in `generate()`.
  ── 1. Failure: conf_int argument works (@test-wrappers.R#141)  ─────────────────
  no_var_equal == var_equal isn't false.
  
  ── 2. Failure: conf_int argument works (@test-wrappers.R#153)  ─────────────────
  shortcut_no_var_equal == shortcut_var_equal isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 347 SKIPPED: 0 FAILED: 2
  1. Failure: conf_int argument works (@test-wrappers.R#141) 
  2. Failure: conf_int argument works (@test-wrappers.R#153) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘influenceR/libs/influenceR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘infotheo/libs/infotheo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘INSPIRE/libs/INSPIRE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
File ‘Interact/libs/Interact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
File ‘intervals/libs/intervals.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘iotools/libs/iotools.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_ReadConnection’,
    ‘R_WriteConnection’
File ‘iotools/libs/iotools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   7.5Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘expm’
  All declared Imports should be used.
File ‘ipfp/libs/ipfp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘RcmdrPlugin.IPSUR’ ‘TeachingDemos’ ‘actuar’ ‘aplpack’
  ‘binom’ ‘boot’ ‘coin’ ‘distrEx’ ‘e1071’ ‘lmtest’ ‘mvtnorm’ ‘prob’
  ‘qcc’ ‘reshape’ ‘scatterplot3d’ ‘vcd’
  All declared Imports should be used.
File ‘iRafNet/libs/iRafNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘irr’
  All declared Imports should be used.
File ‘ISBF/libs/ISBF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
File ‘isingLenzMC/libs/isingLenzMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘IsingSampler/libs/IsingSampler.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   6.1Mb
File ‘isocir/libs/isocir.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Iso/libs/Iso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ISR3/libs/ISR3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘comtradr’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'gurobi', 'Rcplex', 'cplexAPI'
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
File ‘JAGUAR/libs/JAGUAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(janitor)
  > 
  > test_check("janitor")
  ── 1. Failure: users can supply own Ns (@test-adorn-ns.R#129)  ─────────────────
  `%>%`(...) not equal to data.frame(...).
  Component "big": 2 string mismatches
  Component "small": 2 string mismatches
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 438 SKIPPED: 0 FAILED: 1
  1. Failure: users can supply own Ns (@test-adorn-ns.R#129) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘MASS’ ‘ggExtra’ ‘ggplot2’ ‘grid’ ‘gridExtra’ ‘mcmcplots’
  All declared Imports should be used.
File ‘JASPAR/libs/JASPAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Output from running autoreconf:
  configure.ac:103: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
  configure.ac:103: the top level
  configure.ac:103: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
  configure.ac:103: the top level
  configure.ac:103: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
  configure.ac:103: the top level
  configure.ac:103: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
  ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from...
  ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from...
  ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from...
  configure.ac:103: the top level
Non-standard files/directories found at top level:
  ‘getsp.class’ ‘getsp.java’ ‘version’
File ‘JavaGD/libs/JavaGD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘BurStFin’ ‘MASS’ ‘fAssets’ ‘timeDate’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.0Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’
  ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
':::' calls which should be '::':
  ‘jmvcore:::decomposeFormula’ ‘jmvcore:::enquo’
  ‘jmvcore:::marshalData’ ‘jmvcore:::marshalFormula’
  ‘jmvcore:::resolveQuo’
  See the note in ?`:::` about the use of this operator.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.8Mb
Found the following significant warnings:
  jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/jomo.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
File ‘jpeg/libs/jpeg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘JRF/libs/JRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      4.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File ‘kappalab/libs/kappalab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kaps/libs/kaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stinepack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EQL’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   8.8Mb
File ‘Kendall/libs/Kendall.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
File ‘KERE/libs/KERE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
File ‘KernSmoothIRT/libs/KernSmoothIRT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘KFKSDS/libs/KFKSDS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kissmig/libs/kissmig.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kknn/libs/kknn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kml/libs/kml.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘kmlShape/libs/kmlShape.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘knncat/libs/knncat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.9Mb
File ‘kolmim/libs/kolmim.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
File ‘kriging/libs/kriging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.7Mb
Namespace in Imports field not imported from: ‘usethis’
  All declared Imports should be used.
File ‘ktspair/libs/ktspair.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  13.7Mb
File ‘labdsv/libs/labdsv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
File ‘LakeMetabolizer/libs/LakeMetabolizer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/LambertW.Rcheck/00install.out’ for details.
File ‘LambertW/libs/LambertW.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LANDD/libs/LANDD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
Namespaces in Imports field not imported from:
  ‘collections’ ‘repr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    2.4Mb
    help   1.1Mb
File ‘lars/libs/lars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lassoshooting/libs/lassoshooting.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
File ‘lbfgsb3/libs/lbfgsb3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lbfgs/libs/lbfgs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lbiassurv/libs/lbiassurv.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: LCA
> ### Title: Localised Co-dependency Analysis
> ### Aliases: LCA
> 
> ### ** Examples
> 
> ## create a data matrix
> 
> x <- array(runif(1200),dim=c(40,12))
> 
> ## implant similarity across a 'clique'
> 
> clique.cols <- sample(ncol(x),4)
> x[,clique.cols] <- x[,clique.cols] + rnorm(nrow(x))
> 
> ## scale x to (0,1)
> 
> x[x<0] <- 0
> x[x>1] <- 1
> 
> ## choose a 'seed' feature and some partner
> 
> seed.row <- sample(nrow(x),1)
> partner.row <- sample(setdiff(c(1:nrow(x)),seed.row),1)
> 
> x[c(seed.row,partner.row),clique.cols] <- x[c(seed.row,partner.row),clique.cols] + 
+ rep(rnorm(length(clique.cols)),each=2)
> 
> ## calibrate PTL models to dataset
> 
> PTL.fit <- fitPTLmodel(x,nPairs=15)
1 models successfully fitted out of 12 
Error in fitPTLmodel(x, nPairs = 15) : 
  Rerun model calibration (possibly with higher nPairs), no successful fits this time.
Execution halted
File ‘lcopula/libs/lcopula.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lda/libs/lda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘leaderCluster/libs/leaderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘htmlwidgets’ ‘jsonlite’ ‘sf’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘leaflet’
  All declared Imports should be used.
File ‘leaps/libs/leaps.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.o’
File ‘leaps/libs/leaps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘scales’ ‘tibble’
  All declared Imports should be used.
File ‘LearningRlab/libs/LearningRlab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lgarch/libs/lgarch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: clusterCells
> ### Title: Grouping cells into clones.
> ### Aliases: clusterCells
> 
> ### ** Examples
> 
> data(cnps)
> set.seed(2)
> rcells = sample(colnames(cnps), 120)
> outc = clusterCells(cnps[apply(cnps, 1, var)>0, rcells])
[1] "Neither k nor h is set."
[1] "Using Akaike information criterion to decide number of clusters..."
Error in kmeans(t(cnps), centers = x) : 
  more cluster centers than distinct data points.
Calls: clusterCells ... sapply -> lapply -> FUN -> .kmeansAIC -> ncol -> kmeans
Execution halted
File ‘libamtrack/libs/libamtrack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LiblineaR.ACF/libs/LiblineaR.ACF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LiblineaR/libs/LiblineaR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      3.8Mb
    extdata   1.1Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘devtools’ ‘e1071’ ‘glmnet’ ‘hash’ ‘pamr’ ‘randomForest’
  All declared Imports should be used.
File ‘linERR/libs/linERR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘linkcomm/libs/linkcomm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.7Mb
File ‘listdtr/libs/listdtr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
File ‘ljr/libs/ljr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      19.5Mb
    testdata   1.6Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
File ‘lmeNBBayes/libs/lmeNBBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lmeNB/libs/lmeNB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
File ‘lmPerm/libs/lmPerm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shinyjs’
  All declared Imports should be used.
File ‘localgauss/libs/localgauss.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘checkmate’
  All declared Imports should be used.
File ‘locits/libs/locits.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘loe/libs/loe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘logconcens/libs/logconcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘logisticPCA/libs/logisticPCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘logitchoice/libs/logitchoice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LogitNet/libs/LogitNet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘loglognorm/libs/loglognorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lokern/libs/lokern.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lolR)
  > 
  > test_check("lolR")
  ── 1. Failure: Optimal Embedding Dimensions (@test-xval.R#45)  ─────────────────
  result.rs$optimal.lhat not equal to result.rs.noset$optimal.lhat.
  Lengths differ: 2 is not 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 446 SKIPPED: 0 FAILED: 1
  1. Failure: Optimal Embedding Dimensions (@test-xval.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘futile.options’ ‘ggfortify’ ‘grDevices’ ‘stats’
  All declared Imports should be used.
File ‘lorec/libs/lorec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lowmemtkmeans/libs/lowmemtkmeans.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘lpSolveAPI/libs/lpSolveAPI.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lpSolve/libs/lpSolve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LPStimeSeries/libs/LPStimeSeries.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘LRcontrast/libs/LRcontrast.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(lsbclust)
  Loading required package: ggplot2
  > 
  > test_check("lsbclust")
  K-means on overall means...	DONE
  ── 1. Failure: cluster vector (@test_orc.R#29)  ────────────────────────────────
  ovl$cluster not identical to ovltest$cluster.
  24/220 mismatches (average diff: 1.33)
  [1]    8 - 10 == -2
  [14]  10 -  9 ==  1
  [31]   9 -  8 ==  1
  [57]   9 -  8 ==  1
  [61]   8 - 10 == -2
  [64]   8 - 10 == -2
  [77]  10 -  9 ==  1
  [84]  10 -  9 ==  1
  [112]  9 -  8 ==  1
  ...
  
  ── 2. Failure: cluster means (@test_orc.R#33)  ─────────────────────────────────
  ovl$centers not equal to ovltest$centers.
  3/12 mismatches (average diff: 3.68)
  [8]  7.22 - 2.70 ==  4.52
  [9]  2.70 - 1.70 ==  1.00
  [10] 1.70 - 7.22 == -5.52
  
  K-means on row margins...	DONE
  K-means on column margins...	DONE
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 0 FAILED: 2
  1. Failure: cluster vector (@test_orc.R#29) 
  2. Failure: cluster means (@test_orc.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  40.1Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
File ‘ltbayes/libs/ltbayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ltsa/libs/ltsa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘lucr/libs/lucr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.2Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
File ‘lxb/libs/lxb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘polspline’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    TS_files     5.9Mb
    base_files   6.3Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cmprsk’ ‘colorspace’ ‘etm’ ‘fracdiff’ ‘gtable’ ‘munsell’
  ‘numDeriv’ ‘plyr’ ‘quadprog’ ‘scales’ ‘timeDate’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   5.4Mb
File ‘magree/libs/magree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
File ‘MAMSE/libs/MAMSE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Namespaces in Imports field not imported from:
  ‘Metrics’ ‘plyr’ ‘tidyr’
  All declared Imports should be used.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is 40.1Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.5Mb
    libs         36.0Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
File ‘mapfit/libs/mapfit.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
File ‘maptpx/libs/maptpx.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘betareg’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
File ‘marqLevAlg/libs/marqLevAlg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   9.4Mb
File ‘mateable/libs/mateable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘matie/libs/matie.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MAT/libs/MAT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
File ‘MaXact/libs/MaXact.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘effsize’ ‘psych’
  All declared Imports should be used.
File ‘mbrglm/libs/mbrglm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mcclust/libs/mcclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.2Mb
File ‘mcemGLM/libs/mcemGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is 38.4Mb
  sub-directories of 1Mb or more:
    libs  37.4Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
File ‘mco/libs/mco.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mcr/libs/mcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespace in Imports field not imported from: ‘mds’
  All declared Imports should be used.
File ‘meboot/libs/meboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
File ‘MediaK/libs/MediaK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
File ‘MEET/libs/MEET.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RGtk2’ ‘RNifti’ ‘cairoDevice’ ‘gtools’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘foreign’ ‘formattable’ ‘ggplot2’
  ‘haven’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’ ‘shinydashboard’
  ‘shinydashboardPlus’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’
  ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.3Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Running examples in ‘metacart-Ex.R’ failed
The error most likely occurred in:

> ### Name: FEmrt
> ### Title: Fixed effect meta-tree
> ### Aliases: FEmrt
> 
> ### ** Examples
> 
> data(dat.BCT2009)
> FEtree <- FEmrt(g ~ T1 + T2+ T4 + T25, vi = vi, data = dat.BCT2009, c = 0.5)
Warning in FEmrt(g ~ T1 + T2 + T4 + T25, vi = vi, data = dat.BCT2009, c = 0.5) :
  no moderator effect was detected
> print(FEtree)

Fixed Effects Meta-Tree (K = 106 studies); 
FEmrt(formula = g ~ T1 + T2 + T4 + T25, data = dat.BCT2009, vi = vi, 
    c = 0.5)

No moderator effect was detected
use summary() to see the meta-analysis results> summary(FEtree)

Fixed Effects meta-tree (K = 106 studies); 
FEmrt(formula = g ~ T1 + T2 + T4 + T25, data = dat.BCT2009, vi = vi, 
    c = 0.5)

No moderator effect was detected

Test for Heterogeneity under FE assumption:
Q = 253.0357 (df = 105), p-value < 1e-04;

Fixed Effect Meta-analysis Results:
   no.      g     se   zval   pval  ci.lb  ci.ub        
   106  0.229  0.012 18.803  0.000  0.206  0.253    *** 
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 

> plot(FEtree)
Error in `rownames<-`(`*tmp*`, value = rank(as.numeric(rownames(frame)))) : 
  attempt to set 'rownames' on an object with no dimensions
Calls: plot -> plot.FEmrt -> rownames<-
Execution halted
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘reshape’ ‘svglite’
  All declared Imports should be used.
File ‘metafolio/libs/metafolio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MetaheuristicFPA/libs/MetaheuristicFPA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘DT’ ‘GEOmetadb’ ‘RMySQL’ ‘RSQLite’ ‘gplots’ ‘pheatmap’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘shiny’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
File ‘MetaSKAT/libs/MetaSKAT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 56.8Mb
  sub-directories of 1Mb or more:
    libs  56.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
Found the following significant warnings:
  binomial-twostage.cpp:78:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  binomial-twostage.cpp:280:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/mets.Rcheck/00install.out’ for details.
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.1Mb
    libs  18.3Mb
    misc   1.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File ‘mewAvg/libs/mewAvg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mgarchBEKK/libs/mgarchBEKK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MGL/libs/MGL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MGSDA/libs/MGSDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  18.9Mb
File ‘mhsmm/libs/mhsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘copula’
  All declared Imports should be used.
File ‘mht/libs/mht.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
File ‘microclass/libs/microclass.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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’
File ‘MigClim/libs/MigClim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘FactoMineR’ ‘softImpute’
  All declared Imports should be used.
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘jpeg’
  All declared Imports should be used.
File ‘minpack.lm/libs/minpack.lm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.7Mb
File ‘misclassGLM/libs/misclassGLM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MiSPU/libs/MiSPU.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/missDeaths.Rcheck/00install.out’ for details.
installed size is 44.6Mb
  sub-directories of 1Mb or more:
    libs  42.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File ‘MixedDataImpute/libs/MixedDataImpute.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mixedMem/libs/mixedMem.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mixexp/libs/mixexp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rjags’
  All declared Imports should be used.
File ‘mkde/libs/mkde.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘foreach’
  All declared Imports should be used.
File ‘mlbench/libs/mlbench.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘iterators’ ‘parallel’
  All declared Imports should be used.
File ‘MLEcens/libs/MLEcens.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mlmc/libs/mlmc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mlmmm/libs/mlmmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mlogitBMA/libs/mlogitBMA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.0Mb
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘matlib’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘caret’ ‘datasets’ ‘e1071’ ‘nnet’ ‘shiny’ ‘stats’
  All declared Imports should be used.
File ‘mnormpow/libs/mnormpow.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mnormt/libs/mnormt.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rmisc’ ‘amap’ ‘fields’ ‘matrixStats’ ‘mco’ ‘miscTools’ ‘plyr’
  ‘reshape2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bazar’
  All declared Imports should be used.
File ‘ModelGood/libs/ModelGood.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lattice’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.8Mb
    libs   3.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Running ‘testthat.R’ [57s/80s]
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
File ‘MonetDB.R/libs/MonetDB.R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ratelimitr’
  All declared Imports should be used.
File ‘monreg/libs/monreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.7Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.8Mb
File ‘mpbart/libs/mpbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mpmi/libs/mpmi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘mp/libs/mp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
File ‘MRCE/libs/MRCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
File ‘MRH/libs/MRH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mRm/libs/mRm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’
File ‘MRwarping/libs/MRwarping.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘msda/libs/msda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
Packages required but not available: 'mzR', 'xcms'

Depends: includes the non-default packages:
  'amap', 'clValid', 'cluster', 'fpc', 'mzR', 'xcms'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

Package suggested but not available for checking: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
installed size is 43.4Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
File ‘MSGLasso/libs/MSGLasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘msgps/libs/msgps.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘amap’
  All declared Imports should be used.
File ‘MTS/libs/MTS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘capushe’ ‘shiny’
  All declared Imports should be used.
File ‘muhaz/libs/muhaz.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
File ‘MultiBD/libs/MultiBD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘MultiCNVDetect/libs/MultiCNVDetect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cowsay’
  All declared Imports should be used.
File ‘multicool/libs/multicool.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 108.1Mb
  sub-directories of 1Mb or more:
    libs  107.8Mb
Namespace in Imports field not imported from: ‘igraphdata’
  All declared Imports should be used.
File ‘multinomRob/libs/multinomRob.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘multispatialCCM/libs/multispatialCCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘webshot’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Package unavailable to check Rd xrefs: ‘glmulti’
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File ‘MVB/libs/MVB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mvcluster/libs/mvcluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mvnmle/libs/mvnmle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘mvrtn/libs/mvrtn.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
File ‘namespace/libs/namespace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘stats’
  All declared Imports should be used.
File ‘nanop/libs/nanop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘nbpMatching/libs/nbpMatching.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NBPSeq/libs/NBPSeq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘bookdown’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Deriv’ ‘compiler’ ‘stringi’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
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’
File ‘NeatMap/libs/NeatMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘igraph’ ‘rlang’ ‘tidyselect’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘igraph’
  All declared Imports should be used.
File ‘netcoh/libs/netcoh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NetComp/libs/NetComp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘mvrtn’
  All declared Imports should be used.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   6.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
File ‘NetPreProc/libs/NetPreProc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.1Mb
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
File ‘networksis/libs/networksis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘networkTomography/libs/networkTomography.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
File ‘neuroim/libs/neuroim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘lme4’ ‘stringi’
  All declared Imports should be used.
File ‘neuRosim/libs/neuRosim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
File ‘nice/libs/nice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ProjectTemplate’ ‘devtools’ ‘plyr’ ‘survival’
  All declared Imports should be used.
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              5.7Mb
    classic-bugs   1.6Mb
    include        5.8Mb
    libs          16.8Mb
    tests          1.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Namespaces in Imports field not imported from:
  ‘PreciseSums’ ‘numDeriv’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Namespace in Imports field not imported from: ‘deSolve’
  All declared Imports should be used.
File ‘nmfgpu4R/libs/nmfgpu4R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘uroot’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RPostgreSQL’ ‘lwgeom’
  All declared Imports should be used.
File ‘nnls/libs/nnls.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
File ‘noncompliance/libs/noncompliance.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘e1071’ ‘pROC’ ‘purrr’ ‘randomForest’ ‘rlang’
  All declared Imports should be used.
File ‘nontarget/libs/nontarget.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘norm2/libs/norm2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc   8.6Mb
File ‘norm/libs/norm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘NORMT3/libs/NORMT3.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘not/libs/not.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ./SpecialFunctions.h:122:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:153:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:154:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:155:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:197:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./SpecialFunctions.h:198:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/data/gannet/ripley/R/packages/tests-clang/NPBayesImputeCat.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
File ‘NPsimex/libs/NPsimex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘npsp/libs/npsp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘npst/libs/npst.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘xgboost’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’ ‘base’ ‘graphics’ ‘parallel’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘rlang’ ‘tidyverse’ ‘tsibble’
  All declared Imports should be used.
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs  15.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Note: found 13172 marked Latin-1 strings
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.8Mb
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())
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
File ‘oai/libs/oai.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘obliclus/libs/obliclus.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’
File ‘obliclus/libs/obliclus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R            1.5Mb
    test_files   4.2Mb
File ‘OceanView/libs/OceanView.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.5Mb
    help   2.4Mb
    libs   3.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 84.2Mb
  sub-directories of 1Mb or more:
    libs  83.7Mb
File ‘olctools/libs/olctools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘onlinePCA/libs/onlinePCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ontologySimilarity/libs/ontologySimilarity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.8Mb
installed size is 172.4Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    libs    162.3Mb
    models    4.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
File ‘OptGS/libs/OptGS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘OptHedging/libs/OptHedging.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.1Mb
Namespaces in Imports field not imported from:
  ‘boot’ ‘splines’
  All declared Imports should be used.
File ‘optpart/libs/optpart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘orca/libs/orca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Running ‘testthat.R’ [34s/29s]
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")
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ── 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’
File ‘OriGen/libs/OriGen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ORMDR/libs/ORMDR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
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.
File ‘orQA/libs/orQA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
File ‘osDesign/libs/osDesign.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   6.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
installed size is 30.2Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
Package suggested but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.1Mb
Running ‘testthat.R’
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
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Namespace in Imports field not imported from: ‘iterators’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘jcolors’ ‘oompaBase’ ‘palr’ ‘pals’ ‘viridisLite’
  All declared Imports should be used.
File ‘pamr/libs/pamr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PanelCount/libs/PanelCount.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘parma/libs/parma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘parmigene/libs/parmigene.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’
File ‘parmigene/libs/parmigene.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘flexsurv’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tools’
  All declared Imports should be used.
File ‘patchDVI/libs/patchDVI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    data      2.6Mb
    doc       1.3Mb
    extdata   9.5Mb
Namespace in Imports field not imported from: ‘AnnotationDbi’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘glue’ ‘logging’ ‘purrr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘AGread’
  All declared Imports should be used.
File ‘pauwels2014/libs/pauwels2014.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PAWL/libs/PAWL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pbdDEMO/libs/pbdDEMO.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pbdNCDF4/libs/pbdNCDF4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    lib   9.2Mb
File ‘pbivnorm/libs/pbivnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
File ‘PCA4TS/libs/PCA4TS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      2.6Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   6.1Mb
Running examples in ‘pcalg-Ex.R’ failed
The error most likely occurred in:

> ### 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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
File ‘PCICt/libs/PCICt.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PCIT/libs/PCIT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘caret’
  All declared Imports should be used.
File ‘pdc/libs/pdc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pdist/libs/pdist.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
File ‘PDSCE/libs/PDSCE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Packages required but not available: 'MSnbase', 'mzR'

Package suggested but not available for checking: ‘faahKO’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  spectrum.c:707:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:715:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1606:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:63: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/Peaks.Rcheck/00install.out’ for details.
File ‘Peaks/libs/Peaks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PedCNV/libs/PedCNV.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pedigree/libs/pedigree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pedometrics/libs/pedometrics.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespace in Imports field not imported from: ‘lhs’
  All declared Imports should be used.
File ‘PenCoxFrail/libs/PenCoxFrail.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘penMSM/libs/penMSM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘peperr/libs/peperr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘perccal/libs/perccal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PerfMeas/libs/PerfMeas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘rms’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘SnowballC’ ‘cluster’ ‘graph’
  All declared Imports should be used.
File ‘pgee.mixed/libs/pgee.mixed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pGMGM/libs/pGMGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ph2bye/libs/ph2bye.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/PhaseType.Rcheck/00install.out’ for details.
File ‘PhaseType/libs/PhaseType.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘LJMA_arms.o’
File ‘PhaseType/libs/PhaseType.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘phenmod/libs/phenmod.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘jsonlite’ ‘memoise’
  All declared Imports should be used.
File ‘pheno/libs/pheno.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 37.1Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
Namespaces in Imports field not imported from:
  ‘gplots’ ‘phytools’
  All declared Imports should be used.
File ‘phyloland/libs/phyloland.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
File ‘PhyloMeasures/libs/PhyloMeasures.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespace in Imports field not imported from: ‘FrF2.catlg128’
  All declared Imports should be used.
File ‘Pijavski/libs/Pijavski.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
File ‘pirate/libs/pirate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PivotalR/libs/PivotalR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘lubridate’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.0Mb
    doc    3.0Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘stringi’
  All declared Imports should be used.
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    libs  24.5Mb
File ‘plac/libs/plac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘planar/libs/planar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘RColorBrewer’ ‘arm’ ‘epiDisplay’ ‘foreign’ ‘gbm’
  ‘grid’ ‘lattice’ ‘latticeExtra’ ‘lme4’ ‘nnet’ ‘parallel’ ‘splines’
  ‘survey’ ‘twang’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘V8’ ‘devtools’ ‘formatR’ ‘gdata’ ‘rhandsontable’ ‘shinythemes’
  ‘sqldf’
  All declared Imports should be used.
File ‘plgp/libs/plgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘pln/libs/pln.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘mixtools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.2Mb
Running examples in ‘plotrix-Ex.R’ failed
The error most likely occurred in:

> ### 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
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
File ‘plugdensity/libs/plugdensity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘plyr/libs/plyr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.9Mb
Package suggested but not available for checking: ‘enviGCMS’
Error(s) in re-building vignettes:
--- re-building ‘globalstd.Rmd’ using rmarkdown
Quitting from lines 115-119 (globalstd.Rmd) 
Error: processing vignette 'globalstd.Rmd' failed with diagnostics:
there is no package called 'enviGCMS'
--- failed re-building ‘globalstd.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Namespaces in Imports field not imported from:
  ‘GGally’ ‘PKNCA’ ‘grid’ ‘magrittr’ ‘plyr’
  All declared Imports should be used.
File ‘png/libs/png.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
File ‘poilog/libs/poilog.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘car’ ‘lubridate’
  All declared Imports should be used.
File ‘poisDoubleSamp/libs/poisDoubleSamp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘poLCA/libs/poLCA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘polyfreqs/libs/polyfreqs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      6.9Mb
    data   2.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
File ‘pop.wolf/libs/pop.wolf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
File ‘POT/libs/POT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Namespace in Imports field not imported from: ‘shinyWidgets’
  All declared Imports should be used.
Found the following significant warnings:
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/powell.Rcheck/00install.out’ for details.
File ‘powell/libs/powell.so’:
  Found ‘printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘powell.o’
File ‘powell/libs/powell.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
--- finished re-building ‘ppass_par_and_fit.Rmd’

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

Error: Vignette re-building failed.
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
File ‘PPtree/libs/PPtree.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lmtest’ ‘sandwich’
  All declared Imports should be used.
Found the following significant warnings:
  ./shared.h:67:9: warning: result of comparison of constant 2147483648 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/praznik.Rcheck/00install.out’ for details.
File ‘prclust/libs/prclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘TH.data’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘ROCR’ ‘ada’ ‘colourpicker’ ‘corrplot’ ‘e1071’ ‘flexdashboard’
  ‘kknn’ ‘neuralnet’ ‘randomForest’ ‘rattle’ ‘rpart’ ‘scatterplot3d’
  ‘shinyAce’ ‘shinyWidgets’ ‘shinydashboardPlus’ ‘shinyjs’ ‘tidyverse’
  ‘xgboost’ ‘zip’
  All declared Imports should be used.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
File ‘primes/libs/primes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  19.0Mb
File ‘ProbitSpatial/libs/ProbitSpatial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc           6.5Mb
    help          2.1Mb
    htmlwidgets   2.5Mb
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘jtools’ ‘modelr’ ‘prediction’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘clipr’ ‘desc’ ‘devtools’
  All declared Imports should be used.
File ‘profdpm/libs/profdpm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   6.4Mb
    libs      2.4Mb
Package suggested but not available for checking: ‘qtbase’
File ‘proj4/libs/proj4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘distcrete’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.4Mb
File ‘prospectr/libs/prospectr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files which contain pragma(s) suppressing diagnostics:
  ‘src/geobuf.pb.h’ ‘src/rexp.pb.h’
File ‘prototest/libs/prototest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   2.3Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘readr’
  All declared Imports should be used.
File ‘pRSR/libs/pRSR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/PSGExpress.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
File ‘pspearman/libs/pspearman.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: replacing previous import ‘loo::kfold’ by ‘rstanarm::kfold’ when loading ‘psycho’
See ‘/data/gannet/ripley/R/packages/tests-clang/psycho.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     1.7Mb
    doc   2.4Mb
File ‘ptest/libs/ptest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ptinpoly.Rcheck/00install.out’ for details.
File ‘ptinpoly/libs/ptinpoly.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    dict   5.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.5Mb
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘desctable’ ‘effects’ ‘knitr’ ‘latex2exp’ ‘lme4’ ‘nlme’
  ‘nnet’ ‘ordinal’ ‘pander’ ‘papeR’
  All declared Imports should be used.
installed size is 33.6Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
File ‘pullword/libs/pullword.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘FSA’
  All declared Imports should be used.
File ‘PWD/libs/PWD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘PWEALL/libs/PWEALL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
Found the following significant warnings:
  upwindorderedv4.c:509:50: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  upwindorderedv4.c:553:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:553:72: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/QPot.Rcheck/00install.out’ for details.
File ‘QPot/libs/QPot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’
File ‘QPot/libs/upwindorderedv4.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘purrr’ ‘rmarkdown’
  All declared Imports should be used.
File ‘qrencoder/libs/qrencoder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
File ‘QRM/libs/QRM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.8Mb
    doc       3.0Mb
    libs      1.5Mb
File ‘QuACN/libs/QuACN.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.3Mb
    libs  15.2Mb
File ‘quantreg/libs/quantreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘quantspec/libs/quantspec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   4.7Mb
File ‘QUIC/libs/QUIC.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’
File ‘QUIC/libs/QUIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’
File ‘qVarSel/libs/qVarSel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      2.9Mb
File ‘R4dfp/libs/R4dfp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘scran’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
File ‘RAD/libs/RAD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘TCIApathfinder’ ‘xfun’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
File ‘RAHRS/libs/RAHRS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    api           3.2Mb
    htmlwidgets   9.3Mb
File ‘ramsvm/libs/ramsvm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘randaes/libs/randaes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dtplyr’
  All declared Imports should be used.
File ‘randomUniformForest/libs/randomUniformForest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
File ‘Rankcluster/libs/Rankcluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RANKS/libs/RANKS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RANN.L1/libs/RANN.L1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rappdirs/libs/rappdirs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
File ‘RArcInfo/libs/RArcInfo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RaschSampler/libs/RaschSampler.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rasterKernelEstimates/libs/rasterKernelEstimates.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   5.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    etc    1.9Mb
    po     1.2Mb
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs  27.1Mb
Error(s) in re-building vignettes:
--- re-building ‘PoS_codata.Rmd’ using rmarkdown
--- finished re-building ‘PoS_codata.Rmd’

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

--- re-building ‘customizing_plots.Rmd’ using rmarkdown
Loading required package: Rcpp
This is RBesT version 1.3.7
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
Final MCMC sample equivalent to less than 1000 independent draws.
Please consider increasing the MCMC simulation size.
--- finished re-building ‘customizing_plots.Rmd’

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

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

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

--- re-building ‘variances_MAP.Rmd’ using rmarkdown
Quitting from lines 137-148 (variances_MAP.Rmd) 
Error: processing vignette 'variances_MAP.Rmd' failed with diagnostics:
dims [product 2] do not match the length of object [3]
--- failed re-building ‘variances_MAP.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘rBeta2009/libs/rBeta2009.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/Rblpapi.Rcheck/00install.out’ for details.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   6.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
File ‘rbvs/libs/rbvs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RCassandra/libs/RCassandra.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.2Mb
Running examples in ‘rcongresso-Ex.R’ failed
The error most likely occurred in:

> ### Name: fetch_despesas_deputado
> ### Title: Fetches expenditures from deputy
> ### Aliases: fetch_despesas_deputado
> 
> ### ** Examples
> 
> gastos_abel_mesquita <- fetch_despesas_deputado(id = 178957)
Error: Falha na requisicao a API dos Dados Abertos. Erro 400 ao tentar acessar: https://dadosabertos.camara.leg.br/api/v2/deputados/178957/despesas?id=178957
Execution halted
Running ‘testthat.R’ [2s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  ── 1. Error: (unknown) (@test_deputados.R#81)  ─────────────────────────────────
  argument "message" is missing, with no default
  1: skip() at testthat/test_deputados.R:81
  2: structure(list(message = message), class = c("skip", "condition"))
  
  ── 2. Error: (unknown) (@test_proposicoes.R#91)  ───────────────────────────────
  could not find function "FUN1"
  1: check_api() at testthat/test_proposicoes.R:91
  2: tryCatch(setup(), error = function(e) {
         message(e)
         return(FALSE)
     }) at testthat/test_proposicoes.R:15
  3: tryCatchList(expr, classes, parentenv, handlers)
  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5: value[[3L]](cond)
  6: message(e) at testthat/test_proposicoes.R:16
  7: withRestarts({
         signalCondition(cond)
         defaultHandler(cond)
     }, muffleMessage = function() NULL)
  8: withOneRestart(expr, restarts[[1L]])
  9: doWithOneRestart(return(expr), restart)
  
  ── 3. Error: (unknown) (@test_votacoes.R#70)  ──────────────────────────────────
  argument "message" is missing, with no default
  1: skip() at testthat/test_votacoes.R:70
  2: structure(list(message = message), class = c("skip", "condition"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 13 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_deputados.R#81) 
  2. Error: (unknown) (@test_proposicoes.R#91) 
  3. Error: (unknown) (@test_votacoes.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘introducao-rcongresso.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 36-38 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
could not find function "FUN1"
--- failed re-building ‘introducao-rcongresso.Rmd’

--- re-building ‘utilizando-fetch-proposicao.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 57-63 (utilizando-fetch-proposicao.Rmd) 
Error: processing vignette 'utilizando-fetch-proposicao.Rmd' failed with diagnostics:
could not find function "FUN1"
--- failed re-building ‘utilizando-fetch-proposicao.Rmd’

SUMMARY: processing the following files failed:
  ‘introducao-rcongresso.Rmd’ ‘utilizando-fetch-proposicao.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    corpora   7.6Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   5.6Mb
    libs      1.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
File ‘RcppBDT/libs/RcppBDT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RcppDL/libs/RcppDL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RcppEigen’
  All declared Imports should be used.
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     23.5Mb
File ‘RcppExamples/libs/RcppExamples.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RcppFaddeeva/libs/RcppFaddeeva.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 53.3Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      40.1Mb
    libs     11.0Mb
File ‘RcppMLPACK/libs/RcppMLPACK.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs      7.5Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.4Mb
    libs      4.3Mb
Registration problem:
  symbol ‘symbol’ in the local frame:
   .Call(symbol)
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
File ‘RcppXts/libs/RcppXts.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Rcsdp/libs/Rcsdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘smcure’
  All declared Imports should be used.
File ‘rDEA/libs/rDEA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/rdist.Rcheck/00install.out’ for details.
Subdirectory ‘src’ contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
File ‘Rdsdp/libs/Rdsdp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
File ‘Rdtq/libs/Rdtq.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.1Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   7.8Mb
File ‘read.dbc/libs/read.dbc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
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)
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.8Mb
Namespace in Imports field not imported from: ‘RcppRoll’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘readr’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   4.6Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  15.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘rlang’ ‘spatstat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘nnet’ ‘purrr’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘Rcplex’
File ‘relevent/libs/relevent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gWidgetstcltk’
  All declared Imports should be used.
File ‘remMap/libs/remMap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rEMM/libs/rEMM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘remote/libs/remote.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Error(s) in re-building vignettes:
--- re-building ‘rentrez_tutorial.Rmd’ using rmarkdown
Quitting from lines 296-299 (rentrez_tutorial.Rmd) 
Error: processing vignette 'rentrez_tutorial.Rmd' failed with diagnostics:
Error in the HTTP2 framing layer
--- failed re-building ‘rentrez_tutorial.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘ReorderCluster/libs/ReorderCluster.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
File ‘repolr/libs/repolr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  regalg.cpp:215:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
  regalg.cpp:454:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/resemble.Rcheck/00install.out’ for details.
File ‘resemble/libs/resemble.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘segmented’
  All declared Imports should be used.
File ‘restrictedMVN/libs/restrictedMVN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘retimes/libs/retimes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘stringdist’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘bitops’
  All declared Imports should be used.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is 46.7Mb
  sub-directories of 1Mb or more:
    libs  45.4Mb
File ‘RFgroove/libs/RFgroove.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Rfit/libs/Rfit.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
File ‘rgcvpack/libs/rgcvpack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.6Mb
File ‘rgexf/libs/rgexf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc     3.6Mb
    fonts   1.5Mb
    libs    2.5Mb
File ‘Rgnuplot/libs/Rgnuplot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: 'playwith', 'pmg'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
File ‘RGtk2Extras/libs/RGtk2Extras.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘RGtk2Extras-Ex.R’ failed
The error most likely occurred in:

> ### 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
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.5Mb
    libs   8.1Mb
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’
File ‘RGtk2/libs/RGtk2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.2Mb
File ‘RI2by2/libs/RI2by2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gWidgetsRGtk2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
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’
File ‘RInside/libs/RInside.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Rip46/libs/Rip46.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
File ‘rIsing/libs/rIsing.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘gtools’ ‘knitr’ ‘usethis’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
File ‘RJaCGH/libs/RJaCGH.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/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’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rje/libs/rje.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘coda’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘RcppProgress’ ‘magrittr’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    exe  23.8Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
File ‘rkvo/libs/rkvo.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
File ‘rlecuyer/libs/rlecuyer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    libs  50.6Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
File ‘rlm/libs/rlm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘Rlof/libs/Rlof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RLRsim/libs/RLRsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RCarb’ ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Running examples in ‘Rmagic-Ex.R’ failed
The error most likely occurred in:

> ### Name: ggplot.magic
> ### Title: Convert a MAGIC object to a data.frame for ggplot
> ### Aliases: ggplot.magic
> 
> ### ** Examples
> 
> if (reticulate::py_module_available("magic") && require(ggplot2)) {
+ 
+ data(magic_testdata)
+ data_magic <- magic(magic_testdata, genes=c("VIM", "CDH1", "ZEB1"))
+ ggplot(data_magic, aes(VIM, CDH1, colour=ZEB1)) +
+   geom_point()
+ 
+ }
Loading required package: ggplot2
Error in py_get_attr_impl(x, name, silent) : 
  AttributeError: 'module' object has no attribute 'MAGIC'
Calls: magic ... py_get_attr_or_item -> py_get_attr -> py_get_attr_impl
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    rmd   8.3Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Namespaces in Imports field not imported from:
  ‘blogdown’ ‘bookdown’ ‘bookdownplus’ ‘citr’ ‘pagedown’ ‘rticles’
  ‘tinytex’ ‘xaringan’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    libs   5.5Mb
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  36.8Mb
File ‘RMKdiscrete/libs/RMKdiscrete.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### 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: 0x9c7b660>
> 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
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
File ‘rnetcarto/libs/rnetcarto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rngSetSeed/libs/rngSetSeed.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’
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
File ‘rngwell19937/libs/rngwell19937.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doxygen   1.3Mb
    libs      3.2Mb
installed size is 89.4Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     87.2Mb
Namespace in Imports field not imported from: ‘impute’
  All declared Imports should be used.
Running ‘testthat.R’ [11s/26s]
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] 374720 - 888626 == -513906
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test_rnn.R#66) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R  11.2Mb
Found the following significant warnings:
  ./hammock.h:369:15: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/robfilter.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'illuminaHumanv3.db'
Namespace in Imports field not imported from: ‘future’
  All declared Imports should be used.
Running examples in ‘RobRex-Ex.R’ failed
The error most likely occurred in:

> ### Name: rgsOptIC.AL
> ### Title: Computation of the optimally robust IC for AL estimators
> ### Aliases: rgsOptIC.AL
> ### Keywords: robust
> 
> ### ** Examples
> 
> K <- DiscreteDistribution(1:5) # = Unif({1,2,3,4,5})
> IC1 <- rgsOptIC.AL(r = 0.1, K = K)
Found more than one class "ParamFamily" in cache; using the first, from namespace 'ROptEstOld'
Also defined by ‘distrMod’
Found more than one class "ParamFamily" in cache; using the first, from namespace 'ROptEstOld'
Also defined by ‘distrMod’
> checkIC(IC1)
Found more than one class "ParamFamily" in cache; using the first, from namespace 'ROptEstOld'
Also defined by ‘distrMod’
Error in f1(cbind(t(cond), x)) : 
  argument "f1" is missing, with no default
Calls: checkIC ... <Anonymous> -> sapply -> lapply -> FUN -> do.call -> <Anonymous>
Timing stopped at: 0.006 0.001 0.008
Execution halted
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
File ‘robustETM/libs/robustETM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘robustgam/libs/robustgam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘robustHD/libs/robustHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 31.8Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
File ‘robustloggamma/libs/robustloggamma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘robustvarComp/libs/robustvarComp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
File ‘rollply/libs/rollply.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
File ‘Rook/libs/Rook.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rootSolve/libs/rootSolve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
Running examples in ‘ROptRegTS-Ex.R’ failed
The error most likely occurred in:

> ### Name: Av1CondContIC-class
> ### Title: Conditionally centered influence curve of contamination type
> ### Aliases: Av1CondContIC-class CallL2Fam<-,Av1CondContIC-method
> ###   cent,Av1CondContIC-method cent<-,Av1CondContIC-method
> ###   clip,Av1CondContIC-method clip<-,Av1CondContIC-method
> ###   lowerCase,Av1CondContIC-method lowerCase<-,Av1CondContIC-method
> ###   neighborRadius,Av1CondContIC-method
> ###   neighborRadius<-,Av1CondContIC-method stand,Av1CondContIC-method
> ###   stand<-,Av1CondContIC-method
> ###   generateIC,Av1CondContNeighborhood,L2RegTypeFamily-method
> ###   show,Av1CondContIC-method
> ### Keywords: classes robust
> 
> ### ** Examples
> 
> IC1 <- new("Av1CondContIC")
> IC1
An object of class “Av1CondContIC” 
### name:	 conditionally centered IC for average conditional contamination neighborhoods 
Timing stopped at: 0.006 0.001 0.007
Error in f1(cbind(cond, x)) : argument "f1" is missing, with no default
Calls: <Anonymous> ... <Anonymous> -> sapply -> lapply -> FUN -> do.call -> <Anonymous>
Timing stopped at: 0 0.001 0.001
Timing stopped at: 0.07 0.002 0.113
Execution halted
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘methods’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘rstudioapi’ ‘tinytex’
  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   5.3Mb
File ‘rotations/libs/rotations.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RoughSets/libs/RoughSets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘geometry’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
File ‘rpartitions/libs/rpartitions.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.8Mb
File ‘Rphylopars/libs/Rphylopars.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.3Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘testthat’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.4Mb
Namespaces in Imports field not imported from:
  ‘ape’ ‘igraph’
  All declared Imports should be used.
File ‘rPython/libs/rPython.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rrcovNA/libs/rrcovNA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    extdata  12.8Mb
File ‘rredis/libs/rredis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  z.cpp:42:7: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/rrpack.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘data.tree’ ‘penalized’
  All declared Imports should be used.
File ‘rr/libs/rr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rsae/libs/rsae.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    dependencies  21.0Mb
File ‘rscimark/libs/rscimark.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RSclient/libs/RSclient.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘tidyselect’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘randomcoloR’
  All declared Imports should be used.
File ‘rsdepth/libs/rsdepth.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘rsgcc/libs/rsgcc.so’:
  Found ‘rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’
File ‘rsgcc/libs/rsgcc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
File ‘RSKC/libs/RSKC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is 48.9Mb
  sub-directories of 1Mb or more:
    libs  48.3Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Namespace in Imports field not imported from: ‘pkgconfig’
  All declared Imports should be used.
installed size is 154.5Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    libs  151.5Mb
installed size is 167.6Mb
  sub-directories of 1Mb or more:
    libs  165.0Mb
installed size is 80.9Mb
  sub-directories of 1Mb or more:
    libs  79.7Mb
Namespace in Imports field not imported from: ‘loo’
  All declared Imports should be used.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
File ‘RSvgDevice/libs/RSvgDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘RSVGTipsDevice/libs/RSVGTipsDevice.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    Lib  11.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    rmarkdown   5.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.0Mb
    projects   2.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Found the following significant warnings:
  getFunctions.cpp:90:16: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/RTransProb.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘memoise’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.0Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.4Mb
File ‘runjags/libs/runjags.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘RGtk2’
  All declared Imports should be used.
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  37.2Mb
File ‘rvgtest/libs/rvgtest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   2.6Mb
    libs      4.9Mb
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-clang/RVowpalWabbit.Rcheck/00install.out’ for details.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
    test  19.6Mb
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 http://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
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
File ‘rwfec/libs/rwfec.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/RWiener.Rcheck/00install.out’ for details.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  11.5Mb
Namespace in Imports field not imported from: ‘n1qn1’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs    7.6Mb
    yacas   1.5Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘subplex’
  All declared Imports should be used.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SafeBayes.Rcheck/00install.out’ for details.
File ‘SafeBayes/libs/SafeBayes.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SALES/libs/SALES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
File ‘sampling/libs/sampling.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
File ‘sanitizers/libs/sanitizers.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘tidyr’
  All declared Imports should be used.
File ‘sapa/libs/sapa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SAPP/libs/SAPP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘httr’ ‘jsonlite’
  All declared Imports should be used.
File ‘saturnin/libs/saturnin.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SAVE/libs/SAVE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘signal’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
File ‘sbfc/libs/sbfc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sBIC/libs/sBIC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbioPN/libs/sbioPN.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbmSDP/libs/sbmSDP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sbrl/libs/sbrl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SBSA/libs/SBSA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
File ‘scar/libs/scar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
File ‘SCEPtERbinary/libs/SCEPtERbinary.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
File ‘SCEPtER/libs/SCEPtER.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/scio.Rcheck/00install.out’ for details.
File ‘scio/libs/scio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shazam’
  All declared Imports should be used.
Running examples in ‘scorecardModelUtils-Ex.R’ failed
The error most likely occurred in:

> ### Name: scalling
> ### Title: Converting coefficients of logistic regression into scores for
> ###   scorecard building
> ### Aliases: scalling
> 
> ### ** Examples
> 
> data <- iris
> set.seed(11)
> data$Y <- sample(0:1,size=nrow(data),replace=TRUE)
> x <- c("Sepal.Length","Sepal.Width","Petal.Length","Petal.Width")
> iv_table_list <- iv_table(base = data,target = "Y",num_var_name = x,cat_var_name = "Species")
> num_cat <- num_to_cat(base = data,num_woe_table = iv_table_list$num_woe_table)
> log_model <- glm(Y ~ ., data = num_cat, family = "binomial")
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: glm ... model.matrix -> model.matrix.default -> contrasts<-
Execution halted
File ‘scorer/libs/scorer.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘scout/libs/scout.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
File ‘scs/libs/scs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SDDE/libs/SDDE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sde/libs/sde.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
Found the following significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SDMTools.Rcheck/00install.out’ for details.
File ‘SDMTools/libs/SDMTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sdnet/libs/sdnet.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sdprisk/libs/sdprisk.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’ ‘tidyr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/sdwd.Rcheck/00install.out’ for details.
File ‘sdwd/libs/sdwd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
File ‘SearchTrees/libs/SearchTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### 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
File ‘segmag/libs/segmag.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: 'flowMerge', 'flowClust'
Packages unavailable to check Rd xrefs: ‘flowClust’, ‘flowMerge’
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/Segmentor3IsBack.Rcheck/00install.out’ for details.
File ‘Segmentor3IsBack/libs/Segmentor3IsBack.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
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.
File ‘SEL/libs/SEL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘lavaan’ ‘psych’ ‘semPlot’ ‘semTools’ ‘shinyAce’
  All declared Imports should be used.
File ‘semver/libs/semver.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sensitivityPStrat/libs/sensitivityPStrat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.5Mb
File ‘seqCBS/libs/seqCBS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs  12.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
File ‘seqMeta/libs/seqMeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
File ‘sequences/libs/sequences.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
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.
Packages suggested but not available for checking: 'loomR', 'MAST'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    doc     11.2Mb
    libs     6.9Mb
    sqlite   1.5Mb
File ‘sgeostat/libs/sgeostat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.0Mb
Namespaces in Imports field not imported from:
  ‘parallel’ ‘plyr’
  All declared Imports should be used.
File ‘sharpeRratio/libs/sharpeRratio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘htmlwidgets’ ‘jsonlite’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘ggdendro’ ‘gridExtra’ ‘knitr’ ‘latticeExtra’ ‘msm’
  ‘plotly’ ‘shinyBS’ ‘shinydashboard’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    www   8.0Mb
Namespaces in Imports field not imported from:
  ‘CARE1’ ‘LCMCR’ ‘coda’ ‘conting’ ‘dga’ ‘future’ ‘ggplot2’ ‘ipc’
  ‘promises’ ‘reshape’ ‘shinycssloaders’ ‘testthat’
  All declared Imports should be used.
File ‘siar/libs/siar.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘coda’ ‘ellipse’ ‘viridis’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Running ‘testthat.R’ [3s/10s]
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 # 3 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
File ‘signal/libs/signal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
File ‘simFrame/libs/simFrame.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  11.2Mb
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
File ‘simplexreg/libs/simplexreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.9Mb
File ‘SimReg/libs/SimReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘BB’ ‘MASS’ ‘ggplot2’ ‘grid’ ‘triangle’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘bookdownplus’ ‘cowsay’ ‘jsonlite’ ‘pagedown’ ‘xaringan’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   6.0Mb
Namespace in Imports field not imported from: ‘mcmc’
  All declared Imports should be used.
File ‘skda/libs/skda.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.9Mb
File ‘skm/libs/skm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 39.7Mb
  sub-directories of 1Mb or more:
    libs  38.2Mb
File ‘sld/libs/sld.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
File ‘slfm/libs/slfm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SLHD/libs/SLHD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘viridisLite’
  All declared Imports should be used.
File ‘SLOPE/libs/SLOPE.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘slp/libs/slp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
File ‘smac/libs/smac.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘Boruta’ ‘DMwR’ ‘MVN’ ‘NoiseFiltersR’ ‘VIM’ ‘adaptiveGPCA’
  ‘class’ ‘clusterSim’ ‘denoiseR’ ‘discretization’ ‘imbalance’ ‘lle’
  ‘missForest’ ‘missMDA’ ‘outliers’ ‘unbalanced’
  All declared Imports should be used.
Running ‘testthat.R’
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
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SMCP.Rcheck/00install.out’ for details.
File ‘SMCP/libs/SMCP.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SMC/libs/SMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘smds/libs/smds.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [4s/27s]
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
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.4Mb
File ‘sna/libs/sna.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘ggplot2’
  All declared Imports should be used.
File ‘snipEM/libs/snipEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘snnR/libs/snnR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SnowballC/libs/SnowballC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘snpRF/libs/snpRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘snpStatsWriter/libs/snpStatsWriter.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SocialNetworks/libs/SocialNetworks.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SoDA/libs/SoDA.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘softImpute/libs/softImpute.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.2Mb
    libs   5.1Mb
File ‘som/libs/som.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘soobench/libs/soobench.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SoundexBR/libs/SoundexBR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘gtools’ ‘hashmap’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
File ‘SpaCCr/libs/SpaCCr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘spacejam/libs/spacejam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘space/libs/space.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘spacodiR/libs/spacodiR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
installed size is 31.6Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs  29.4Mb
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
Running examples in ‘spa-Ex.R’ failed
The error most likely occurred in:

> ### 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
File ‘sparcl/libs/sparcl.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparc/libs/sparc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SparseFactorAnalysis/libs/SparseFactorAnalysis.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
File ‘sparseLTSEigen/libs/sparseLTSEigen.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparsereg/libs/sparsereg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘sparseSEM/libs/sparseSEM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SparseTSCGM/libs/SparseTSCGM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘spate/libs/spate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
  ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
  ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
  All declared Imports should be used.
File ‘spatialfil/libs/spatialfil.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘spatialTailDep/libs/spatialTailDep.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  15.1Mb
File ‘SpaTimeClus/libs/SpaTimeClus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    R      5.2Mb
    doc    4.9Mb
    help   5.1Mb
    libs   2.0Mb
installed size is 27.8Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
File ‘spcr/libs/spcr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
File ‘SpeciesMix/libs/SpeciesMix.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SPECIES/libs/SPECIES.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: 'xcms', 'MAIT'

Package suggested but not available for checking: ‘rcytoscapejs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘spectral/libs/spectral.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘usethis’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘Spectrum_vignette.Rmd’ using rmarkdown
tlmgr search --file --global '/framed.sty'
TeX Live 2018 is frozen forever and will no
longer be updated.  This happens in preparation for a new release.

If you're interested in helping to pretest the new release (when
pretests are available), please read https://tug.org/texlive/pretest.html.
Otherwise, just wait, and the new release will be ready in due time.
Trying to automatically install missing LaTeX packages...
tlmgr install framed
TeX Live 2018 is frozen forever and will no
longer be updated.  This happens in preparation for a new release.

If you're interested in helping to pretest the new release (when
pretests are available), please read https://tug.org/texlive/pretest.html.
Otherwise, just wait, and the new release will be ready in due time.
tlmgr: package repository http://mirror.ox.ac.uk/sites/ctan.org/systems/texlive/tlnet (verified)
tlmgr install: package already present: framed
tlmgr path add
add_link_dir_dir: /usr/local/share/info/dir exists; not making symlink.
tlmgr search --file --global '/framed.sty'
TeX Live 2018 is frozen forever and will no
longer be updated.  This happens in preparation for a new release.

If you're interested in helping to pretest the new release (when
pretests are available), please read https://tug.org/texlive/pretest.html.
Otherwise, just wait, and the new release will be ready in due time.
! LaTeX Error: File `framed.sty' not found.

! Emergency stop.
<read *> 

Error: processing vignette 'Spectrum_vignette.Rmd' failed with diagnostics:
Failed to compile Spectrum_vignette.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See Spectrum_vignette.log for more info.
--- failed re-building ‘Spectrum_vignette.Rmd’

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

Error: Vignette re-building failed.
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.
File ‘spe/libs/spe.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  All declared Imports should be used.
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  22.0Mb
File ‘spikeslab/libs/spikeslab.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(splitstackshape)
  > 
  > test_check("splitstackshape")
  OMP: Warning #96: Cannot form a team with 24 threads, using 2 instead.
  OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
  ── 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
File ‘splus2R/libs/splus2R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
File ‘SPODT/libs/SPODT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   8.0Mb
Namespaces in Imports field not imported from:
  ‘extrafont’ ‘ggplot2’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  12.8Mb
Namespaces in Imports field not imported from:
  ‘BayesX’ ‘BayesXsrc’ ‘automap’ ‘plyr’ ‘rgdal’ ‘splines’
  All declared Imports should be used.
File ‘sROC/libs/sROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
File ‘SSL/libs/SSL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 67.7Mb
  sub-directories of 1Mb or more:
    libs  67.4Mb
File ‘sspline/libs/sspline.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘stabledist’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘stacomir.Rmd’ using rmarkdown
Quitting from lines 281-303 (stacomir.Rmd) 
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
round(sum(datasub$value, na.rm = TRUE), 2) and round(sum(datasub2$value, na.rm = TRUE), 2) are not equal:
  Mean relative difference: 0.000996741
--- failed re-building ‘stacomir.Rmd’

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

Error: Vignette re-building failed.
Execution halted
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.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    include   9.9Mb
    lib       2.3Mb
File ‘starma/libs/starma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
File ‘STAR/libs/STAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    doc  10.3Mb
    nc    3.5Mb
Error(s) in re-building vignettes:
--- re-building ‘HTML_special_features.Rmd’ using rmarkdown
--- finished re-building ‘HTML_special_features.Rmd’

--- re-building ‘Rmarkdown.Rmd’ using rmarkdown
pandoc: Cannot decode byte '\xa9': Data.Text.Internal.Encoding.streamDecodeUtf8With: Invalid UTF-8 stream
Error: processing vignette 'Rmarkdown.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘Rmarkdown.Rmd’

--- re-building ‘code_chunks.Rmd’ using rmarkdown
OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
pandoc: Cannot decode byte '\xa9': Data.Text.Internal.Encoding.streamDecodeUtf8With: Invalid UTF-8 stream
Error: processing vignette 'code_chunks.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘code_chunks.Rmd’

--- re-building ‘stationery.Rnw’ using Sweave
--- finished re-building ‘stationery.Rnw’

SUMMARY: processing the following files failed:
  ‘Rmarkdown.Rmd’ ‘code_chunks.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘staTools/libs/staTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gbm’ ‘ggfortify’ ‘tibble’
  All declared Imports should be used.
File ‘STB/libs/STB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘steadyICA/libs/steadyICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘rlist’ ‘tm’ ‘zoo’
  All declared Imports should be used.
File ‘steepness/libs/steepness.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘igraph’ ‘methods’ ‘plyr’ ‘rgdal’ ‘scales’ ‘sp’
  All declared Imports should be used.
File ‘stepwise/libs/stepwise.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘StepwiseTest/libs/StepwiseTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘readr’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Namespace in Imports field not imported from: ‘knitcitations’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  BIRCH/CFTree.cpp:18:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/stream.Rcheck/00install.out’ for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   8.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
File ‘strum/libs/strum.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘gWidgets2tcltk’
  All declared Imports should be used.
File ‘stsm/libs/stsm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘geoR’ ‘gridBase’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘V8’ ‘bsplus’ ‘colourpicker’ ‘dplyr’ ‘grDevices’ ‘graphics’
  ‘jsonlite’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    2.5Mb
File ‘Sunder/libs/Sunder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘supclust/libs/supclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SuppDists.Rcheck/00install.out’ for details.
File ‘SuppDists/libs/SuppDists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘matrixStats’ ‘nloptr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiceOptim’ ‘GPareto’ ‘rgenoud’
  All declared Imports should be used.
File ‘survAUC/libs/survAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘survC1/libs/survC1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.5Mb
File ‘surveybootstrap/libs/surveybootstrap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 134.5Mb
  sub-directories of 1Mb or more:
    libs  133.1Mb
File ‘survIDINRI/libs/survIDINRI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘cowplot’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
File ‘survivalROC/libs/survivalROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
File ‘survSNP/libs/survSNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘svcm/libs/svcm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/svd.Rcheck/00install.out’ for details.
File ‘svmadmm/libs/svmadmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SVMMatch/libs/SVMMatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘svmpath/libs/svmpath.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
File ‘svmpath/libs/svmpath.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/SWATmodel.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tailDepFun/libs/tailDepFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘devEMF’ ‘segmented’ ‘smoother’ ‘tools’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.2Mb
Namespace in Imports field not imported from: ‘jiebaR’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘dplyr’ ‘igraph’ ‘tm’ ‘wordcloud2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
File ‘tbart/libs/tbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tbltools)
  > 
  > test_check("tbltools")
  ── 1. Failure: filter_data, arrange_data (@test-tbl.R#60)  ─────────────────────
  nrow(filter_data(d, d$abc == "a")) not equal to 34.
  1/1 mismatches
  [1] 30 - 34 == -4
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 99 SKIPPED: 0 FAILED: 1
  1. Failure: filter_data, arrange_data (@test-tbl.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    libs  29.7Mb
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
File ‘TDboost/libs/TDboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    apps   2.8Mb
    libs   7.7Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  15.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
File ‘tensorA/libs/tensorA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TESS/libs/TESS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘stringi’ ‘utils’
  All declared Imports should be used.
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Found the following significant warnings:
  GloveFitter.cpp:80:7: warning: explicitly assigning value of variable of type 'GloveFit' to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/text2vec.Rcheck/00install.out’ for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   5.0Mb
Namespace in Imports field not imported from: ‘irlba’
  All declared Imports should be used.
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘forecast’ ‘lars’ ‘parallel’ ‘tau’ ‘tsDyn’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
File ‘textreuse/libs/textreuse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
File ‘tgp/libs/tgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    7.1Mb
Namespace in Imports field not imported from: ‘tiff’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘splancs’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mix’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘dials’ ‘parsnip’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
Namespaces in Imports field not imported from:
  ‘here’ ‘htmltools’ ‘scales’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dbplyr’ ‘reprex’ ‘rlang’
  All declared Imports should be used.
Found the following significant warnings:
  ref.cpp:24:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:35:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:50:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:61:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
See ‘/data/gannet/ripley/R/packages/tests-clang/tidyxl.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.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.
File ‘tiff/libs/tiff.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘forecast’
  All declared Imports should be used.
File ‘timma/libs/timma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    rmarkdown   1.3Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘tibble’
  All declared Imports should be used.
File ‘TKF/libs/TKF.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tkrplot/libs/tkrplot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    examples  13.8Mb
    include    3.0Mb
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
File ‘tmg/libs/tmg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvtnorm/libs/tmvtnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘cowplot’ ‘ggplot2’ ‘jsonlite’
  All declared Imports should be used.
File ‘TopKLists/libs/TopKLists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
Note: found 64 marked Latin-1 strings
  Note: found 548 marked UTF-8 strings
Running examples in ‘TPmsm-Ex.R’ failed
The error most likely occurred in:

> ### Name: transLS
> ### Title: Location-Scale transition probabilities
> ### Aliases: transLS
> ### Keywords: dplot nonparametric smooth survival
> 
> ### ** Examples
> 
> # Set the number of threads
> nth <- setThreadsTP(2)
> 
> # Create survTP object
> data(bladderTP)
> bladderTP_obj <- with(bladderTP, survTP(time1, event1, Stime, event))
> 
> # Compute transition probabilities
> LS0 <- transLS(object=bladderTP_obj, s=5, t=59, h=c(0.25, 2.5), nh=25, ncv=50, conf=FALSE)
> print(LS0)
Location-Scale transition probabilities

Estimates of P(5, 59)
          1         2         3
1 0.5036414 0.1602728 0.3360858
2 0.0000000 0.3617209 0.6382791
3 0.0000000 0.0000000 1.0000000
> 
> # Compute transition probabilities with confidence band
> h <- with( LS0, c( rep(h[1], 2), rep(h[2], 2) ) )
> transLS(object=bladderTP_obj, s=5, t=59, h=h, conf=TRUE,
+ conf.level=0.95, method.boot="percentile", boot.cv=FALSE)

 *** caught segfault ***
address 0x88, cause 'memory not mapped'

Traceback:
 1: TransPROB.LS(object, UT, nboot = nboot, ...)
 2: TransPROB(object, UT, nboot = nboot, ...)
 3: TPBoot.cboot(object, UT, n.boot, ...)
 4: TPBoot(object, UT, n.boot, ...)
 5: TransBoot.TP(object, s, t, state.names, n.boot, conf.level, method.boot,     ...)
 6: TransBoot(object, s, t, state.names, n.boot, conf.level, method.boot,     ...)
 7: TransMethod.TP(object, s, t, state.names, conf, n.boot, conf.level,     method.boot, h = h, nh = nh, ncv = ncv, window = window,     bootcv = boot.cv, cvfull = cv.full)
 8: TransMethod(object, s, t, state.names, conf, n.boot, conf.level,     method.boot, h = h, nh = nh, ncv = ncv, window = window,     bootcv = boot.cv, cvfull = cv.full)
 9: transLS(object = bladderTP_obj, s = 5, t = 59, h = h, conf = TRUE,     conf.level = 0.95, method.boot = "percentile", boot.cv = FALSE)
An irrecoverable exception occurred. R is aborting now ...
File ‘tpr/libs/tpr.so’:
  Found ‘_ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    data      2.1Mb
    doc       2.7Mb
    extdata   8.4Mb
Namespace in Imports field not imported from: ‘neuralnet’
  All declared Imports should be used.
File ‘trapezoid/libs/trapezoid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘nlme’
  All declared Imports should be used.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    extdata   1.4Mb
    libs     11.7Mb
File ‘treeperm/libs/treeperm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: sim.bd.age
> ### Title: sim.bd.age: Simulating birth-death trees of a fixed age.
> ### Aliases: sim.bd.age
> 
> ### ** Examples
> 
> age<-2
> lambda <- 2.0
> mu <- 0.5
> frac <-0.6
> numbsim<-3
> 
> ##
> # Simulating trees with time age since the origin:
> 
> sim.bd.age(age,numbsim,lambda,mu,mrca=FALSE,complete=TRUE)
[[1]]

Phylogenetic tree with 117 tips and 116 internal nodes.

Tip labels:
	t51, t46, t102, t11, t8, t87, ...

Rooted; includes branch lengths.

[[2]]
[1] 0

[[3]]
[1] 0

> sim.bd.age(age,numbsim,lambda,mu,frac,mrca=FALSE,complete=FALSE)
Warning in max(oldnodes) :
  no non-missing arguments to max; returning -Inf
Error in integer(max(oldnodes)) : vector size cannot be infinite
Calls: sim.bd.age ... drop.extinct -> .drop.tip -> collapse.singles -> integer
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is 53.2Mb
  sub-directories of 1Mb or more:
    libs  51.7Mb
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘triebeard/libs/triebeard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘trimTrees/libs/trimTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tripack/libs/tripack.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘Hmisc’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
File ‘truncgof/libs/truncgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
File ‘tsc/libs/tsc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   7.4Mb
Namespace in Imports field not imported from: ‘gsDesign’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘forecast’
  All declared Imports should be used.
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘colormap’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘shinyAce’ ‘shinyjs’
  All declared Imports should be used.
File ‘tvd/libs/tvd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TwoCop/libs/TwoCop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TwoPhaseInd/libs/TwoPhaseInd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘ucminf/libs/ucminf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs       20.2Mb
File ‘udunits2/libs/udunits2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘viridis’
  All declared Imports should be used.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    8.3Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
Running ‘test_unifDAG.R’ [6s/14s]
Running the tests in ‘tests/test_unifDAG.R’ failed.
Complete output:
  > library(unifDAG)
  > 
  > my.wgtMatrix <- function(g, transpose = TRUE) {
  +   res <- as(g, "matrix") # from 'graph' package, now reliable (we hope)
  +   if (transpose) ## default!
  +     t(res) else res
  + }
  > 
  > ## exact
  > set.seed(123)
  > n <- 2
  > reps <- 100
  > res <- matrix(0, reps, 3)
  > for (i in 1:reps) {
  +     gAM <- unifDAG(n)
  +     wm <- my.wgtMatrix(gAM)
  +     if (wm[1,2] != 0) {
  +         res[i,1] <- 1
  +     } else {
  +           if (wm[2,1] != 0) {
  +               res[i,2] <- 1
  +           } else {
  +                 res[i,3] <- 1
  +             }
  +       }
  + }
  > if (!all(round(colMeans(res), 2) == c(0.41, 0.31, 0.28))) {
  +     stop("test_unifDAG: Saved result could not be reproduced (unifDAG).")
  + }
  Error: test_unifDAG: Saved result could not be reproduced (unifDAG).
  Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.6Mb
    libs   4.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespace in Imports field not imported from: ‘mcmcplots’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
File ‘urca/libs/urca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘uroot/libs/uroot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
File ‘uuid/libs/uuid.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’
File ‘uuid/libs/uuid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘validatejsonr/libs/validatejsonr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("vanddraabe")
  Loading required package: vanddraabe
  ── 1. Failure: the correct mobility values are returned (@test-BoundWaterEnviron
  Mobility(Bvalues, occupancy) not equal to `mobility.answer`.
  14/14 mismatches (average diff: 0.0382)
  [1] 0.224 - 0.225 == -0.00168
  [2] 0.373 - 0.375 == -0.00280
  [3] 0.471 - 0.474 == -0.00354
  [4] 0.621 - 0.626 == -0.00467
  [5] 0.706 - 0.676 ==  0.03025
  [6] 0.824 - 0.876 == -0.05229
  [7] 0.993 - 0.948 ==  0.04521
  [8] 1.006 - 1.013 == -0.00756
  [9] 1.242 - 1.126 ==  0.11578
  ...
  
  ── 2. Failure: counting AtomTypes works (@test-utilities.R#102)  ───────────────
  getAtomTypeCounts(atom.types) not equal to `ATCounts.answer`.
  56/167 mismatches (average diff: 5.09)
  [4]  0 - 1 == -1
  [9]  0 - 8 == -8
  [11] 0 - 7 == -7
  [14] 7 - 1 ==  6
  [15] 1 - 0 ==  1
  [18] 0 - 1 == -1
  [21] 0 - 1 == -1
  [23] 0 - 4 == -4
  [31] 1 - 0 ==  1
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 63 SKIPPED: 0 FAILED: 2
  1. Failure: the correct mobility values are returned (@test-BoundWaterEnvironments.R#71) 
  2. Failure: counting AtomTypes works (@test-utilities.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
File ‘vbdm/libs/vbdm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘VBLPCM/libs/VBLPCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vbsr/libs/vbsr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘freetypeharfbuzz’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    doc    1.2Mb
    help   2.8Mb
File ‘VIFCP/libs/VIFCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘VIGoR/libs/VIGoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

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

> ### Name: generateRandomSp
> ### Title: Generate a random virtual species distribution from
> ###   environmental variables
> ### Aliases: generateRandomSp
> 
> ### ** Examples
> 
> # Create an example stack with six environmental variables
> a <- matrix(rep(dnorm(1:100, 50, sd = 25)), 
+             nrow = 100, ncol = 100, byrow = TRUE)
> env <- stack(raster(a * dnorm(1:100, 50, sd = 25)),
+              raster(a * 1:100),
+              raster(a * logisticFun(1:100, alpha = 10, beta = 70)),
+              raster(t(a)),
+              raster(exp(a)),
+              raster(log(a)))
> names(env) <- paste("Var", 1:6, sep = "")   
> 
> # More than 6 variables: by default a PCA approach will be used
> generateRandomSp(env)
 - Perfoming the pca

 - Defining the response of the species along PCA axes

 - Calculating suitability values

 - Converting into Presence - Absence

   --- Determing species.prevalence automatically according to alpha and beta


Virtual species generated from 6 variables:
 Var1, Var2, Var3, Var4, Var5, Var6

- Approach used: Response to axes of a PCA
- Axes:  1, 2 ;  81.71 % explained by these axes
- Responses to axes:
   .Axis 1  [min=-3.52; max=3.55] : dnorm (mean=1.399218; sd=2.969177)
   .Axis 2  [min=-1.74; max=3.75] : dnorm (mean=0.2190712; sd=1.881691)
- Environmental suitability was rescaled between 0 and 1

- Converted into presence-absence:
   .Method = probability
   .alpha (slope)           = -0.1
   .beta  (inflexion point) = 0.128128128128128
   .species prevalence      = 0.914> 
> # Manually choosing a response approach
> generateRandomSp(env, approach = "response")
 - Determining species' response to predictor variables

Error in seq.default(cur.rast@data@min, cur.rast@data@max, length = 1000) : 
  'from' must be a finite number
Calls: generateRandomSp -> sample -> seq -> seq.default
Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc           4.2Mb
    docjs         1.4Mb
    htmlwidgets   4.0Mb
Namespace in Imports field not imported from: ‘rpart’
  All declared Imports should be used.
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘purrr’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘XML’ ‘checkmate’ ‘gstat’ ‘intervals’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tibble’
  All declared Imports should be used.
File ‘waffect/libs/waffect.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’
File ‘waffect/libs/waffect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 53.8Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  51.7Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘XML’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘rmarkdown’ ‘shinyjs’
  ‘shinythemes’ ‘spThin’ ‘spocc’ ‘zip’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
File ‘wand/libs/wand.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   4.0Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘waveslim/libs/waveslim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘wavethresh/libs/wavethresh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘zoo’
  All declared Imports should be used.
File ‘wbs/libs/wbs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.2Mb
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/WhopGenome.Rcheck/00install.out’ for details.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
File ‘widals/libs/widals.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘widenet/libs/widenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘drc’ ‘imputeTestbench’
  All declared Imports should be used.
File ‘wingui/libs/wingui.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘DescTools’ ‘HydeNet’ ‘RBGL’ ‘Rgraphviz’ ‘arules’ ‘bnlearn’
  ‘dplyr’ ‘graph’ ‘igraph’ ‘linkcomm’ ‘missRanger’ ‘parallel’ ‘psych’
  ‘rhandsontable’ ‘rintrojs’ ‘shinyBS’ ‘shinyWidgets’ ‘shinyalert’
  ‘shinycssloaders’ ‘shinydashboard’ ‘tools’ ‘visNetwork’
  All declared Imports should be used.
File ‘WMCapacity/libs/WMCapacity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
File ‘wordspace/libs/wordspace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
File ‘wskm/libs/wskm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.4Mb
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
File ‘XMRF/libs/XMRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘xseq/libs/xseq.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘Usingxtractomatic.Rmd’ using rmarkdown
date	lon	lat	lowLon	higLon	lowLat	higLat
4/23/2003	203.899	19.664	203.899	203.899	19.664	19.664
4/24/2003	204.151	19.821	203.912597	204.389403	18.78051934	20.86148066
4/30/2003	203.919	20.351	203.6793669	204.1586331	18.79728188	21.90471812
5/1/2003	204.229	20.305	203.9943343	204.4636657	18.90440013	21.70559987
Quitting from lines 818-843 (Usingxtractomatic.Rmd) 
Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
(converted from warning) Removed 4070 rows containing missing values (geom_raster).
--- failed re-building ‘Usingxtractomatic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
File ‘yakmoR/libs/yakmoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘ghyp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘MatchIt’ ‘WhatIf’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
Found the following significant warnings:
  analyzeFMRI.c:948:3: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  analyzeFMRI.c:975:5: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/AnalyzeFMRI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mcmc.c:337:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/BayHap.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘bdlp.Rmd’ using rmarkdown
Loading required namespace: RSQLite
Warning: call dbDisconnect() when finished working with a connection
Quitting from lines 197-211 (bdlp.Rmd) 
Error: processing vignette 'bdlp.Rmd' failed with diagnostics:
miller2012.R:7:208: unexpected '{'
6:  
7: miller2012 <- function(setnr = NULL, seedinfo = list(100, "3.7.0", c("Mersenne-Twister", "Inversion", "Rejection", metaseedinfo = list(100, "3.7.0", c("Mersenne-Twister", "Inversion", "Rejecti
                                                                                                                                                                                                                  ^
--- failed re-building ‘bdlp.Rmd’

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

Error: Vignette re-building failed.
Execution halted
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
Running ‘testthat.R’ [225s/246s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BMSC)
  Loading required package: Rcpp
  > 
  > test_check("BMSC")
  ── 1. Failure: A message is returned if some rows are missing (@test_missingValu
  `BMSC:::handleMissingData(data, formula, yUncertainty)$data` produced unexpected messages.
  Expected match: 7 rows \\(9.33% of the data\\) were excluded due to missing values.
  Actual values:
  * 8 rows (10.67% of the data) were excluded due to missing values.
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 61 SKIPPED: 1 FAILED: 1
  1. Failure: A message is returned if some rows are missing (@test_missingValuesHandling.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘test-all.R’ [35s/80s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  ── 1. Error: tidy.htest/oneway.test (@test-stats-htest.R#14)  ──────────────────
  object 'extra' not found
  1: oneway.test(extra ~ group, data = sleep) at testthat/test-stats-htest.R:14
  2: eval(m, parent.frame())
  3: eval(m, parent.frame())
  4: stats::model.frame(formula = extra ~ group, data = sleep)
  5: model.frame.default(formula = extra ~ group, data = sleep)
  6: eval(predvars, data, env)
  7: eval(predvars, data, env)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 976 SKIPPED: 2 FAILED: 1
  1. Error: tidy.htest/oneway.test (@test-stats-htest.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/C50.Rcheck/00install.out’ for details.
---- unloading

(R:37887): GLib-CRITICAL **: 17:27:58.150: g_main_loop_quit: assertion 'loop != NULL' failed
Found the following significant warnings:
  catnet_rexport.cpp:202:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:206:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:213:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:216:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:217:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:232:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:231:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/catnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  MLEEstimator.cpp:81:17: warning: catching polymorphic type ‘class std::domain_error’ by value [-Wcatch-value=]
  MLEEstimator.cpp:127:17: warning: catching polymorphic type ‘class std::domain_error’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/catSurv.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clhs)
  > 
  > test_check("clhs")
  ── 1. Failure: basic clhs on a data.frame works (@test-clhs-data.frame.R#15)  ──
  `res` not equal to c(188, 657, 140, 301, 817).
  5/5 mismatches (average diff: 210)
  [1]  97 - 188 == -91
  [2] 903 - 657 == 246
  [3] 539 - 140 == 399
  [4] 451 - 301 == 150
  [5] 979 - 817 == 162
  
  ── 2. Failure: DLHS method on a data.frame works (@test-method_DLHS.R#17)  ─────
  `res` not equal to c(214, 40, 702, 919, 521).
  5/5 mismatches (average diff: 211)
  [1] 412 - 214 ==  198
  [2] 170 -  40 ==  130
  [3] 196 - 702 == -506
  [4] 820 - 919 ==  -99
  [5] 641 - 521 ==  120
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 2
  1. Failure: basic clhs on a data.frame works (@test-clhs-data.frame.R#15) 
  2. Failure: DLHS method on a data.frame works (@test-method_DLHS.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:

  Warning: 'survConcordance' is deprecated.
  Warning: 'survConcordance' is deprecated.
  Warning: 'survConcordance' is deprecated.
  Warning: 'survConcordance' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/Cubist.Rcheck/00install.out’ for details.
Running examples in ‘degenes-Ex.R’ failed
The error most likely occurred in:

> ### Name: deg
> ### Title: Detection of differentially expressed genes.
> ### Aliases: deg
> 
> ### ** Examples
> 
> X1 = matrix(rnorm(2000, 0, 1), 200, 10)
> X2 = matrix(rnorm(2000, 0, 1), 200, 10)
> index = sample(1:200, 5, replace=FALSE)
> X2[index,] = X2[index,] + 5
> D = deg(X1, X2)
Sun Mar 24 18:21:48 2019
Calculation of Z
Calculation of z
Calculation of the kernel estimator
Calculation of the kernel estimator
Determination of the rejection region
Error in if (integral > single.alpha) c1 <- c : 
  missing value where TRUE/FALSE needed
Calls: deg
Execution halted
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/deisotoper.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/Delaporte.Rcheck/00install.out’ for details.
Found the following significant warnings:
  GetData.c:342:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
  GetData.c:355:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/DetSel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/dggridR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/dpglasso.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [16s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.9.1") {
  +   library(testthat)
  +   test_check("emil")
  + }
  Loading required package: emil
  
  Attaching package: 'emil'
  
  The following object is masked from 'package:base':
  
      mode
  
  ── 1. Failure: k-NN imputation (@test-preprocess.r#30)  ────────────────────────
  sets$test$x[na.ind] not equivalent to ifelse(na.ind[, 2] <= 3, 5, 4.5).
  3/10 mismatches (average diff: 0.5)
  [5]  5 - 4.5 == 0.5
  [7]  5 - 4.5 == 0.5
  [10] 5 - 4.5 == 0.5
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 183 SKIPPED: 1 FAILED: 1
  1. Failure: k-NN imputation (@test-preprocess.r#30) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘BiocParallel’ ‘broom’ ‘reshape2’ ‘rmarkdown’
  All declared Imports should be used.
Found the following significant warnings:
  main.c:334:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:575:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:518:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:805:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:755:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1034:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:983:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1377:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1279:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1678:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1962:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1912:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2316:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2212:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/enviPat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  epanet.c:999:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1000:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1492:3: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2308:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2309:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:454:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:455:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input3.c:604:2: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/epanet2toolkit.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘labels-support.Rmd’ using rmarkdown

Use 'expss_output_rnotebook()' to display tables inside R Notebooks.
 To return to the console output, use 'expss_output_default()'.

--- finished re-building ‘labels-support.Rmd’

--- re-building ‘tables-with-labels.Rmd’ using rmarkdown
Quitting from lines 79-138 (tables-with-labels.Rmd) 
Error: processing vignette 'tables-with-labels.Rmd' failed with diagnostics:
<text>:1:12: unexpected symbol
1: Miles/(US) gallon
               ^
--- failed re-building ‘tables-with-labels.Rmd’

--- re-building ‘xlsx-export.Rmd’ using rmarkdown
--- finished re-building ‘xlsx-export.Rmd’

SUMMARY: processing the following file failed:
  ‘tables-with-labels.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-devel/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  gropt/src/SmartSpace.cpp:142:24: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/fdasrvf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  RngStream.c:275:7: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/freeknotsplines.Rcheck/00install.out’ for details.
Found the following significant warnings:
  hap_c.c:380:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  hap_c.c:392:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/gap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Gdmlib.cpp:2352:19: warning: ‘%lf’ directive writing between 3 and 317 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/gdm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/gglasso.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/glmulti.Rcheck/00install.out’ for details.
Running examples in ‘gremlin-Ex.R’ failed
The error most likely occurred in:

> ### Name: gremlin-package
> ### Title: Mixed-Effects REML Incorporating Generalized Inverses
> ### Aliases: gremlin-package _PACKAGE
> 
> ### ** Examples
> 
>   require(nadiv)
Loading required package: nadiv
>   Ainv <- makeAinv(Mrode3[-c(1:2), 1:3])$Ainv
>   mod11 <- gremlinR(WWG11 ~ sex - 1,
+ random = ~ calf,
+ data = Mrode11,
+ ginverse = list(calf = Ainv),
+ Gstart = matrix(0.2), Rstart = matrix(0.4),
+ maxit = 10, v = 2)
gremlin started:		 20:13:43 
   1 of max 10 			 20:13:44 
	EM to find next theta
Element 0.2124631 must be a symmetric matrix or a number
Error in FUN(X[[i]], ...) : 
Calls: gremlinR -> sapply -> lapply -> FUN
Execution halted
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Running ‘testthat.R’ [28s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(harvestr)
  > foreach::registerDoSEQ()
  > test_check("harvestr")
  ── 1. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42)  
  RNGkind() not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  ── 2. Failure: gather replaces seed. (@test-gather.R#57)  ──────────────────────
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ── 3. Failure: get.seed retrieves properly (@test-seeds.R#14)  ─────────────────
  `seed` not identical to `eseed`.
  Mean relative difference: 0.9608917
  
  ── 4. Failure: replace.seed (@test-seeds.R#29)  ────────────────────────────────
  `k` not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ── 5. Failure: replace.seed (@test-seeds.R#30)  ────────────────────────────────
  `l` not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  ── 6. Failure: withseed replaces previous seed. (@test-seeds.R#56)  ────────────
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 119 SKIPPED: 5 FAILED: 6
  1. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42) 
  2. Failure: gather replaces seed. (@test-gather.R#57) 
  3. Failure: get.seed retrieves properly (@test-seeds.R#14) 
  4. Failure: replace.seed (@test-seeds.R#29) 
  5. Failure: replace.seed (@test-seeds.R#30) 
  6. Failure: withseed replaces previous seed. (@test-seeds.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  readstat/readstat_writer.c:82:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/readstat_writer.c:276:5: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
  readstat/readstat_writer.c:331:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/sas/readstat_sas7bcat_write.c:108:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:284:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:337:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 31 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:156:5: warning: ‘strncpy’ output may be truncated copying 9 bytes from a string of length 9 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:164:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 8 [-Wstringop-truncation]
  readstat/spss/readstat_por_write.c:205:5: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/haven.Rcheck/00install.out’ for details.
Found the following significant warnings:
  gener.c:39:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/hier.part.Rcheck/00install.out’ for details.
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
Running examples in ‘IBDsim-Ex.R’ failed
The error most likely occurred in:

> ### Name: oneLocusIBD
> ### Title: Estimating pairwise IBD coefficients
> ### Aliases: oneLocusIBD
> ### Keywords: math
> 
> ### ** Examples
> 
> ### Example 1: Full siblings
> x <- nuclearPed(2) 
> Nsim <- 100 # Should be increased substantially
> 
> # Autosomal kappa: Estimate vs exact 
> k_est = oneLocusIBD(x, ind1=3, ind2=4, Nsim=Nsim, seed=123)
---------------
Performing unconditional simulation
Mode: autosomal 
Recombination model: haldane (poisson process) 
Number of simulations: 100 
Simulation finished. Time used: 0.077 seconds
---------------
IBD analysis finished. Total time used: 0.08 seconds.
> k_exact = c(0.25, 0.5, 0.25)
> stopifnot(all(round(k_est - k_exact, 1) == 0))
Error: all(round(k_est - k_exact, 1) == 0) is not TRUE
Execution halted
Running ‘testthat.R’ [14s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(infer)
  > 
  > test_check("infer")
  Setting `type = "permute"` in `generate()`.
  ── 1. Failure: conf_int argument works (@test-wrappers.R#141)  ─────────────────
  no_var_equal == var_equal isn't false.
  
  ── 2. Failure: conf_int argument works (@test-wrappers.R#153)  ─────────────────
  shortcut_no_var_equal == shortcut_var_equal isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 347 SKIPPED: 0 FAILED: 2
  1. Failure: conf_int argument works (@test-wrappers.R#141) 
  2. Failure: conf_int argument works (@test-wrappers.R#153) 
  
  Error: testthat unit tests failed
  Execution halted
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
Running ‘testthat.R’ [5s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(kiwisR)
  > 
  > test_check("kiwisR")
  ── 1. Error: check_hub accepts defaults and returns URL (@test_utils.R#6)  ─────
  OpenSSL SSL_read: SSL_ERROR_SYSCALL, errno 104
  1: check_hub("swmc") at testthat/test_utils.R:6
  2: httr::http_status(httr::GET(paste0(api_url, "datasource=0&service=kisters&type=queryServices&request=getrequestinfo")))
  3: status_code(x)
  4: httr::GET(paste0(api_url, "datasource=0&service=kisters&type=queryServices&request=getrequestinfo"))
  5: request_perform(req, hu$handle$handle)
  6: request_fetch(req$output, req$url, handle)
  7: request_fetch.write_memory(req$output, req$url, handle)
  8: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 46 SKIPPED: 0 FAILED: 1
  1. Error: check_hub accepts defaults and returns URL (@test_utils.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
comp.npci: no visible global function definition for ‘qnorm’
epband.fun: no visible global function definition for ‘data’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.90’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.95’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.99’
hall.wellner.fun: no visible global function definition for ‘data’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.90’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.95’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.99’
lrt.confints: no visible global function definition for ‘qchisq’
rothman.fun: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Found the following significant warnings:
  /data/gannet/ripley/R/test-3.6/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-3.6/BH/include/boost/container/detail/copy_move_algo.hpp:897:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-3.6/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/lolog.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/maGUI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/ManifoldOptim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  MatFile.cpp:40:16: warning: converting to non-pointer type ‘char’ from NULL [-Wconversion-null]
  MatFile.cpp:65:16: warning: converting to non-pointer type ‘char’ from NULL [-Wconversion-null]
See ‘/data/gannet/ripley/R/packages/tests-devel/MetaSKAT.Rcheck/00install.out’ for details.
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 ‘/data/gannet/ripley/R/packages/tests-devel/MigClim.Rcheck/00install.out’ for details.
listGenoToTable: no visible binding for global variable ‘dummy’
Undefined global functions or variables:
  dummy
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 ‘/data/gannet/ripley/R/packages/tests-devel/MonetDBLite.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [59s/155s]
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
Running ‘testthat.R’ [76s/184s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mvtboost)
  > 
  > test_check("mvtboost")
  ── 1. Failure: covex-E (@test_covex.R#54)  ─────────────────────────────────────
  covex[covex > 0.01] not equal to rep(a, 3).
  1/3 mismatches
  [2] 0.811 - 0.899 == -0.0886
  0.5
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 174 SKIPPED: 2 FAILED: 1
  1. Failure: covex-E (@test_covex.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘NNMIS-Ex.R’ failed
The error most likely occurred in:

> ### Name: km.pool
> ### Title: Perform Kaplan-Meier estmation over the multiply imputed
> ###   survival data sets
> ### Aliases: km.pool
> 
> ### ** Examples
> 
> 
> # load required packages
> library(NNMIS)
> library(survival)
> 
> # load data set - stanford2 in package 'survival'
> data("stanford2")
> head(stanford2)
     id time status age   t5
139 139   86      1  12 1.26
159 159   10      1  13 1.49
181 181   60      0  13   NA
119 119 1116      0  14 0.54
74   74 2006      0  15 1.26
120 120 1107      0  18 0.25
> attach(stanford2)
> 
> # performance multiple imputation on missing covariate t5 and
> # censored observations based on the imputed missing covariates
> imp.dat <- NNMIS(t5, xa=age, xb=age, time=time, event=status, imputeCT=TRUE, Seed = 1234)
Request for 1 threads.
Only 1 thread is used.
> 
> # check imputation results
> head(imp.dat$dat.T.NNMI)
    M1   M2   M3   M4   M5   M6   M7   M8   M9  M10
1   86   86   86   86   86   86   86   86   86   86
2   10   10   10   10   10   10   10   10   10   10
3 2313 1232  227 2006 2006  227 2006 2006 2006 1232
4 2723 2984 2127 2984 2313 2984 2723 1634 1634 2127
5 2723 3410 3695 3410 3695 3695 2723 2127 3410 2127
6 2984 1232 2127 2984 2984 1232 2723 2984 2984 2127
> 
> # combine inference from imputed data sets using Rubin's rules
> # Kaplan-Meier estimates
> kmfit <- km.pool(imp.dat, time, status)
> plotKM(kmfit)
Error in ssurv[who, j] : subscript out of bounds
Calls: plotKM -> <Anonymous> -> plot.survfit
Execution halted
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 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 ‘/data/gannet/ripley/R/packages/tests-devel/odbc.Rcheck/00install.out’ for details.
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 significant warnings:
  opus_miner.cpp:90:15: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/opusminer.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [33s/27s]
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
Found the following significant warnings:
  ../osqp_sources//include/glob_opts.h:173:50: warning: ISO C does not support ‘__FUNCTION__’ predefined identifier [-Wpedantic]
See ‘/data/gannet/ripley/R/packages/tests-devel/osqp.Rcheck/00install.out’ for details.
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 ‘/data/gannet/ripley/R/packages/tests-devel/PGRdup.Rcheck/00install.out’ for details.
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
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 ‘/data/gannet/ripley/R/packages/tests-devel/PRIMME.Rcheck/00install.out’ for details.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/PSGExpress.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘loo::kfold’ by ‘rstanarm::kfold’ when loading ‘psycho’
See ‘/data/gannet/ripley/R/packages/tests-devel/psycho.Rcheck/00install.out’ for details.
Found the following file(s) containing GNU extensions:
  src-build/Makefile
  tools/kdebindings-build/Makefile
  tools/kdebindings-build/generator/Makefile
  tools/kdebindings-build/generator/generators/Makefile
  tools/kdebindings-build/generator/generators/dump/Makefile
  tools/kdebindings-build/generator/generators/smoke/Makefile
  tools/kdebindings-build/generator/parser/Makefile
  tools/kdebindings-build/smoke/Makefile
  tools/kdebindings-build/smoke/qt/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section ‘Writing portable
packages’ in the ‘Writing R Extensions’ manual.
Note: information on .o files is not available
File ‘qtpaint/libs/qtpaint.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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 ‘/data/gannet/ripley/R/packages/tests-devel/R4dfp.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘BiocManager’ ‘stringi’
  All declared Imports should be used.
.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 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 ‘/data/gannet/ripley/R/packages/tests-devel/RArcInfo.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/Rblpapi.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  ── 1. Error: (unknown) (@test_deputados.R#81)  ─────────────────────────────────
  argument "message" is missing, with no default
  1: skip() at testthat/test_deputados.R:81
  2: structure(list(message = message), class = c("skip", "condition"))
  
  ── 2. Error: (unknown) (@test_proposicoes.R#91)  ───────────────────────────────
  could not find function "FUN1"
  1: check_api() at testthat/test_proposicoes.R:91
  2: tryCatch(setup(), error = function(e) {
         message(e)
         return(FALSE)
     }) at testthat/test_proposicoes.R:15
  3: tryCatchList(expr, classes, parentenv, handlers)
  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5: value[[3L]](cond)
  6: message(e) at testthat/test_proposicoes.R:16
  7: withRestarts({
         signalCondition(cond)
         defaultHandler(cond)
     }, muffleMessage = function() NULL)
  8: withOneRestart(expr, restarts[[1L]])
  9: doWithOneRestart(return(expr), restart)
  
  ── 3. Error: (unknown) (@test_votacoes.R#70)  ──────────────────────────────────
  argument "message" is missing, with no default
  1: skip() at testthat/test_votacoes.R:70
  2: structure(list(message = message), class = c("skip", "condition"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 13 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_deputados.R#81) 
  2. Error: (unknown) (@test_proposicoes.R#91) 
  3. Error: (unknown) (@test_votacoes.R#70) 
  
  Error: testthat unit tests 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 ‘/data/gannet/ripley/R/packages/tests-devel/Rdsdp.Rcheck/00install.out’ for details.
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 ‘/data/gannet/ripley/R/packages/tests-devel/re2r.Rcheck/00install.out’ for details.
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 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 ‘/data/gannet/ripley/R/packages/tests-devel/rioja.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/rJava.Rcheck/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’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rlecuyer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  DbResult.cpp:81:41: warning: catching polymorphic type ‘class MariaResultPrep::UnsupportedPS’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/RMariaDB.Rcheck/00install.out’ for details.
Running examples in ‘rms-Ex.R’ failed
The error most likely occurred in:

> ### 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: 0x995f178>
> 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
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 ‘/data/gannet/ripley/R/packages/tests-devel/rncl.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [11s/13s]
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] 374720 - 888626 == -513906
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test_rnn.R#66) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  robust.cpp:665:25: warning: catching polymorphic type ‘class std::exception’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/robfilter.Rcheck/00install.out’ for details.
Running examples in ‘RobRex-Ex.R’ failed
The error most likely occurred in:

> ### Name: rgsOptIC.AL
> ### Title: Computation of the optimally robust IC for AL estimators
> ### Aliases: rgsOptIC.AL
> ### Keywords: robust
> 
> ### ** Examples
> 
> K <- DiscreteDistribution(1:5) # = Unif({1,2,3,4,5})
> IC1 <- rgsOptIC.AL(r = 0.1, K = K)
Found more than one class "ParamFamily" in cache; using the first, from namespace 'ROptEstOld'
Also defined by ‘distrMod’
Found more than one class "ParamFamily" in cache; using the first, from namespace 'ROptEstOld'
Also defined by ‘distrMod’
> checkIC(IC1)
Found more than one class "ParamFamily" in cache; using the first, from namespace 'ROptEstOld'
Also defined by ‘distrMod’
Error in f1(cbind(t(cond), x)) : 
  argument "f1" is missing, with no default
Calls: checkIC ... <Anonymous> -> sapply -> lapply -> FUN -> do.call -> <Anonymous>
Timing stopped at: 0.007 0.001 0.008
Execution halted
Running examples in ‘ROptRegTS-Ex.R’ failed
The error most likely occurred in:

> ### Name: Av1CondContIC-class
> ### Title: Conditionally centered influence curve of contamination type
> ### Aliases: Av1CondContIC-class CallL2Fam<-,Av1CondContIC-method
> ###   cent,Av1CondContIC-method cent<-,Av1CondContIC-method
> ###   clip,Av1CondContIC-method clip<-,Av1CondContIC-method
> ###   lowerCase,Av1CondContIC-method lowerCase<-,Av1CondContIC-method
> ###   neighborRadius,Av1CondContIC-method
> ###   neighborRadius<-,Av1CondContIC-method stand,Av1CondContIC-method
> ###   stand<-,Av1CondContIC-method
> ###   generateIC,Av1CondContNeighborhood,L2RegTypeFamily-method
> ###   show,Av1CondContIC-method
> ### Keywords: classes robust
> 
> ### ** Examples
> 
> IC1 <- new("Av1CondContIC")
> IC1
An object of class “Av1CondContIC” 
### name:	 conditionally centered IC for average conditional contamination neighborhoods 
Timing stopped at: 0.006 0.001 0.006
Error in f1(cbind(cond, x)) : argument "f1" is missing, with no default
Calls: <Anonymous> ... <Anonymous> -> sapply -> lapply -> FUN -> do.call -> <Anonymous>
Timing stopped at: 0.001 0 0.001
Timing stopped at: 0.067 0.001 0.069
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 ‘/data/gannet/ripley/R/packages/tests-devel/rphast.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-devel/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  RngStreams.c:332:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/rstream.Rcheck/00install.out’ for details.
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 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 ‘/data/gannet/ripley/R/packages/tests-devel/rtfbs.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/data/gannet/ripley/R/packages/tests-devel/RVowpalWabbit.Rcheck/00install.out’ for details.
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 ‘/data/gannet/ripley/R/packages/tests-devel/s2.Rcheck/00install.out’ for details.
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 significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/scio.Rcheck/00install.out’ for details.
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 ‘/data/gannet/ripley/R/packages/tests-devel/sdnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/sdwd.Rcheck/00install.out’ for details.
Running ‘testthat.R’
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 # 3 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
Running ‘testthat.R’ [4s/25s]
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
Running ‘testthat.R’
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
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 ‘/data/gannet/ripley/R/packages/tests-devel/SSN.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘HTML_special_features.Rmd’ using rmarkdown
--- finished re-building ‘HTML_special_features.Rmd’

--- re-building ‘Rmarkdown.Rmd’ using rmarkdown
pandoc: Cannot decode byte '\xa9': Data.Text.Internal.Encoding.streamDecodeUtf8With: Invalid UTF-8 stream
Error: processing vignette 'Rmarkdown.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘Rmarkdown.Rmd’

--- re-building ‘code_chunks.Rmd’ using rmarkdown
pandoc: Cannot decode byte '\xa9': Data.Text.Internal.Encoding.streamDecodeUtf8With: Invalid UTF-8 stream
Error: processing vignette 'code_chunks.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
--- failed re-building ‘code_chunks.Rmd’

--- re-building ‘stationery.Rnw’ using Sweave
--- finished re-building ‘stationery.Rnw’

SUMMARY: processing the following files failed:
  ‘Rmarkdown.Rmd’ ‘code_chunks.Rmd’

Error: Vignette re-building failed.
Execution halted
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 ‘/data/gannet/ripley/R/packages/tests-devel/strum.Rcheck/00install.out’ for details.
Found the following significant warnings:
  rapi.cc:191:12: warning: catching polymorphic type ‘struct subprocess::subprocess_exception’ by value [-Wcatch-value=]
See ‘/data/gannet/ripley/R/packages/tests-devel/subprocess.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-devel/SWATmodel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /data/gannet/ripley/R/test-3.6/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
  /data/gannet/ripley/R/test-3.6/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, float>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/text2vec.Rcheck/00install.out’ for details.
Found the following significant warnings:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/TPmsm.Rcheck/00install.out’ for details.
File ‘tpr/libs/tpr.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/TukeyRegion.Rcheck/00install.out’ for details.
Running ‘test_unifDAG.R’
Running the tests in ‘tests/test_unifDAG.R’ failed.
Complete output:
  > library(unifDAG)
  > 
  > my.wgtMatrix <- function(g, transpose = TRUE) {
  +   res <- as(g, "matrix") # from 'graph' package, now reliable (we hope)
  +   if (transpose) ## default!
  +     t(res) else res
  + }
  > 
  > ## exact
  > set.seed(123)
  > n <- 2
  > reps <- 100
  > res <- matrix(0, reps, 3)
  > for (i in 1:reps) {
  +     gAM <- unifDAG(n)
  +     wm <- my.wgtMatrix(gAM)
  +     if (wm[1,2] != 0) {
  +         res[i,1] <- 1
  +     } else {
  +           if (wm[2,1] != 0) {
  +               res[i,2] <- 1
  +           } else {
  +                 res[i,3] <- 1
  +             }
  +       }
  + }
  > if (!all(round(colMeans(res), 2) == c(0.41, 0.31, 0.28))) {
  +     stop("test_unifDAG: Saved result could not be reproduced (unifDAG).")
  + }
  Error: test_unifDAG: Saved result could not be reproduced (unifDAG).
  Execution halted
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/data/gannet/ripley/R/packages/tests-devel/validatejsonr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  tabix/razf.c:188:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/data/gannet/ripley/R/packages/tests-devel/WhopGenome.Rcheck/00install.out’ for details.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.1Mb
    libs                    3.5Mb
asp: no visible global function definition for 'as.formula'
asp: no visible global function definition for 'var'
aspm: no visible binding for global variable 'X.Declan'
aspm: no visible binding for global variable 'Z.Jaida'
aspm: no visible binding for global variable 'group.vec.Handan'
aspm: no visible global function definition for 'as.formula'
aspm: no visible global function definition for 'glm'
aspm: no visible global function definition for 'binomial'
aspm: no visible global function definition for 'poisson'
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/AdaSampling.Rcheck/00install.out' for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.7Mb
    pictures   2.1Mb
Running examples in 'adehabitatMA-Ex.R' failed
The error most likely occurred in:

> ### Name: buffer
> ### Title: Compute Buffers Regions
> ### Aliases: buffer
> ### Keywords: spatial
> 
> ### ** Examples
> 
> 
> data(lynxjura)
> 
> # locs is the SpatialPointsDataFrame containing the
> # locations of lynx indices in the Jura mountains
> locs <- lynxjura$locs
> head(locs)
        coordinates     Date Type
3 (856208, 2135450) 19801231   EP
4 (852942, 2134370) 19810101   EP
5 (857408, 2134780) 19810101    E
7 (857425, 2135190) 19810114    E
8 (853543, 2133730) 19810114    E
9 (852771, 2132560) 19810114    E
Coordinate Reference System (CRS) arguments: NA 
> 
> ## just for the sake of illustration: sample 100 points
> set.seed(233)
> locs <- locs[sample(1:nrow(locs), 100),]
> 
> # sa is the SpatialPixelsDataFrame object containing
> # maps of the study area
> sa <- lynxjura$map
> 
> # Buffer of 2000 m from all points
> bu <- buffer(locs, sa, 2000)
> image(bu)
> 
> # displays all the pixels of the study area within 2000 m
> # of a point, for each type of indices (see ?lynxjura)
> buani <- buffer(locs[,2], sa, 2000)
> buani
Object of class "SpatialPixelsDataFrame" (package sp):

Grid parameters:
  cellcentre.offset cellsize cells.dim
x            828916      500        96
y           2130700      500        90

Variables measured:
  D E EF EO EP L O OP P
1 0 0  0  0  0 0 0  0 0
2 0 0  0  0  0 0 0  0 0
3 0 0  0  0  0 0 0  0 0
4 0 0  0  0  0 0 0  0 0
5 0 0  0  0  0 0 0  0 0
6 0 0  0  0  0 0 0  0 0
...

> par(mar=c(0,0,2,0))
> opar<-par(mfrow=c(3,4))
> lapply(1:11, function(i) {
+    image(buani, i)
+    title(main = names(slot(buani, "data"))[i])
+ })
Error in `[.data.frame`(x@data, , i, drop = FALSE) : 
  undefined columns selected
Calls: lapply ... matrix -> t -> matrix -> [ -> [ -> [ -> [.data.frame
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.2Mb
Found a 'configure.in' file: 'configure.ac' has long been preferred.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Running examples in 'AMR-Ex.R' failed
The error most likely occurred in:

> ### Name: ggplot_rsi
> ### Title: AMR plots with 'ggplot2'
> ### Aliases: ggplot_rsi geom_rsi facet_rsi scale_y_percent
> ###   scale_rsi_colours theme_rsi labels_rsi_count
> 
> ### ** Examples
> 
> library(dplyr)
Warning: package 'dplyr' was built under R version 3.7.0

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)
Warning: package 'ggplot2' was built under R version 3.7.0
> 
> # get antimicrobial results for drugs against a UTI:
> ggplot(septic_patients %>% select(amox, nitr, fosf, trim, cipr)) +
+   geom_rsi()
Error in valid.units(units) : Invalid unit
Calls: <Anonymous> ... unit.c -> unit -> valid.unit -> structure -> valid.units
Execution halted
annot : annotlist: no visible global function definition for
  'read.table'
annot : annotlist: no visible global function definition for
  'write.table'
annot: no visible global function definition for 'flush.console'
annot: no visible global function definition for 'read.table'
annot: no visible global function definition for 'choose.dir'
Undefined global functions or variables:
  choose.dir flush.console read.table write.table
Consider adding
  importFrom("utils", "choose.dir", "flush.console", "read.table",
             "write.table")
to your NAMESPACE file.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(anonymizer)
  > 
  > test_check("anonymizer")
  -- 1. Failure: Produces the correct output. (@test-anonymize.R#5)  -------------
  anonymize("a", .seed = 1) not equal to "ed879445e47969394b3f8eb818501976bed22b9ab0e7f7c5fdf2a96df0aec80e".
  1/1 mismatches
  x[1]: "6ae80dd07643618a5ea6ac83b506fd367d81f86e5f5650a42045ca7ebe516602"
  y[1]: "ed879445e47969394b3f8eb818501976bed22b9ab0e7f7c5fdf2a96df0aec80e"
  
  -- 2. Failure: Produces the correct output. (@test-salt.R#6)  ------------------
  salt("a", .seed = 1, .n_chars = 1) not equal to "gag".
  1/1 mismatches
  x[1]: "yay"
  y[1]: "gag"
  
  -- 3. Failure: Produces the correct output. (@test-salt.R#7)  ------------------
  salt("a", .seed = 2, .n_chars = 1) not equal to "eae".
  1/1 mismatches
  x[1]: "uau"
  y[1]: "eae"
  
  == testthat results  ===========================================================
  OK: 12 SKIPPED: 1 FAILED: 3
  1. Failure: Produces the correct output. (@test-anonymize.R#5) 
  2. Failure: Produces the correct output. (@test-salt.R#6) 
  3. Failure: Produces the correct output. (@test-salt.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:212:44: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:213:53: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/anytime.Rcheck/00install.out' for details.
installed size is 73.0Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.8Mb
Running examples in 'archetypes-Ex.R' failed
The error most likely occurred in:

> ### Name: simplexplot
> ### Title: Simplex visualization
> ### Aliases: simplexplot
> 
> ### ** Examples
> 
> ### This example reproduces parts of the Figure 7 shown in
>   ### "Probabilistic Archetypal Analysis" by Seth and Eugster (2014)
> 
>   data("toy", package = "archetypes")
> 
>   set.seed(1234); a3 <- archetypes(toy, k = 3)
>   set.seed(1237); a4 <- archetypes(toy, k = 4)
>   set.seed(1238); a5 <- archetypes(toy, k = 5)
Warning in archetypes(toy, k = 5) :
  k=5: Error in qr.solve(alphas %*% t(alphas)): singular matrix 'a' in solve

> 
>   simplexplot(a3)
>   simplexplot(a3, show_direction = TRUE, show_points = FALSE)
>   simplexplot(a4, projection = tspsimplex_projection)
Loading required package: TSP
>   simplexplot(a5, show_direction = TRUE, show_points = FALSE,
+     direction_length = 2, directions_col = "black")
Error in rep(points_col, nrow(coef(object))) : invalid 'times' argument
Calls: simplexplot
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    help   1.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Package suggested but not available for checking: 'REBayes'
Running examples in 'assist-Ex.R' failed
The error most likely occurred in:

> ### Name: anova.ssr
> ### Title: Testing a Non-parametric Function Fitted via Smoothing Splines
> ### Aliases: anova.ssr
> ### Keywords: file
> 
> ### ** Examples
> 
> data(acid)
> 
> # fit a partial thin-plate spline
> temp <- ssr(ph~t1+x1+x2, rk=tp(t1), data=acid, spar="m")
At line 1992 of file rkpk1.f
Fortran runtime error: Index '2' of dimension 1 of array 'jpvt' above upper bound of 1
Package which this enhances but not available for checking: 'rPython'
Found the following significant warnings:
  Warning: package 'spam' was built under R version 3.7.0
  Warning: package 'dotCall64' was built under R version 3.7.0
See 'd:/Rcompile/CRANpkg/local/3.6/autoFRK.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/AutoStepwiseGLM.Rcheck/00install.out' for details.
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  46.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    java   7.4Mb
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R Under development (unstable) (2019-03-24 r76263) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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

  Natural language support but running in an English locale

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

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

> pkgname <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   1.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.0Mb
Packages which this enhances but not available for checking:
  'doMC', 'rPython'
Package suggested but not available for checking: 'doMC'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/BayClone2.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.2Mb
NeedsCompilation field should likely be 'yes'
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   4.1Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/BayesXsrc.Rcheck/00install.out' for details.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
File 'BayHap/libs/i386/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'
File 'BayHap/libs/x64/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Packages suggested but not available for checking: 'bcmapsdata', 'doMC'
Error(s) in re-building vignettes:
--- re-building 'bdlp.Rmd' using rmarkdown
Loading required namespace: RSQLite
Warning: call dbDisconnect() when finished working with a connection
Quitting from lines 197-211 (bdlp.Rmd) 
Error: processing vignette 'bdlp.Rmd' failed with diagnostics:
miller2012.R:7:208: unexpected '{'
6:  
7: miller2012 <- function(setnr = NULL, seedinfo = list(100, "3.6.0", c("Mersenne-Twister", "Inversion", "Rejection", metaseedinfo = list(100, "3.6.0", c("Mersenne-Twister", "Inversion", "Rejecti
                                                                                                                                                                                                                  ^
--- failed re-building 'bdlp.Rmd'

Warning in file.remove(f) :
  cannot remove file 'dangl2014_set_1_seed_100.db', reason 'Permission denied'
SUMMARY: processing the following file failed:
  'bdlp.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 150.5Mb
  sub-directories of 1Mb or more:
    include  149.5Mb
Error(s) in re-building vignettes:
--- re-building 'bib2df.Rmd' using rmarkdown
Quitting from lines 68-77 (bib2df.Rmd) 
Error: processing vignette 'bib2df.Rmd' failed with diagnostics:
Invalid URL: File is not readable.
--- failed re-building 'bib2df.Rmd'

SUMMARY: processing the following file failed:
  'bib2df.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:212:44: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:213:53: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/bigalgebra.Rcheck/00install.out' for details.
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:212:44: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:213:53: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/biganalytics.Rcheck/00install.out' for details.
bigglm.RODBC: no visible global function definition for 'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'odbcQuery'
bigglm.RODBC : chunk: no visible global function definition for
  'sqlGetResults'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbSendQuery'
bigglm,ANY-DBIConnection: no visible global function definition for
  'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbClearResult'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'dbSendQuery'
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for 'fetch'
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      1.7Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
Found the following additional notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/bigmemory.Rcheck/00install.out' for details.
Running examples in 'BiG-Ex.R' failed
The error most likely occurred in:

> ### Name: BiG_DA
> ### Title: BiG with half-t prior through a data augmentation approach
> ### Aliases: BiG_DA
> 
> ### ** Examples
> 
> set.seed(1234)
> sim = sim_lvm(G=25, S=6, n_p1=3, rho=runif(6,min=0.3,max=0.9), p_p1=0.6, p_p2=0.8, 
+       lambda=runif(6,min=0.6,max=0.8), n_T=sample(c(5,10,15),6,replace=TRUE))
> BiG_DA(r=sim$r, n_T=sim$n_T, n_p1=3, M=100, burnin=50)
Warning in max(W[which(r[, s] == (n_T[s] + 1)), s]) :
  no non-missing arguments to max; returning -Inf
Error in truncnorm::rtruncnorm(sum(r[, s] == n_T[s] + 1, na.rm = TRUE),  : 
  length(mean) > 0 is not TRUE
Calls: BiG_DA -> <Anonymous> -> stopifnot
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.9Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:151:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:159:9: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:184:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/interprocess/detail/win32_api.hpp:186:7: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:212:44: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/winapi/basic_types.hpp:213:53: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/bigtabulate.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/BioMedR.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.5Mb
Depends: includes the non-default packages:
  'colorspace', 'deldir', 'rgl', 'tcltk', 'tcltk2', 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'colorspace'
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
install_blat: no visible global function definition for 'download.file'
install_blat: no visible global function definition for 'unzip'
Undefined global functions or variables:
  download.file unzip
Consider adding
  importFrom("utils", "download.file", "unzip")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   1.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Running 'testthat.R' [196s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BMSC)
  Loading required package: Rcpp
  > 
  > test_check("BMSC")
  -- 1. Failure: A message is returned if some rows are missing (@test_missingValu
  `BMSC:::handleMissingData(data, formula, yUncertainty)$data` produced unexpected messages.
  Expected match: 7 rows \\(9.33% of the data\\) were excluded due to missing values.
  Actual values:
  * 8 rows (10.67% of the data) were excluded due to missing values.
  
  
  == testthat results  ===========================================================
  OK: 61 SKIPPED: 1 FAILED: 1
  1. Failure: A message is returned if some rows are missing (@test_missingValuesHandling.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [200s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(BMSC)
  Loading required package: Rcpp
  > 
  > test_check("BMSC")
  -- 1. Failure: A message is returned if some rows are missing (@test_missingValu
  `BMSC:::handleMissingData(data, formula, yUncertainty)$data` produced unexpected messages.
  Expected match: 7 rows \\(9.33% of the data\\) were excluded due to missing values.
  Actual values:
  * 8 rows (10.67% of the data) were excluded due to missing values.
  
  
  == testthat results  ===========================================================
  OK: 61 SKIPPED: 1 FAILED: 1
  1. Failure: A message is returned if some rows are missing (@test_missingValuesHandling.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/BonEV.Rcheck/00install.out' for details.
installed size is 83.8Mb
  sub-directories of 1Mb or more:
    include   3.0Mb
    lib      80.4Mb
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     3.0Mb
    doc   2.4Mb
Running 'test-all.R' [32s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  -- 1. Error: tidy.htest/oneway.test (@test-stats-htest.R#14)  ------------------
  object 'extra' not found
  1: oneway.test(extra ~ group, data = sleep) at testthat/test-stats-htest.R:14
  2: eval(m, parent.frame())
  3: eval(m, parent.frame())
  4: stats::model.frame(formula = extra ~ group, data = sleep)
  5: model.frame.default(formula = extra ~ group, data = sleep)
  6: eval(predvars, data, env)
  7: eval(predvars, data, env)
  
  == testthat results  ===========================================================
  OK: 976 SKIPPED: 2 FAILED: 1
  1. Error: tidy.htest/oneway.test (@test-stats-htest.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Foreign function calls to a different package:
  .C("CharArray", ..., PACKAGE = "libOpenBUGS")
  .C("CmdInterpreter", ..., PACKAGE = "libOpenBUGS")
  .C("Integer", ..., PACKAGE = "libOpenBUGS")
  .C("RealArray", ..., PACKAGE = "libOpenBUGS")
  .C("SetTempDir", ..., PACKAGE = "libOpenBUGS")
  .C("SetWorkingDir", ..., PACKAGE = "libOpenBUGS")
Undeclared package in foreign function calls:
   'libOpenBUGS'
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Error(s) in re-building vignettes:
--- re-building 'usage.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 67-71 (usage.Rmd) 
Error: processing vignette 'usage.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building 'usage.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/C50.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'FastRWeb'
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/Cairo.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R        1.1Mb
    data     1.5Mb
    models   2.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   2.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.2Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/Ckmeans.1d.dp.Rcheck/00install.out' for details.
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clhs)
  > 
  > test_check("clhs")
  -- 1. Failure: basic clhs on a data.frame works (@test-clhs-data.frame.R#15)  --
  `res` not equal to c(188, 657, 140, 301, 817).
  5/5 mismatches (average diff: 210)
  [1]  97 - 188 == -91
  [2] 903 - 657 == 246
  [3] 539 - 140 == 399
  [4] 451 - 301 == 150
  [5] 979 - 817 == 162
  
  -- 2. Failure: DLHS method on a data.frame works (@test-method_DLHS.R#17)  -----
  `res` not equal to c(214, 40, 702, 919, 521).
  5/5 mismatches (average diff: 211)
  [1] 412 - 214 ==  198
  [2] 170 -  40 ==  130
  [3] 196 - 702 == -506
  [4] 820 - 919 ==  -99
  [5] 641 - 521 ==  120
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 0 FAILED: 2
  1. Failure: basic clhs on a data.frame works (@test-clhs-data.frame.R#15) 
  2. Failure: DLHS method on a data.frame works (@test-method_DLHS.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/clustcurv.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: package 'Rcpp' was built under R version 3.7.0
See 'd:/Rcompile/CRANpkg/local/3.6/clusternor.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
Package suggested but not available for checking: 'moe430a.db'
Error(s) in re-building vignettes:
--- re-building 'commonsMath.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 32-37 (commonsMath.Rmd) 
Error: processing vignette 'commonsMath.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building 'commonsMath.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.0Mb
Package suggested but not available for checking: 'ProData'
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.3Mb
Error(s) in re-building vignettes:
--- re-building 'crfsuite-nlp.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
trying URL 'https://raw.githubusercontent.com/bnosac-dev/nltk_data/gh-pages/packages/corpora/conll2002.zip'
Content type 'application/zip' length 1867449 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

Downloading udpipe model from https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.3/master/inst/udpipe-ud-2.3-181115/dutch-alpino-ud-2.3-181115.udpipe to d:/RCompile/CRANpkg/local/3.6/crfsuite.Rcheck/vign_test/crfsuite/vignettes/dutch-alpino-ud-2.3-181115.udpipe
trying URL 'https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.3/master/inst/udpipe-ud-2.3-181115/dutch-alpino-ud-2.3-181115.udpipe'
Quitting from lines 213-222 (crfsuite-nlp.Rmd) 
Error: processing vignette 'crfsuite-nlp.Rmd' failed with diagnostics:
cannot open URL 'https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.3/master/inst/udpipe-ud-2.3-181115/dutch-alpino-ud-2.3-181115.udpipe'
--- failed re-building 'crfsuite-nlp.Rmd'

SUMMARY: processing the following file failed:
  'crfsuite-nlp.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.9Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/Cubist.Rcheck/00install.out' for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File 'curl/libs/i386/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'
File 'curl/libs/x64/curl.dll':
  Found non-API call to R: 'R_new_custom_connection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   1.9Mb
Running examples in 'CVXR-Ex.R' failed
The error most likely occurred in:

> ### Name: conv
> ### Title: Discrete Convolution
> ### Aliases: conv
> 
> ### ** Examples
> 
> x <- Variable(5)
> h <- matrix(stats::rnorm(2), nrow = 2, ncol = 1)
> prob <- Problem(Minimize(sum(conv(h, x))))
> result <- solve(prob)
Error in valuesById(object, results_dict, sym_data, solver) : 
  Solver failed. Try another.
Calls: solve ... solve.Problem -> <Anonymous> -> <Anonymous> -> valuesById
Execution halted
Running examples in 'D2C-Ex.R' failed
The error most likely occurred in:

> ### Name: predict,D2C-method
> ### Title: predict if there is a connection between node i and node j
> ### Aliases: predict,D2C-method
> 
> ### ** Examples
> 
> require(RBGL)
Loading required package: RBGL
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 object is masked from 'package:randomForest':

    combine

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

> require(gRbase)
Loading required package: gRbase
> require(foreach)
Loading required package: foreach
> data(example)
> ## load the D2C object
> testDAG<-new("simulatedDAG",NDAG=1, N=50,noNodes=5,
+            functionType = "linear", seed=1,sdn=c(0.25,0.5))
simulatedDAG: DAG number: 1 generated: #nodes= 5 # edges= 0 # samples= 50 
> ## creates a simulatedDAG object for testing
> plot(testDAG@list.DAGs[[1]])
Error in testDAG@list.DAGs[[1]] : subscript out of bounds
Calls: plot
Execution halted
.onLoad : <anonymous>: no visible global function definition for
  'read.table'
.onLoad : <anonymous>: no visible global function definition for
  'dbConnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbListTables'
.onLoad : <anonymous>: no visible global function definition for
  'dbExistsTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbReadTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbWriteTable'
.onLoad : <anonymous>: no visible global function definition for
  'dbDisconnect'
.onLoad : <anonymous>: no visible global function definition for
  'dbRemoveTable'
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.1Mb
browse: no visible global function definition for 'slot'
browse: no visible global function definition for 'page'
default.options: no visible binding for global variable 'object.size'
heat.view: no visible global function definition for 'head'
heat.view: no visible global function definition for 'tail'
whos: no visible global function definition for 'slotNames'
whos : <anonymous> : <anonymous>: no visible global function definition
  for 'slot'
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.3Mb
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11180 (sockconn)
Execution halted
Running examples in 'DCEM-Ex.R' failed
The error most likely occurred in:

> ### Name: dcem_train
> ### Title: dcem_train: Part of DCEM package.
> ### Aliases: dcem_train
> 
> ### ** Examples
> 
> # Simulating a mixture of univariate samples from three distributions
> # with mean as 20, 70 and 100 and standard deviation as 10, 100 and 40 respectively.
> sample_uv_data = as.data.frame(c(rnorm(1000, 20, 10), rnorm(500, 70, 100),
+ rnorm(2000, 100, 40)), row=3500)
Warning in as.data.frame.numeric(c(rnorm(1000, 20, 10), rnorm(500, 70, 100),  :
  'row.names' is not a character vector of length 3500 -- omitting it. Will be an error!
> 
> # Randomly shuffle the samples.
> sample_uv_data = as.data.frame(sample_uv_data[sample(1:nrow(sample_uv_data)),],
+ row=nrow(sample_uv_data))
Warning in as.data.frame.numeric(sample_uv_data[sample(1:nrow(sample_uv_data)),  :
  'row.names' is not a character vector of length 3500 -- omitting it. Will be an error!
> 
> # Calling the dcem_train() function on the simulated data with threshold of
> # 0.000001 and iteration count of 1000 respectively.
> sample_uv_out = dcem_train(sample_uv_data, num_clusters = 3, iteration_count = 1000,
+ threshold = 0.000001)
Error in if (mean_diff < threshold) { : 
  missing value where TRUE/FALSE needed
Calls: dcem_train -> dcem_cluster_uv
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'new'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'new'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'new'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'new'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'new'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava winMenuAdd winMenuAddItem
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in 'degenes-Ex.R' failed
The error most likely occurred in:

> ### Name: deg
> ### Title: Detection of differentially expressed genes.
> ### Aliases: deg
> 
> ### ** Examples
> 
> X1 = matrix(rnorm(2000, 0, 1), 200, 10)
> X2 = matrix(rnorm(2000, 0, 1), 200, 10)
> index = sample(1:200, 5, replace=FALSE)
> X2[index,] = X2[index,] + 5
> D = deg(X1, X2)
Sun Mar 24 02:41:36 2019
Calculation of Z
Calculation of z
Calculation of the kernel estimator
Calculation of the kernel estimator
Determination of the rejection region
Error in if (integral > single.alpha) c1 <- c : 
  missing value where TRUE/FALSE needed
Calls: deg
Execution halted
Running examples in 'deisotoper-Ex.R' failed
The error most likely occurred in:

> ### Name: deisotope
> ### Title: Deisotope a Mass Spectrum
> ### Aliases: deisotope
> 
> ### ** Examples
> 
> 
> x <- list(mZ = c(1, 2, 2.5, 3), intensity = rep(1, 4), pepmass=600, charge=2)
> 
> xd <- deisotope(dtoper <- deisotoper(), x)
> plot.deisotoper(x, xd)
> summary(dtoper)
  NumberOfIsotopicSets NumberOfIsotopicClusters NumberOfPeaksInIsotopicClusters
1                    1                        2                               4
  NumberOfPeaks
1             4
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	Summary (textConnection)
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Bootstrapping.CI: no visible global function definition for 'quantile'
D.Jost: no visible global function definition for 'read.table'
D.Jost: no visible global function definition for 'write.table'
Dv.locis.corrected.calc: no visible global function definition for
  'p.adjust'
Gst.Nei: no visible global function definition for 'read.table'
Gst.Nei: no visible global function definition for 'write.table'
H.out: no visible global function definition for 'write.table'
Hardy.calc: no visible global function definition for 'chisq.test'
critical.ci.values: no visible global function definition for
  'quantile'
inputformat: no visible global function definition for 'read.table'
inputformat: no visible global function definition for 'write.table'
over.all.pops: no visible global function definition for 'write.table'
p.value.correcture: no visible global function definition for
  'p.adjust'
pair.pops: no visible global function definition for 'write.table'
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Running examples in 'dendroTools-Ex.R' failed
The error most likely occurred in:

> ### Name: glimpse_daily_data
> ### Title: glimpse_daily_data
> ### Aliases: glimpse_daily_data
> 
> ### ** Examples
> 
> data("LJ_daily_temperatures")
> glimpse_daily_data(env_data = LJ_daily_temperatures, tidy_env_data = FALSE, na.color = "white")
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
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.6Mb
    help   1.4Mb
    libs   2.0Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.8Mb
Running examples in 'dgmb-Ex.R' failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("Tktable") : Tcl package 'Tktable' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "table".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/diffMeanVar.Rcheck/00install.out' for details.
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

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

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

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11417 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11417 (sockconn)
Execution halted
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

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

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

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11911 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11911 (sockconn)
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
Found the following significant warnings:
  Warning: package 'distr' was built under R version 3.7.0
  Warning: package 'sfsmisc' was built under R version 3.7.0
See 'd:/Rcompile/CRANpkg/local/3.6/distrEx.Rcheck/00install.out' for details.
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    include  15.9Mb
    libs      1.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.1Mb
    libs   2.0Mb
Package suggested but not available for checking: 'rPython'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/doremi.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   6.6Mb
File 'DPpackage/libs/i386/DPpackage.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'
File 'DPpackage/libs/x64/DPpackage.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o',
      'ToolsLDTFP.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    appinformation   9.6Mb
    media            1.1Mb
Running examples in 'DTRlearn-Ex.R' failed
The error most likely occurred in:

> ### Name: Olearning_Single
> ### Title: Improved single stage O-learning with cross validation
> ### Aliases: Olearning_Single
> 
> ### ** Examples
> 
> n_cluster=5
> pinfo=10
> pnoise=10
> n_sample=50
> set.seed(3)
> example=make_classification(n_cluster,pinfo,pnoise,n_sample)
> pi=list()
> pi[[2]]=pi[[1]]=rep(1,n_sample)
> modelrbf=Olearning_Single(example$X,example$A,example$R,kernel='rbf',m=3,sigma=0.05)
[1] 0.5
[1] NA
Error in svd(rbind(rho, tau, matrix(alpha), nu)) : 
  infinite or missing values in 'x'
Calls: Olearning_Single -> wsvm -> ipop -> ipop -> svd
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.1Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.6Mb
    libs   5.4Mb
Running examples in 'easyalluvial-Ex.R' failed
The error most likely occurred in:

> ### Name: alluvial_wide
> ### Title: alluvial plot of data in wide format
> ### Aliases: alluvial_wide
> 
> ### ** Examples
> 
> 
> require(magrittr)
Loading required package: magrittr
> 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

> 
> data = as_tibble(mtcars)
> categoricals = c('cyl', 'vs', 'am', 'gear', 'carb')
> numericals = c('mpg', 'cyl', 'disp', 'hp', 'drat', 'wt', 'qsec')
> max_variables = 5
> 
> data = data %>%
+   mutate_at( vars(categoricals), as.factor )
> 
> 
> alluvial_wide( data = data
+                 , max_variables = max_variables
+                 , fill_by = 'first_variable' )
Error: No role currently exists for column(s): 'easyalluvialid'. Please use `update_role()` instead.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    hac    4.0Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/EcoHydRology.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/EdSurvey.Rcheck/00install.out' for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (packageVersion("testthat") >= "0.9.1") {
  +   library(testthat)
  +   test_check("emil")
  + }
  Loading required package: emil
  
  Attaching package: 'emil'
  
  The following object is masked from 'package:base':
  
      mode
  
  -- 1. Failure: k-NN imputation (@test-preprocess.r#30)  ------------------------
  sets$test$x[na.ind] not equivalent to ifelse(na.ind[, 2] <= 3, 5, 4.5).
  3/10 mismatches (average diff: 0.5)
  [5]  5 - 4.5 == 0.5
  [7]  5 - 4.5 == 0.5
  [10] 5 - 4.5 == 0.5
  
  == testthat results  ===========================================================
  OK: 179 SKIPPED: 1 FAILED: 1
  1. Failure: k-NN imputation (@test-preprocess.r#30) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > if (packageVersion("testthat") >= "0.9.1") {
  +   library(testthat)
  +   test_check("emil")
  + }
  Loading required package: emil
  
  Attaching package: 'emil'
  
  The following object is masked from 'package:base':
  
      mode
  
  -- 1. Failure: k-NN imputation (@test-preprocess.r#30)  ------------------------
  sets$test$x[na.ind] not equivalent to ifelse(na.ind[, 2] <= 3, 5, 4.5).
  3/10 mismatches (average diff: 0.5)
  [5]  5 - 4.5 == 0.5
  [7]  5 - 4.5 == 0.5
  [10] 5 - 4.5 == 0.5
  
  == testthat results  ===========================================================
  OK: 179 SKIPPED: 1 FAILED: 1
  1. Failure: k-NN imputation (@test-preprocess.r#30) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Found the following significant warnings:
  Warning: package 'rjags' was built under R version 3.7.0
  Warning: package 'coda' was built under R version 3.7.0
See 'd:/Rcompile/CRANpkg/local/3.6/EWOC2.Rcheck/00install.out' for details.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/excursions.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
File 'fastmatch/libs/i386/fastmatch.dll':
  Found non-API call to R: 'match5'
File 'fastmatch/libs/x64/fastmatch.dll':
  Found non-API call to R: 'match5'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
Found the following file(s) containing GNU extensions:
  src/feather/Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif, .NOTPARALLEL See section 'Writing portable
packages' in the 'Writing R Extensions' manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    libs   1.7Mb
Packages suggested but not available for checking: 'doMC', 'RSvgDevice'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R   6.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Package which this enhances but not available for checking: 'doMC'
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs  10.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
Package suggested but not available for checking: 'dggrids'
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
    libs   1.4Mb
Found the following significant warnings:
  Warning: package 'flexclust' was built under R version 3.7.0
See 'd:/Rcompile/CRANpkg/local/3.6/funcy.Rcheck/00install.out' for details.
Running examples in 'funHDDC-Ex.R' failed
The error most likely occurred in:

> ### Name: predict.funHDDC
> ### Title: Predict new results from a funHDDC model
> ### Aliases: predict.funHDDC
> 
> ### ** Examples
> 
> ##Univariate example
>     data("trigo")
>     basis<- create.bspline.basis(c(0,1), nbasis=25)
>     z<-sample(1:100,0.8*100,replace=FALSE)
>     var1_train<-smooth.basis(argvals=seq(0,1,length.out = 100),y=t(trigo[z,1:100]),
+                              fdParobj=basis)$fd
>     var1_test<-smooth.basis(argvals=seq(0,1,length.out = 100),y=t(trigo[-z,1:100]),
+                             fdParobj=basis)$fd
> 
>     model<-funHDDC(var1_train,K=2)
      model K threshold complexity         BIC
1 AKJBKQKDK 2       0.2        103 -373,867.94

SELECTED: model  AKJBKQKDK  with  2  clusters.
Selection Criterion: BIC.
>     pred<-predict(model,var1_test)
> 
> ##Multivariate example
>     data("triangle")
>     basis<- create.bspline.basis(c(1,21), nbasis=25)
>     z<-sample(1:100,0.8*100,replace=FALSE)
>     var1_train<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[z,1:101]),
+                               fdParobj=basis)$fd
>     var1_test<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[-z,1:101]),
+                             fdParobj=basis)$fd
>     var2_train<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[z,102:202]),
+                             fdParobj=basis)$fd
>     var2_test<-smooth.basis(argvals=seq(1,21,length.out = 101),y=t(triangle[-z,102:202]),
+                             fdParobj=basis)$fd
> 
>     model<-funHDDC(list(var1_train,var2_train),K=3)
Warning in funHDDC(list(var1_train, var2_train), K = 3) :
  All models diverged.
>     pred<-predict(model,list(var1_test,var2_test))
Error in UseMethod("predict") : 
  no applicable method for 'predict' applied to an object of class "list"
Calls: predict
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      1.5Mb
finterp.data.frame: no visible global function definition for
  'as.formula'
finterp.data.frame: no visible global function definition for 'terms'
finterp.data.frame: no visible global function definition for
  'model.matrix'
finterp.data.frame: no visible global function definition for
  'model.frame'
finterp.default: no visible global function definition for 'terms'
finterp.default: no visible global function definition for
  'model.matrix'
finterp.default: no visible global function definition for
  'model.frame'
gamlss.nl: no visible global function definition for 'nlm'
nl: no visible global function definition for 'is'
nlgamlss: no visible global function definition for 'NO'
nlgamlss: no visible global function definition for 'as.gamlss.family'
nlgamlss: no visible global function definition for 'nlm'
nlgamlss: no visible global function definition for 'cov2cor'
summary.nlgamlss: no visible global function definition for 'coef'
summary.nlgamlss: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.7Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   3.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R         6.1Mb
    extdata   1.3Mb
Found the following significant warnings:
  Warning: package 'sp' was built under R version 3.7.0
See 'd:/Rcompile/CRANpkg/local/3.6/georob.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/gginnards.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.7Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   9.0Mb
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
installed size is 23.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  21.2Mb
Package suggested but not available for checking: 'cplexAPI'
File 'gnmf/libs/i386/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'
File 'gnmf/libs/x64/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/gprofiler2.Rcheck/00install.out' for details.
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    R  27.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   1.6Mb
Running examples in 'gremlin-Ex.R' failed
The error most likely occurred in:

> ### Name: gremlin-package
> ### Title: Mixed-Effects REML Incorporating Generalized Inverses
> ### Aliases: gremlin-package _PACKAGE
> 
> ### ** Examples
> 
>   require(nadiv)
Loading required package: nadiv
>   Ainv <- makeAinv(Mrode3[-c(1:2), 1:3])$Ainv
>   mod11 <- gremlinR(WWG11 ~ sex - 1,
+ random = ~ calf,
+ data = Mrode11,
+ ginverse = list(calf = Ainv),
+ Gstart = matrix(0.2), Rstart = matrix(0.4),
+ maxit = 10, v = 2)
gremlin started:		 05:14:13 
   1 of max 10 			 05:14:13 
	EM to find next theta
Element 0.2124631 must be a symmetric matrix or a number
Error in FUN(X[[i]], ...) : 
Calls: gremlinR -> sapply -> lapply -> FUN
Execution halted
Running examples in 'GREP2-Ex.R' failed
The error most likely occurred in:

> ### Name: get_metadata
> ### Title: Download metadata from GEO and SRA
> ### Aliases: get_metadata
> 
> ### ** Examples
> 
> 
> get_metadata(geo_series_acc="GSE102170",destdir=tempdir(),
+ geo_only=TRUE,download_method="auto")
Error in download.file(myurl, destfile, mode = mode, quiet = TRUE, method = getOption("download.file.method.GEOquery")) : 
  cannot open URL 'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE102nnn/GSE102170/soft/GSE102170_family.soft.gz'
Calls: get_metadata -> <Anonymous> -> getGEOfile -> download.file
Execution halted
Running examples in 'groupedSurv-Ex.R' failed
The error most likely occurred in:

> ### Name: groupedSurvFam
> ### Title: Compute the Efficient Score Statistic for the Frailty Model
> ### Aliases: groupedSurvFam
> 
> ### ** Examples
> 
> # Generate dummy data
> set.seed(111)
> n <- 24
> 
> # effect size
> beta <- 0.3
> 
> # covariate parameters
> theta <- c(0.2, 0.2)
> 
> # variable of interest
> MAF <- 0.05
> x <- matrix(rbinom(n, 2, MAF), ncol = 1)
> 
> # covariate data (centered at 0)
> z1 <- rnorm(n)
> z2 <- rbinom(n, 1, 0.5) - 0.5
> Z  <- matrix(cbind(z1, z2), ncol = 2)
> 
> # continuous survival time
> lam0 <- 1
> cmax <- 3
> lami <- lam0 * exp(x*beta + Z[,1]*theta[1]+Z[,2]*theta[2])
> stime <- rexp(n, lami)
> ctime <- runif(n, 0, cmax)
> delta <- stime < ctime
> otime <- pmin(stime, ctime)
> 
> # number of observation times
> ntps <- 5
> 
> # number of intervals
> r <- ntps + 1
> 
> # last observation time
> maxbreakq <- 0.85
> maxbreak <- qexp(maxbreakq, lam0)
> 
> # grouped failure times
> breaks <- (1:ntps) * (maxbreak/ntps)
> gtime <- findInterval(otime, breaks) + 1
> delta[gtime == r] <- FALSE
> dctime <- findInterval(ctime, breaks) + 1
> delta[gtime == dctime] <- FALSE
> delta <- as.numeric(delta)
> 
> # family-specific information
> m <- n/3
> fam_role <- rep(c("o","f","m"),m)
> fam_group <- as.character(rep(1:m,rep(3,m)))
> 
> # nuisance parameters
> alpha <- thetaEst(Z, gtime,delta)$alpha
> var <- 0.2
> 
> # compute efficient score statistics
> res   <- groupedSurvFam(x, fam_group, fam_role, alpha, var, gtime, delta) 
> res
            [,1]
[1,] -0.09108599
[2,] -0.03535880
[3,] -0.05805514
[4,] -0.07539618
[5,]  0.09537326
[6,]  0.50679716
[7,] -0.01163486
[8,] -0.02150784
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11275 (sockconn)
Execution halted
Running examples in 'groupedSurv-Ex.R' failed
The error most likely occurred in:

> ### Name: groupedSurvFam
> ### Title: Compute the Efficient Score Statistic for the Frailty Model
> ### Aliases: groupedSurvFam
> 
> ### ** Examples
> 
> # Generate dummy data
> set.seed(111)
> n <- 24
> 
> # effect size
> beta <- 0.3
> 
> # covariate parameters
> theta <- c(0.2, 0.2)
> 
> # variable of interest
> MAF <- 0.05
> x <- matrix(rbinom(n, 2, MAF), ncol = 1)
> 
> # covariate data (centered at 0)
> z1 <- rnorm(n)
> z2 <- rbinom(n, 1, 0.5) - 0.5
> Z  <- matrix(cbind(z1, z2), ncol = 2)
> 
> # continuous survival time
> lam0 <- 1
> cmax <- 3
> lami <- lam0 * exp(x*beta + Z[,1]*theta[1]+Z[,2]*theta[2])
> stime <- rexp(n, lami)
> ctime <- runif(n, 0, cmax)
> delta <- stime < ctime
> otime <- pmin(stime, ctime)
> 
> # number of observation times
> ntps <- 5
> 
> # number of intervals
> r <- ntps + 1
> 
> # last observation time
> maxbreakq <- 0.85
> maxbreak <- qexp(maxbreakq, lam0)
> 
> # grouped failure times
> breaks <- (1:ntps) * (maxbreak/ntps)
> gtime <- findInterval(otime, breaks) + 1
> delta[gtime == r] <- FALSE
> dctime <- findInterval(ctime, breaks) + 1
> delta[gtime == dctime] <- FALSE
> delta <- as.numeric(delta)
> 
> # family-specific information
> m <- n/3
> fam_role <- rep(c("o","f","m"),m)
> fam_group <- as.character(rep(1:m,rep(3,m)))
> 
> # nuisance parameters
> alpha <- thetaEst(Z, gtime,delta)$alpha
> var <- 0.2
> 
> # compute efficient score statistics
> res   <- groupedSurvFam(x, fam_group, fam_role, alpha, var, gtime, delta) 
> res
            [,1]
[1,] -0.09108599
[2,] -0.03535880
[3,] -0.05805514
[4,] -0.07539618
[5,]  0.09537326
[6,]  0.50679716
[7,] -0.01163486
[8,] -0.02150784
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11253 (sockconn)
Execution halted
Package suggested but not available for checking: 'dse1'
Running examples in 'GSE-Ex.R' failed
The error most likely occurred in:

> ### Name: TSGS
> ### Title: Two-Step Generalized S-Estimator for cell- and case-wise
> ###   outliers
> ### Aliases: TSGS
> 
> ### ** Examples
> 
> set.seed(12345)
> 
> # Generate 5% cell-wise contaminated normal data
> # using a random correlation matrix with condition number 100
> x <- generate.cellcontam(n=100, p=10, cond=100, contam.size=5, contam.prop=0.05)
> 
> ## Using MLE
> slrt( cov(x$x), x$A)
[1] 61.72234
> 
> ## Using Fast-S
> slrt( rrcov:::CovSest(x$x)@cov, x$A)
[1] 33.86437
> 
> ## Using 2SGS
> slrt( TSGS(x$x)@S, x$A)
Error: 'DetectDeviatingCells' is not an exported object from 'namespace:cellWise'
Execution halted
Running examples in 'GSE-Ex.R' failed
The error most likely occurred in:

> ### Name: TSGS
> ### Title: Two-Step Generalized S-Estimator for cell- and case-wise
> ###   outliers
> ### Aliases: TSGS
> 
> ### ** Examples
> 
> set.seed(12345)
> 
> # Generate 5% cell-wise contaminated normal data
> # using a random correlation matrix with condition number 100
> x <- generate.cellcontam(n=100, p=10, cond=100, contam.size=5, contam.prop=0.05)
> 
> ## Using MLE
> slrt( cov(x$x), x$A)
[1] 69.01395
> 
> ## Using Fast-S
> slrt( rrcov:::CovSest(x$x)@cov, x$A)
[1] 44.9836
> 
> ## Using 2SGS
> slrt( TSGS(x$x)@S, x$A)
Error: 'DetectDeviatingCells' is not an exported object from 'namespace:cellWise'
Execution halted
normalweight: no visible binding for global variable 'NW_above'
normalweight: no visible binding for global variable 'NW_below'
obese: no visible global function definition for 'data'
obese: no visible binding for global variable 'OB_above'
obese: no visible binding for global variable 'OB_below'
overweight: no visible global function definition for 'data'
overweight: no visible binding for global variable 'OW_above'
overweight: no visible binding for global variable 'OW_below'
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(harvestr)
  > foreach::registerDoSEQ()
  > test_check("harvestr")
  -- 1. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42)  
  RNGkind() not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  -- 2. Failure: gather replaces seed. (@test-gather.R#57)  ----------------------
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  -- 3. Failure: get.seed retrieves properly (@test-seeds.R#14)  -----------------
  `seed` not identical to `eseed`.
  Mean relative difference: 0.9608917
  
  -- 4. Failure: replace.seed (@test-seeds.R#29)  --------------------------------
  `k` not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  -- 5. Failure: replace.seed (@test-seeds.R#30)  --------------------------------
  `l` not identical to c("L'Ecuyer-CMRG", "Inversion").
  Lengths differ: 3 is not 2
  
  -- 6. Failure: withseed replaces previous seed. (@test-seeds.R#56)  ------------
  RNGkind() not identical to c("Mersenne-Twister", "Box-Muller").
  Lengths differ: 3 is not 2
  
  == testthat results  ===========================================================
  OK: 119 SKIPPED: 5 FAILED: 6
  1. Failure: gather gives the appropriate kinds of seed. (@test-gather.R#42) 
  2. Failure: gather replaces seed. (@test-gather.R#57) 
  3. Failure: get.seed retrieves properly (@test-seeds.R#14) 
  4. Failure: replace.seed (@test-seeds.R#29) 
  5. Failure: replace.seed (@test-seeds.R#30) 
  6. Failure: withseed replaces previous seed. (@test-seeds.R#56) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   4.0Mb
Error(s) in re-building vignettes:
--- re-building 'ctstm.Rmd' using rmarkdown
Loading required package: survival
Quitting from lines 189-206 (ctstm.Rmd) 
Error: processing vignette 'ctstm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building 'ctstm.Rmd'

--- re-building 'icea.Rmd' using rmarkdown
Quitting from lines 169-177 (icea.Rmd) 
Error: processing vignette 'icea.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building 'icea.Rmd'

--- re-building 'intro.Rmd' using rmarkdown
Loading required package: survival
Quitting from lines 262-269 (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 'psm.Rmd' using rmarkdown
Loading required package: survival
Quitting from lines 179-198 (psm.Rmd) 
Error: processing vignette 'psm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building 'psm.Rmd'

SUMMARY: processing the following files failed:
  'ctstm.Rmd' 'icea.Rmd' 'intro.Rmd' 'psm.Rmd'

Error: Vignette re-building failed.
Execution halted
PlotOptPower: no visible global function definition for 'bmp'
PlotOptPower: no visible global function definition for
  'filled.contour'
PlotOptPower: no visible global function definition for 'title'
PlotOptPower: no visible global function definition for 'grey.colors'
PlotOptPower: no visible global function definition for 'axis'
PlotOptPower: no visible global function definition for 'polygon'
PlotOptPower: no visible global function definition for 'legend'
PlotOptPower: no visible global function definition for 'mtext'
PlotOptPower: no visible global function definition for 'dev.off'
PlotOptPower: no visible global function definition for
  'terrain.colors'
ShowOptDesign: no visible global function definition for 'head'
diffVariantError: no visible global function definition for 'pbinom'
predictPoolNCP: no visible global function definition for 'data'
probDetEqual3: no visible global function definition for 'dbinom'
probDetEqual3: no visible global function definition for 'pbinom'
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.5Mb
    libs   1.5Mb
File 'hSDM/libs/i386/hSDM.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'useful.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'hSDM.Nmixture.o', 'hSDM.Nmixture.iCAR.o', 'hSDM.ZIB.o',
      'hSDM.ZIB.iCAR.alteration.o', 'hSDM.ZIB.iCAR.o', 'hSDM.ZIP.o',
      'hSDM.ZIP.iCAR.alteration.o', 'hSDM.ZIP.iCAR.o',
      'hSDM.binomial.o', 'hSDM.binomial.iCAR.o', 'hSDM.poisson.o',
      'hSDM.poisson.iCAR.o', 'hSDM.siteocc.o', 'hSDM.siteocc.iCAR.o'
File 'hSDM/libs/x64/hSDM.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'useful.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'hSDM.Nmixture.o', 'hSDM.Nmixture.iCAR.o', 'hSDM.ZIB.o',
      'hSDM.ZIB.iCAR.alteration.o', 'hSDM.ZIB.iCAR.o', 'hSDM.ZIP.o',
      'hSDM.ZIP.iCAR.alteration.o', 'hSDM.ZIP.iCAR.o',
      'hSDM.binomial.o', 'hSDM.binomial.iCAR.o', 'hSDM.poisson.o',
      'hSDM.poisson.iCAR.o', 'hSDM.siteocc.o', 'hSDM.siteocc.iCAR.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data  12.0Mb
    doc    2.2Mb
Error(s) in re-building vignettes:
--- re-building 'DecisionNetworks.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: nnet
--- finished re-building 'DecisionNetworks.Rmd'

--- re-building 'GettingStartedWithHydeNet.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'GettingStartedWithHydeNet.Rmd'

--- re-building 'HydeNetPlots.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 158-167 (HydeNetPlots.Rmd) 
Error: processing vignette 'HydeNetPlots.Rmd' failed with diagnostics:
Blackjack rules URL does not exist.  Find a new link
--- failed re-building 'HydeNetPlots.Rmd'

--- re-building 'WorkingWithHydeNetObjects.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
--- finished re-building 'WorkingWithHydeNetObjects.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(hyphenatr)
  > 
  > test_check("hyphenatr")
  -- 1. Failure: we can do something (@test-hyphenatr.R#16)  ---------------------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "tÃ¤=gelÃ®ch"
  y[1]: "tä=gelîch"
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: we can do something (@test-hyphenatr.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   2.1Mb
Running examples in 'IBDsim-Ex.R' failed
The error most likely occurred in:

> ### Name: oneLocusIBD
> ### Title: Estimating pairwise IBD coefficients
> ### Aliases: oneLocusIBD
> ### Keywords: math
> 
> ### ** Examples
> 
> ### Example 1: Full siblings
> x <- nuclearPed(2) 
> Nsim <- 100 # Should be increased substantially
> 
> # Autosomal kappa: Estimate vs exact 
> k_est = oneLocusIBD(x, ind1=3, ind2=4, Nsim=Nsim, seed=123)
---------------
Performing unconditional simulation
Mode: autosomal 
Recombination model: haldane (poisson process) 
Number of simulations: 100 
Simulation finished. Time used: 0.03 seconds
---------------
IBD analysis finished. Total time used: 0.05 seconds.
> k_exact = c(0.25, 0.5, 0.25)
> stopifnot(all(round(k_est - k_exact, 1) == 0))
Error: all(round(k_est - k_exact, 1) == 0) is not TRUE
Execution halted
Running examples in 'IBDsim-Ex.R' failed
The error most likely occurred in:

> ### Name: oneLocusIBD
> ### Title: Estimating pairwise IBD coefficients
> ### Aliases: oneLocusIBD
> ### Keywords: math
> 
> ### ** Examples
> 
> ### Example 1: Full siblings
> x <- nuclearPed(2) 
> Nsim <- 100 # Should be increased substantially
> 
> # Autosomal kappa: Estimate vs exact 
> k_est = oneLocusIBD(x, ind1=3, ind2=4, Nsim=Nsim, seed=123)
---------------
Performing unconditional simulation
Mode: autosomal 
Recombination model: haldane (poisson process) 
Number of simulations: 100 
Simulation finished. Time used: 0.05 seconds
---------------
IBD analysis finished. Total time used: 0.05 seconds.
> k_exact = c(0.25, 0.5, 0.25)
> stopifnot(all(round(k_est - k_exact, 1) == 0))
Error: all(round(k_est - k_exact, 1) == 0) is not TRUE
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/icd.Rcheck/00install.out' for details.
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    R     14.5Mb
    doc    4.8Mb
    libs   2.9Mb
Error(s) in re-building vignettes:
--- re-building 'CMS-HCC.Rmd' using rmarkdown
--- finished re-building 'CMS-HCC.Rmd'

--- re-building 'ICD-10.Rmd' using rmarkdown
--- finished re-building 'ICD-10.Rmd'

--- re-building 'PCCC.Rmd' using rmarkdown
--- finished re-building 'PCCC.Rmd'

--- re-building 'charlson-scores.Rmd' using rmarkdown
--- finished re-building 'charlson-scores.Rmd'

--- re-building 'compare-maps.Rmd' using rmarkdown
--- finished re-building 'compare-maps.Rmd'

--- re-building 'efficiency.Rmd' using rmarkdown
Error: processing vignette 'efficiency.Rmd' failed with diagnostics:
pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
--- failed re-building 'efficiency.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

--- re-building 'ranges.Rmd' using rmarkdown
--- finished re-building 'ranges.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/igraph.Rcheck/00install.out' for details.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.9Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.3Mb
    include   2.8Mb
    libs     12.9Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/iMediate.Rcheck/00install.out' for details.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(infer)
  > 
  > test_check("infer")
  Setting `type = "permute"` in `generate()`.
  -- 1. Failure: conf_int argument works (@test-wrappers.R#141)  -----------------
  no_var_equal == var_equal isn't false.
  
  -- 2. Failure: conf_int argument works (@test-wrappers.R#153)  -----------------
  shortcut_no_var_equal == shortcut_var_equal isn't false.
  
  == testthat results  ===========================================================
  OK: 347 SKIPPED: 0 FAILED: 2
  1. Failure: conf_int argument works (@test-wrappers.R#141) 
  2. Failure: conf_int argument works (@test-wrappers.R#153) 
  
  Error: testthat unit tests failed
  Execution halted
Missing or unexported object: 'devtools::find_rtools'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/intensity.analysis.Rcheck/00install.out' for details.
ClearBottomMenuPlot: no visible global function definition for 'rect'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertX'
InteractiveIGraph : mousedown: no visible global function definition
  for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertX'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'grconvertY'
InteractiveIGraph : dragmousemove: no visible global function
  definition for 'polygon'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertX'
InteractiveIGraph : mouseup: no visible global function definition for
  'grconvertY'
InteractiveIGraph : keybd: no visible global function definition for
  'readClipboard'
InteractiveIGraph : keybd: no visible global function definition for
  'par'
PlotRegionGeneral: no visible global function definition for 'polygon'
plot.InteractiveIGraph: no visible global function definition for
  'plot'
plot.InteractiveIGraph: no visible global function definition for 'par'
plot.Menu: no visible global function definition for 'par'
plot.Menu: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'strwidth'
plot.MenuItem: no visible binding for global variable 'strheight'
plot.MenuItem: no visible binding for global variable 'rect'
plot.MenuItem: no visible binding for global variable 'text'
plot.MenuLine: no visible binding for global variable 'rect'
Undefined global functions or variables:
  grconvertX grconvertY par plot polygon readClipboard rect strheight
  strwidth text
Consider adding
  importFrom("graphics", "grconvertX", "grconvertY", "par", "plot",
             "polygon", "rect", "strheight", "strwidth", "text")
  importFrom("utils", "readClipboard")
to your NAMESPACE file.
Interpol: no visible global function definition for 'splinefun'
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
File 'iotools/libs/i386/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'
File 'iotools/libs/x64/iotools.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_ReadConnection',
    'R_WriteConnection'

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

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

> ### Name: idstrsplit
> ### Title: Create an iterator for splitting binary or character input into
> ###   a dataframe
> ### Aliases: idstrsplit
> ### Keywords: iterator
> 
> ### ** Examples
> 
> col_names <- names(iris)
> write.csv(iris, file="iris.csv", row.names=FALSE)
> it <- idstrsplit("iris.csv", col_types=c(rep("numeric", 4), "character"), 
+                  sep=",")
> # Get the elements
> iris_read <- it$nextElem()[-1,]
> # or with the iterators package
> # nextElem(it)
> names(iris_read) <- col_names
> print(head(iris_read))
  Sepal.Length Sepal.Width Petal.Length Petal.Width  Species
2          5.1         3.5          1.4         0.2 "setosa"
3          4.9         3.0          1.4         0.2 "setosa"
4          4.7         3.2          1.3         0.2 "setosa"
5          4.6         3.1          1.5         0.2 "setosa"
6          5.0         3.6          1.4         0.2 "setosa"
7          5.4         3.9          1.7         0.4 "setosa"
> unlink("iris.csv")
> 
> 
> 
> cleanEx()
Error: connections left open:
	iris.csv (file)
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    extdata   7.5Mb
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 293
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11163 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11163 (sockconn)
Execution halted
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11037 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11037 (sockconn)
Execution halted
Running examples in 'iterators-Ex.R' failed
The error most likely occurred in:

> ### Name: ireadLines
> ### Title: Iterator over Lines of Text from a Connection
> ### Aliases: ireadLines
> ### Keywords: utilities
> 
> ### ** Examples
> 
>   # create an iterator over the lines of COPYING
>   it <- ireadLines(file.path(R.home(), 'COPYING'))
>   nextElem(it)
[1] "\t\t    GNU GENERAL PUBLIC LICENSE"
>   nextElem(it)
[1] "\t\t       Version 2, June 1991"
>   nextElem(it)
[1] ""
> 
> 
> 
> cleanEx()
Error: connections left open:
	D:/RCompile/recent/R/COPYING (file)
Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(janitor)
  > 
  > test_check("janitor")
  -- 1. Failure: users can supply own Ns (@test-adorn-ns.R#129)  -----------------
  `%>%`(...) not equal to data.frame(...).
  Component "big": 2 string mismatches
  Component "small": 2 string mismatches
  
  == testthat results  ===========================================================
  OK: 438 SKIPPED: 0 FAILED: 1
  1. Failure: users can supply own Ns (@test-adorn-ns.R#129) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/JavaGD.Rcheck/00install.out' for details.
Package unavailable to check Rd xrefs: 'doMC'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
comp.npci: no visible global function definition for 'qnorm'
epband.fun: no visible global function definition for 'data'
epband.fun: no visible binding for global variable
  'critical.value.nair.90'
epband.fun: no visible binding for global variable
  'critical.value.nair.95'
epband.fun: no visible binding for global variable
  'critical.value.nair.99'
hall.wellner.fun: no visible global function definition for 'data'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.90'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.95'
hall.wellner.fun: no visible binding for global variable
  'critical.value.hall.99'
lrt.confints: no visible global function definition for 'qchisq'
rothman.fun: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.1Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:72:36: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:96:9: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/LANDD.Rcheck/00install.out' for details.
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Running examples in 'LCA-Ex.R' failed
The error most likely occurred in:

> ### Name: LCA
> ### Title: Localised Co-dependency Analysis
> ### Aliases: LCA
> 
> ### ** Examples
> 
> ## create a data matrix
> 
> x <- array(runif(1200),dim=c(40,12))
> 
> ## implant similarity across a 'clique'
> 
> clique.cols <- sample(ncol(x),4)
> x[,clique.cols] <- x[,clique.cols] + rnorm(nrow(x))
> 
> ## scale x to (0,1)
> 
> x[x<0] <- 0
> x[x>1] <- 1
> 
> ## choose a 'seed' feature and some partner
> 
> seed.row <- sample(nrow(x),1)
> partner.row <- sample(setdiff(c(1:nrow(x)),seed.row),1)
> 
> x[c(seed.row,partner.row),clique.cols] <- x[c(seed.row,partner.row),clique.cols] + 
+ rep(rnorm(length(clique.cols)),each=2)
> 
> ## calibrate PTL models to dataset
> 
> PTL.fit <- fitPTLmodel(x,nPairs=15)
1 models successfully fitted out of 12 
Error in fitPTLmodel(x, nPairs = 15) : 
  Rerun model calibration (possibly with higher nPairs), no successful fits this time.
Execution halted
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/liayson.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
    libs   1.5Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/liquidSVM.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.2Mb
    testdata   1.6Mb
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lolR)
  > 
  > test_check("lolR")
  -- 1. Failure: Optimal Embedding Dimensions (@test-xval.R#45)  -----------------
  result.rs$optimal.lhat not equal to result.rs.noset$optimal.lhat.
  Lengths differ: 2 is not 1
  
  == testthat results  ===========================================================
  OK: 446 SKIPPED: 0 FAILED: 1
  1. Failure: Optimal Embedding Dimensions (@test-xval.R#45) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(loose.rock)
  > 
  > test_check("loose.rock")
  -- 1. Error: coding genes retrieves some genes (@test-coding.genes.R#4)  -------
  replacement has 0 rows, data has 86
  1: coding.genes(verbose = FALSE) at testthat/test-coding.genes.R:4
  2: `$<-`(`*tmp*`, "ccds_status", value = structure(integer(0), .Label = character(0), class = "factor"))
  3: `$<-.data.frame`(`*tmp*`, "ccds_status", value = structure(integer(0), .Label = character(0), class = "factor"))
  4: stop(sprintf(ngettext(N, "replacement has %d row, data has %d", "replacement has %d rows, data has %d"), 
         N, nrows), domain = NA)
  
  == testthat results  ===========================================================
  OK: 145 SKIPPED: 2 FAILED: 1
  1. Error: coding genes retrieves some genes (@test-coding.genes.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: package 'data.table' was built under R version 3.7.0
  Warning: package 'FactoMineR' was built under R version 3.7.0
  Warning: package 'rARPACK' was built under R version 3.7.0
  Warning: package 'svd' was built under R version 3.7.0
See 'd:/Rcompile/CRANpkg/local/3.6/lori.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.5Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lsbclust)
  Loading required package: ggplot2
  > 
  > test_check("lsbclust")
  K-means on overall means...	DONE
  -- 1. Failure: cluster vector (@test_orc.R#29)  --------------------------------
  ovl$cluster not identical to ovltest$cluster.
  24/220 mismatches (average diff: 1.33)
  [1]    8 - 10 == -2
  [14]  10 -  9 ==  1
  [31]   9 -  8 ==  1
  [57]   9 -  8 ==  1
  [61]   8 - 10 == -2
  [64]   8 - 10 == -2
  [77]  10 -  9 ==  1
  [84]  10 -  9 ==  1
  [112]  9 -  8 ==  1
  ...
  
  -- 2. Failure: cluster means (@test_orc.R#33)  ---------------------------------
  ovl$centers not equal to ovltest$centers.
  3/12 mismatches (average diff: 3.68)
  [8]  7.22 - 2.70 ==  4.52
  [9]  2.70 - 1.70 ==  1.00
  [10] 1.70 - 7.22 == -5.52
  
  K-means on row margins...	DONE
  K-means on column margins...	DONE
  == testthat results  ===========================================================
  OK: 34 SKIPPED: 0 FAILED: 2
  1. Failure: cluster vector (@test_orc.R#29) 
  2. Failure: cluster means (@test_orc.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lucr)
  > 
  > test_check("lucr")
  -- 1. Failure: Simple amounts can be converted (@test_conversion.R#4)  ---------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12.00"
  y[1]: "£12.00"
  
  -- 2. Failure: Complex amounts can be converted (@test_conversion.R#8)  --------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12,000.00"
  y[1]: "£12,000.00"
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 2
  1. Failure: Simple amounts can be converted (@test_conversion.R#4) 
  2. Failure: Complex amounts can be converted (@test_conversion.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   1.6Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
    proj   5.0Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    TS_files     5.8Mb
    base_files   6.3Mb
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs  34.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs          7.7Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/maps.Rcheck/00install.out' for details.
Running examples in 'markmyassignment-Ex.R' failed
The error most likely occurred in:

> ### Name: mark_my_file
> ### Title: Mark assignment file
> ### Aliases: mark_my_file
> 
> ### ** Examples
> 
> assignment_path <- 
+   paste0(system.file(package = "markmyassignment"), "/extdata/example_assignment01.yml")
> file_path <- paste0(system.file(package = "markmyassignment"), "/extdata/example_lab_file.R")
> mark_my_file(mark_file = file_path, assignment_path = assignment_path)
v | OK F W S | Context

/ |  0       | task1
- |  1       | task1
\ |  2       | task1
| |  3       | task1
v |  3       | task1

/ |  0       | task2a
- |  1       | task2a
\ |  2       | task2a
| |  3       | task2a
v |  3       | task2a

/ |  0       | task2b
- |  1       | task2b
\ |  2       | task2b
| |  3       | task2b
/ |  4       | task2b
v |  4       | task2b

/ |  0       | Mandatory tests
- |  1       | Mandatory tests
v |  1       | Mandatory tests

== Results =====================================================================
OK:       11
Failed:   0
Warnings: 0
Skipped:  0
Keep up the good work!> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	lines (textConnection)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'GSoC-2017_additions.Rmd' using rmarkdown
Package:  markovchain
Version:  0.6.9.14
Date:     2019-01-20
BugReport: http://github.com/spedygiorgio/markovchain/issues

--- finished re-building 'GSoC-2017_additions.Rmd'

--- re-building 'an_introduction_to_markovchain_package.Rmd' using rmarkdown
Error: processing vignette 'an_introduction_to_markovchain_package.Rmd' failed with diagnostics:
pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
--- failed re-building 'an_introduction_to_markovchain_package.Rmd'

--- re-building 'complicateSteadyStates.Rmd' using rmarkdown
Package:  markovchain
Version:  0.6.9.14
Date:     2019-01-20
BugReport: http://github.com/spedygiorgio/markovchain/issues

--- finished re-building 'complicateSteadyStates.Rmd'

--- re-building 'higher_order_markov_chains.Rmd' using rmarkdown
Error: processing vignette 'higher_order_markov_chains.Rmd' failed with diagnostics:
pandoc version 2.2 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
--- failed re-building 'higher_order_markov_chains.Rmd'

--- re-building 'markovchainCrashIntro.Rmd' using rmarkdown
--- finished re-building 'markovchainCrashIntro.Rmd'

SUMMARY: processing the following files failed:
  'an_introduction_to_markovchain_package.Rmd'
  'higher_order_markov_chains.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
Depends: includes the non-default packages:
  'MASS', 'boot', 'RColorBrewer', 'scatterplot3d', 'tcltk', 'tcltk2',
  'tkrplot', 'rpanel', 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.0Mb
Error(s) in re-building vignettes:
--- re-building 'metaBMA.Rmd' using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
INFORMATION: Es konnten keine Dateien mit dem angegebenen
Muster gefunden werden.
Quitting from lines 63-72 (metaBMA.Rmd) 
Error: processing vignette 'metaBMA.Rmd' failed with diagnostics:
Unable to call JAGS
--- failed re-building 'metaBMA.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Running examples in 'metacart-Ex.R' failed
The error most likely occurred in:

> ### Name: FEmrt
> ### Title: Fixed effect meta-tree
> ### Aliases: FEmrt
> 
> ### ** Examples
> 
> data(dat.BCT2009)
> FEtree <- FEmrt(g ~ T1 + T2+ T4 + T25, vi = vi, data = dat.BCT2009, c = 0.5)
Warning in FEmrt(g ~ T1 + T2 + T4 + T25, vi = vi, data = dat.BCT2009, c = 0.5) :
  no moderator effect was detected
> print(FEtree)

Fixed Effects Meta-Tree (K = 106 studies); 
FEmrt(formula = g ~ T1 + T2 + T4 + T25, data = dat.BCT2009, vi = vi, 
    c = 0.5)

No moderator effect was detected
use summary() to see the meta-analysis results> summary(FEtree)

Fixed Effects meta-tree (K = 106 studies); 
FEmrt(formula = g ~ T1 + T2 + T4 + T25, data = dat.BCT2009, vi = vi, 
    c = 0.5)

No moderator effect was detected

Test for Heterogeneity under FE assumption:
Q = 253.0357 (df = 105), p-value < 1e-04;

Fixed Effect Meta-analysis Results:
   no.      g     se   zval   pval  ci.lb  ci.ub        
   106  0.229  0.012 18.803  0.000  0.206  0.253    *** 
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

> plot(FEtree)
Error in `rownames<-`(`*tmp*`, value = rank(as.numeric(rownames(frame)))) : 
  attempt to set 'rownames' on an object with no dimensions
Calls: plot -> plot.FEmrt -> rownames<-
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Packages suggested but not available for checking: 'doMC', 'doSMP'
Found the following significant warnings:
  MatFile.cpp:40:14: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null]
  MatFile.cpp:65:14: warning: converting to non-pointer type 'char' from NULL [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/3.6/MetaSKAT.Rcheck/00install.out' for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.1Mb
    libs   4.5Mb
    misc   1.1Mb
File 'MigClim/libs/i386/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.o'
File 'MigClim/libs/x64/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:72:36: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/BH/include/boost/math/special_functions/detail/bernoulli_details.hpp:96:9: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/mixedMem.Rcheck/00install.out' for details.
Package unavailable to check Rd xrefs: 'REBayes'
listGenoToTable: no visible binding for global variable 'dummy'
Undefined global functions or variables:
  dummy
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/mma.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.8Mb
    libs   1.9Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/MonetDBLite.Rcheck/00install.out' for details.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Running 'testthat.R' [161s]
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: 296 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
Running 'testthat.R' [181s]
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: 296 SKIPPED: 16 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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Running examples in 'mptools-Ex.R' failed
The error most likely occurred in:

> ### Name: kch
> ### Title: Extract Metapop KCH
> ### Aliases: kch
> 
> ### ** Examples
> 
> mp <- system.file('example.mp', package='mptools')
> k <- kch(meta=meta(mp), path=dirname(mp))
Extracting population metadata from file:
D:/temp/Rtmp0WTcJZ/RLIBS_1758850a8896/mptools/example.mp
> 
> 
> 
> cleanEx()
Error: connections left open:
	pops[1] (textConnection)
Execution halted
File 'MRwarping/libs/i386/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'
File 'MRwarping/libs/x64/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Running examples in 'msgpack-Ex.R' failed
The error most likely occurred in:

> ### Name: msgConnection
> ### Title: Read and write msgpack formatted messages over R connections.
> ### Aliases: msgConnection close.msgConnection partial
> ###   partial.msgConnection readMsgs status status.msgConnection
> ###   seek.msgConnection readMsg writeMsg writeMsgs
> 
> ### ** Examples
> 
> out <- rawConnection(raw(0), open="wb")
> apply(quakes, 1, function(x) writeMsg(x, out))
NULL
> length(rawConnectionValue(out))
[1] 57300
> inn <- msgConnection(rawConnection(rawConnectionValue(out), open="rb"))
> readMsg(inn)
     lat     long    depth      mag stations 
  -20.42   181.62   562.00     4.80    41.00 
> readMsgs(inn, 3)
[[1]]
     lat     long    depth      mag stations 
  -20.62   181.03   650.00     4.20    15.00 

[[2]]
     lat     long    depth      mag stations 
   -26.0    184.1     42.0      5.4     43.0 

[[3]]
     lat     long    depth      mag stations 
  -17.97   181.66   626.00     4.10    19.00 

> 
> 
> 
> cleanEx()
Error: connections left open:
	raw(0) (rawConnection)
	rawConnectionValue(out) (rawConnection)
Execution halted
Found the following significant warnings:
  Warning: unable to re-encode 'dfgps.R' line 51
  Warning: unable to re-encode 'msgps.R' line 98
  Warning: unable to re-encode 'plot.msgps.R' line 60
  Warning: unable to re-encode 'print.msgps.R' line 36
  Warning: unable to re-encode 'summary.msgps.R' line 45
See 'd:/Rcompile/CRANpkg/local/3.6/msgps.Rcheck/00install.out' for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/mvabund.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
    libs   1.5Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
File 'NeatMap/libs/i386/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'
File 'NeatMap/libs/x64/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/3.6/NestedCategBayesImpute.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/nimble.Rcheck/00install.out' for details.
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    CppCode   2.7Mb
    R         5.7Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    3.8Mb
    libs   2.5Mb
installed size is 38.9Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
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.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
File 'obliclus/libs/i386/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'
File 'obliclus/libs/x64/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.5Mb
    help   2.5Mb
    libs   2.3Mb
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.
MLparameters: no visible global function definition for 'optim'
comp.freq: no visible global function definition for 'x11'
comp.freq: no visible global function definition for 'par'
comp.freq: no visible global function definition for 'plot'
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Running examples in 'openair-Ex.R' failed
The error most likely occurred in:

> ### 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: 'unix'
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.1Mb
    models   4.7Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   5.6Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/ore.Rcheck/00install.out' for details.
Running 'testthat.R' [27s]
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: 33 SKIPPED: 1 FAILED: 1
  1. Failure: CV MSE matches previous value (@test-overall.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
File 'OriGen/libs/i386/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'
File 'OriGen/libs/x64/OriGen.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'OriGen.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'OriGen.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   7.2Mb
Package suggested but not available for checking: 'Rcplex'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.8Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/PAC.Rcheck/00install.out' for details.
Running 'testthat.R' [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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.3Mb
    extdata   9.5Mb
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > std_getwd <- function() 
  + {
  +   pwd <- getwd()
  +   # Enforce upper case Windows drive letters
  +   substring(pwd, 1, 1) <- toupper(substring(pwd, 1, 1))
  +   pwd
  + }
  > 
  > test_check("pathological")
  Loading required package: pathological
  -- 1. Failure: decompose_path handles paths with a unicode directory name. (@tes
  actual$dirname not equal to expected$dirname.
  1/1 mismatches
  x[1]: "D:/Rcompile/CRANpkg/local/3.6/pathological.Rcheck/tests/testthat/CRAN"
  y[1]: "D:/Rcompile/CRANpkg/local/3.6/pathological.Rcheck/tests/testthat/CRAN"
  
  -- 2. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.6/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.6/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 186 SKIPPED: 18 FAILED: 2
  1. Failure: decompose_path handles paths with a unicode directory name. (@test_decompose_path.R#466) 
  2. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/pbdBASE.Rcheck/00install.out' for details.
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
Not exits: C:/Program Files/netCDF 4.3.2
Not exits: C:/Program Files/netCDF 4.3.2/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcp100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/msvcr100.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/zlib.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5.dll
Not exits: C:/Program Files/netCDF 4.3.2/deps/x64/bin/hdf5_hl.dll
Not exits: C:/Program Files/netCDF 4.3.2/bin/netcdf.dll
===== WARNING =====
- netCDF 4.3.2 may not install at compile time.
- Environment variables may not be correct at compile and run time.
- pbdNCDF4 binary may not link with netCDF.
- Please consider to rebuild from source.
===================
get.sysenv: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/pbdSLAP.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      1.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   2.3Mb
Running examples in 'pcalg-Ex.R' failed
The error most likely occurred in:

> ### 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
Running examples in 'pcnetmeta-Ex.R' failed
The error most likely occurred in:

> ### Name: absolute.plot
> ### Title: Plotting Treatment-Specific 95% Credible Intervals
> ### Aliases: absolute.plot
> 
> ### ** Examples
> 
> data(smoke)
> # increase n.iter to reach convergence
> # increase n.adapt to enhance efficiency
> set.seed(1234)
> nma.out <- nma.ab.bin(s.id, t.id, r, n, data = smoke,
+   trtname = c("NC", "SH", "IC", "GC"), param= "AR",
+   model = "het_cor", n.adapt = 400, n.iter = 100, n.chains = 1)
Start running MCMC...
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 50
   Unobserved stochastic nodes: 29
   Total graph size: 611

Initializing model

> absolute.plot(nma.out)
The absolute plot is saved in your working directory:
d:/Rcompile/CRANpkg/local/3.6/pcnetmeta.Rcheck
> absolute.plot(nma.out, alphabetic = FALSE)
The absolute plot is saved in your working directory:
d:/Rcompile/CRANpkg/local/3.6/pcnetmeta.Rcheck
> 
> 
> 
> cleanEx()
Error: connections left open:
	modelstring (textConnection)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'pct-international.Rmd' using rmarkdown
Warning in st_centroid.sf(zones) :
  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
--- finished re-building 'pct-international.Rmd'

--- re-building 'pct.Rmd' using rmarkdown
Quitting from lines 321-337 (pct.Rmd) 
Error: processing vignette 'pct.Rmd' failed with diagnostics:
Invalid unit
--- failed re-building 'pct.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs   13.3Mb
    share  11.9Mb
Package suggested but not available for checking: 'faahKO'
Malformed Title field: should not end in a period.
'LinkingTo' for 'ggplot2' is unused as it has no 'include' directory
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11353 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11353 (sockconn)
Execution halted
File 'PhaseType/libs/i386/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'
File 'PhaseType/libs/x64/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/photobiologySun.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/phylobase.Rcheck/00install.out' for details.
Running examples in 'phylosim-Ex.R' failed
The error most likely occurred in:

> ### Name: getLogLevel.PhyloSim
> ### Title: Get the log level from a PhyloSim object
> ### Aliases: getLogLevel.PhyloSim PhyloSim.getLogLevel
> ###   getLogLevel,PhyloSim-method
> 
> ### ** Examples
> 
> 	# Create a PhyloSim object
> 	sim<-PhyloSim();
> 	# get/set log level
> 	getLogLevel(sim)
[1] -1
> 	setLogLevel(sim,0)
[1] 0
> 	# set/get log level via virtual field
> 	sim$logLevel<- -1
> 	sim$logLevel
[1] -1
> 	# clean up
> 	unlink(sim$logFile)
>  
> 
> 
> cleanEx()
Error: connections left open:
	PhyloSim_Anonymous_247066536.log (file)
Execution halted
Running examples in 'plater-Ex.R' failed
The error most likely occurred in:

> ### Name: add_plate
> ### Title: Read a plater-formatted file and combine it with an existing
> ###   data frame.
> ### Aliases: add_plate
> 
> ### ** Examples
> 
> # Part of the data is tidy
> file <- system.file("extdata", "example-2-part-A.csv", package = "plater")
> data <- read.csv(file)
> 
> # Part of the data is plate-shaped
> plate_shaped <- system.file("extdata", "example-2-part-B.csv", package = "plater")
> 
> # Combine the two
> data <- add_plate(
+    data = data, 
+    file = plate_shaped,
+    well_ids_column = "Wells")
> 
> # Now data are tidy
> head(data)
  Wells Killing Drug Concentration Bacteria
1   A01      98    A       100.000  E. coli
2   A02      95    A        20.000  E. coli
3   A03      92    A         4.000  E. coli
4   A04      41    A         0.800  E. coli
5   A05      17    A         0.160  E. coli
6   A06       2    A         0.032  E. coli
> 
> 
> 
> cleanEx()
Error: connections left open:
	plate (textConnection)
	plate (textConnection)
	plate (textConnection)
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.0Mb
Running examples in 'plotrix-Ex.R' failed
The error most likely occurred in:

> ### 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
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Running examples in 'popRange-Ex.R' failed
The error most likely occurred in:

> ### Name: popRangeSim
> ### Title: popRangeSim
> ### Aliases: popRangeSim
> 
> ### ** Examples
>  
> ## Example: In this scenario, we are simulating a 3x3 grid of populations for 50 
> ## generations. Each population starts with 100 diploid individuals. Each individual 
> ## has a 0.01 probability of migrating away from their populations. There are 100 
> ## SNPs that all have a starting frequency of 0.5, and the program outputs the standard 
> ## "results" file, as well as a PLINK file. 
> 
> ## Commands
> 
> mat = matrix(1,nrow=3,ncol=3) 
> popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,
+               mig = 0.01, SNP_model = 0, nSNPs = 100, SNPs_starting_freq = 0.5, 
+               outfile= "outFile1", PLINK=TRUE)
Error in find_python_cmd(minimum_version = minimum_version, maximum_version = maximum_version,  : 
  Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary')  or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 2.7 Python must be at most version 3.4 Python must have access to the modules: numpy
[1] "Could not find an acceptable version of python with numpy installed. This should be able to locate python \n      anywhere on your computer, but perhaps try adding python to your PATH if you think this message is an error."
Error in popRangeSim(world = mat, popSize = 100, diploid = TRUE, nGens = 50,  : 
  
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
File 'powell/libs/i386/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'
File 'powell/libs/x64/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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 '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
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/3.6/PPRL.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.6Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc           6.5Mb
    help          2.1Mb
    htmlwidgets   2.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    extdata   6.4Mb
    libs      1.6Mb
Package suggested but not available for checking: 'qtbase'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.3Mb
Found the following significant warnings:
  Warning: replacing previous import 'loo::kfold' by 'rstanarm::kfold' when loading 'psycho'
See 'd:/Rcompile/CRANpkg/local/3.6/psycho.Rcheck/00install.out' for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.3Mb
    libs   3.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'

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

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

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    Output   2.2Mb
    bin      9.3Mb
Running examples in 'R2HTML-Ex.R' failed
The error most likely occurred in:

> ### Name: HTM2clip
> ### Title: Wrapper around HTML() to save output to the clipboard
> ### Aliases: HTML2clip
> ### Keywords: print IO file
> 
> ### ** Examples
> 
> if (.Platform$OS == "windows")
+ 	HTML2clip(summary(lm(rating ~., attitude)))
> 
> 
> 
> cleanEx()
Error: connections left open:
	clipboard (clipboard)
Execution halted
Packages suggested but not available for checking: 'rcom', 'RDCOMClient'
'library' or 'require' calls in package code:
  'RDCOMClient' 'rcom'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
PPT.AddBlankSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'comIsValidHandle'
PPT.AddDataFrame: no visible global function definition for
  'write.table'
PPT.AddDataFrame: no visible global function definition for 'write.csv'
PPT.AddGraphicstoSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.cur'
PPT.AddGraphicstoSlide: no visible global function definition for
  'dev.list'
PPT.AddGraphicstoSlide: no visible global function definition for
  'savePlot'
PPT.AddTextSlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleOnlySlide: no visible global function definition for
  'comIsValidHandle'
PPT.AddTitleSlide: no visible global function definition for
  'comIsValidHandle'
PPT.ApplyTemplate: no visible global function definition for
  'comIsValidHandle'
PPT.Close: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'comCreateObject'
PPT.Init: no visible global function definition for 'comIsValidHandle'
PPT.Init: no visible global function definition for 'COMCreate'
PPT.Present: no visible global function definition for
  'comIsValidHandle'
PPT.SaveAs: no visible global function definition for
  'comIsValidHandle'
PPT.getAbsolutePath : PPT.filePath: no visible global function
  definition for 'readWindowsShortcut'
Undefined global functions or variables:
  COMCreate comCreateObject comIsValidHandle dev.cur dev.list
  readWindowsShortcut savePlot write.csv write.table
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "savePlot")
  importFrom("utils", "write.csv", "write.table")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   8.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   3.0Mb
.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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/randstr.Rcheck/00install.out' for details.
Found the following significant warnings:
  congruRand.c:180:3: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:187:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:188:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:189:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/3.6/randtoolbox.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   2.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.8Mb
Error(s) in re-building vignettes:
--- re-building 'PoS_codata.Rmd' using rmarkdown
--- finished re-building 'PoS_codata.Rmd'

--- re-building 'PoS_interim.Rmd' using rmarkdown
--- finished re-building 'PoS_interim.Rmd'

--- re-building 'customizing_plots.Rmd' using rmarkdown
Loading required package: Rcpp
This is RBesT version 1.3.7
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
Final MCMC sample equivalent to less than 1000 independent draws.
Please consider increasing the MCMC simulation size.
--- finished re-building 'customizing_plots.Rmd'

--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

--- re-building 'introduction_normal.Rmd' using rmarkdown
--- finished re-building 'introduction_normal.Rmd'

--- re-building 'robustMAP.Rmd' using rmarkdown
--- finished re-building 'robustMAP.Rmd'

--- re-building 'variances_MAP.Rmd' using rmarkdown
Quitting from lines 137-148 (variances_MAP.Rmd) 
Error: processing vignette 'variances_MAP.Rmd' failed with diagnostics:
dims [product 2] do not match the length of object [3]
--- failed re-building 'variances_MAP.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/Rblpapi.Rcheck/00install.out' for details.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/RCA.Rcheck/00install.out' for details.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
Running 'testthat.R' [73s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcmdcheck)
  > 
  > test_check("rcmdcheck")
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.1Mb
Running examples in 'rcongresso-Ex.R' failed
The error most likely occurred in:

> ### Name: fetch_despesas_deputado
> ### Title: Fetches expenditures from deputy
> ### Aliases: fetch_despesas_deputado
> 
> ### ** Examples
> 
> gastos_abel_mesquita <- fetch_despesas_deputado(id = 178957)
Error: Falha na requisicao a API dos Dados Abertos. Erro 400 ao tentar acessar: https://dadosabertos.camara.leg.br/api/v2/deputados/178957/despesas?id=178957
Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Error: (unknown) (@test_deputados.R#81)  ---------------------------------
  argument "message" is missing, with no default
  1: skip() at testthat/test_deputados.R:81
  2: structure(list(message = message), class = c("skip", "condition"))
  
  -- 2. Error: (unknown) (@test_proposicoes.R#91)  -------------------------------
  could not find function "FUN1"
  1: check_api() at testthat/test_proposicoes.R:91
  2: tryCatch(setup(), error = function(e) {
         message(e)
         return(FALSE)
     }) at testthat/test_proposicoes.R:15
  3: tryCatchList(expr, classes, parentenv, handlers)
  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  5: value[[3L]](cond)
  6: message(e) at testthat/test_proposicoes.R:16
  7: withRestarts({
         signalCondition(cond)
         defaultHandler(cond)
     }, muffleMessage = function() NULL)
  8: withOneRestart(expr, restarts[[1L]])
  9: doWithOneRestart(return(expr), restart)
  
  -- 3. Error: (unknown) (@test_votacoes.R#70)  ----------------------------------
  argument "message" is missing, with no default
  1: skip() at testthat/test_votacoes.R:70
  2: structure(list(message = message), class = c("skip", "condition"))
  
  == testthat results  ===========================================================
  OK: 13 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_deputados.R#81) 
  2. Error: (unknown) (@test_proposicoes.R#91) 
  3. Error: (unknown) (@test_votacoes.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'introducao-rcongresso.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 36-38 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
could not find function "FUN1"
--- failed re-building 'introducao-rcongresso.Rmd'

--- re-building 'utilizando-fetch-proposicao.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 57-63 (utilizando-fetch-proposicao.Rmd) 
Error: processing vignette 'utilizando-fetch-proposicao.Rmd' failed with diagnostics:
could not find function "FUN1"
--- failed re-building 'utilizando-fetch-proposicao.Rmd'

SUMMARY: processing the following files failed:
  'introducao-rcongresso.Rmd' 'utilizando-fetch-proposicao.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    corpora   7.4Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    include   5.8Mb
    libs      1.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib       3.9Mb
    libs      2.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   6.3Mb
    libs      1.7Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib       8.9Mb
    libs      1.0Mb
installed size is 35.0Mb
  sub-directories of 1Mb or more:
    include   8.8Mb
    libs     26.1Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    include   6.3Mb
    libs      2.0Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/RCurl.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("rdefra")
  > 
  > test_check("rdefra")
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  -- 1. Failure: Metadata should be in the right format (@test-data.R#44)  -------
  `x` not equal to `expected`.
  1 element mismatch
  
  Error in file(file, "rt") : cannot open the connection
  -- 2. Failure: Data should be in the right format (@test-data.R#55)  -----------
  `x` not equal to `expected`.
  'is.NA' value mismatch: 0 in current 1 in target
  
  == testthat results  ===========================================================
  OK: 39 SKIPPED: 1 FAILED: 2
  1. Failure: Metadata should be in the right format (@test-data.R#44) 
  2. Failure: Data should be in the right format (@test-data.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'rdefra_vignette.Rmd' using knitr
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine sichere in eine nicht sichere Verbindung.'
No data available for station MY1
Warning: Unknown or uninitialised column: 'unit'.
Warning: Unknown or uninitialised column: 'unit'.

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Warning: Unknown or uninitialised column: 'datetime'.
Quitting from lines 118-124 (rdefra_vignette.Rmd) 
Error: processing vignette 'rdefra_vignette.Rmd' failed with diagnostics:
do not know how to convert 'df$datetime' to class "POSIXlt"
--- failed re-building 'rdefra_vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.6Mb
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.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Package which this enhances but not available for checking: 'Rcplex'
CA: no visible global function definition for 'readClipboard'
LL: no visible global function definition for 'readClipboard'
US: no visible global function definition for 'readClipboard'
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'
latexlist: no visible global function definition for 'readClipboard'
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'
strWrap: no visible global function definition for 'readClipboard'
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 readClipboard tail unzip
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "download.file", "head", "menu", "readClipboard",
             "tail", "unzip")
to your NAMESPACE file.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is 80.3Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.8Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/rgl.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc     3.6Mb
    fonts   1.5Mb
    libs    2.0Mb
Packages suggested but not available for checking: 'pmg', 'SVGAnnotation'
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
Running examples in 'RGtk2Extras-Ex.R' failed
The error most likely occurred in:

> ### 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
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.6Mb
    libs   5.1Mb
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: '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.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    lib    3.5Mb
    libs   4.8Mb
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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 notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.6/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.6/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Mallows: no visible global function definition for 'runif'
Mallows: no visible global function definition for 'x11'
Mallows: no visible global function definition for 'plot'
Mallows: no visible global function definition for 'dev.off'
UpdateLambda: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    rmd   8.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   2.1Mb
Running examples in 'rms-Ex.R' failed
The error most likely occurred in:

> ### 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: 0x069a1320>
> 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
Running examples in 'rms-Ex.R' failed
The error most likely occurred in:

> ### 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: 0x000000000e1bdd58>
> 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
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Running 'testthat.R' [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
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.5Mb
Running 'testthat.R' [14s]
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] 209284 - 888626 == -679342
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test_rnn.R#66) 
  
  Error: testthat unit tests failed
  Execution halted
'LinkingTo' for 'mgcv' is unused as it has no 'include' directory
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   2.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.7Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/RQuantLib.Rcheck/00install.out' for details.
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
Error(s) in re-building vignettes:
--- re-building 'rscala.Rnw' using Sweave

Error: processing vignette 'rscala.Rnw' failed with diagnostics:
 chunk 7 (label = Instantiate a bridge for this document) 
Error in scalaConnect(details) : missing value where TRUE/FALSE needed

--- failed re-building 'rscala.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
Found the following additional notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/Rserve.Rcheck/00install.out' for details.
Rserve: no visible global function definition for 'shortPathName'
Undefined global functions or variables:
  shortPathName
Consider adding
  importFrom("utils", "shortPathName")
to your NAMESPACE file.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.6/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.6/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/Rssa.Rcheck/00install.out' for details.
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  17.6Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
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
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Running 'test-all.R' [45s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("rtext")
  Loading required package: rtext
  Loading required package: stringb
  -- 1. Failure: easy examples work properly (@test_tools.R#336)  ----------------
  which_token(x = 1:2, y1 = c(2, 1), y2 = c(2, 1)) not equal to c(2, 1).
  Lengths differ: 1 is not 2
  
  == testthat results  ===========================================================
  OK: 282 SKIPPED: 0 FAILED: 1
  1. Failure: easy examples work properly (@test_tools.R#336) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.7Mb
Running examples in 'rtson-Ex.R' failed
The error most likely occurred in:

> ### Name: readTSON
> ### Title: Deserialize a connection
> ### Aliases: readTSON
> 
> ### ** Examples
> 
> ## Example
> 
> library(rtson)
> 
> list = list(integer=42L,
+             double=42,
+             bool=TRUE,
+             uint8=tson.uint8.vec(c(42,0)),
+             uint16=tson.uint16.vec(c(42,0)),
+             uint32=tson.uint32.vec(c(42,0)),
+             int8=tson.int8.vec(c(42,0)),
+             int16=tson.int16.vec(c(42,0)),
+             int32=as.integer(c(42,0)),
+             float32=tson.float32.vec(c(0.0, 42.0)),
+             float64=c(42.0,42.0),
+             map=list(x=42, y=42, label="42"),
+             list=list("42",42)
+ )
> 
> con = rawConnection(raw(0), "r+")
> writeTSON(list, con)
<Serializer>
  Public:
    addBool: function (object) 
    addDouble: function (object) 
    addDoubleList: function (object) 
    addFloat32List: function (object) 
    addFloat64List: function (object) 
    addInt16List: function (object) 
    addInt32List: function (object) 
    addInt8List: function (object) 
    addInteger: function (object) 
    addIntegerList: function (object) 
    addLength: function (len) 
    addList: function (object) 
    addListOrMap: function (object) 
    addMap: function (object) 
    addNull: function () 
    addObject: function (object) 
    addRootObject: function (object) 
    addString: function (object) 
    addStringList: function (object) 
    addType: function (type) 
    addUInt16List: function (object) 
    addUInt32List: function (object) 
    addUInt8List: function (object) 
    clone: function (deep = FALSE) 
    con: 3
    initialize: function (object, con) 
> bytes = rawConnectionValue(con)
> close(con)
> con = rawConnection(bytes, "r")
> object = readTSON(con)
> 
> 
> 
> cleanEx()
Error: connections left open:
	bytes (rawConnection)
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.2Mb
Package suggested but not available for checking: 'gpuR'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    include   5.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs      8.1Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
File 'RWinEdt/R/zzz.R':
  .onAttach calls:
    writeLines(edtFile, con = send2RedtLoc)
    writeLines(edtFile, con = send2RedtLoc)

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  Warning message:
  package 'testthat' was built under R version 3.7.0 
  > library(Rxnat)
  > 
  > test_check("Rxnat")
  -- 1. Error: xnat_api (@test-xnat-api.R#7)  ------------------------------------
  error during HTTP request
  1: testthat::expect_is(nitrc$experiments(), "data.frame") at testthat/test-xnat-api.R:7
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: nitrc$experiments()
  5: xnat_call("/data/search?format=csv", data = in_data)
  6: stop("error during HTTP request")
  
  == testthat results  ===========================================================
  OK: 5 SKIPPED: 0 FAILED: 1
  1. Error: xnat_api (@test-xnat-api.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'SnakeCharmR'
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/RxODE.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   5.0Mb
Running examples in 'sapfluxnetr-Ex.R' failed
The error most likely occurred in:

> ### Name: sfn_plot
> ### Title: plot method for sfn_data class
> ### Aliases: sfn_plot
> 
> ### ** Examples
> 
> library(ggplot2)
Warning: package 'ggplot2' was built under R version 3.7.0
> 
> # data
> data('ARG_TRE', package = 'sapfluxnetr')
> 
> # plotting directly
> sfn_plot(ARG_TRE, type = 'sapf')
Error in valid.units(units) : Invalid unit
Calls: <Anonymous> ... unit.c -> unit -> valid.unit -> structure -> valid.units
Execution halted
Error(s) in re-building vignettes:
--- re-building 'custom-aggregation.Rmd' using rmarkdown
--- finished re-building 'custom-aggregation.Rmd'

--- re-building 'data-flags.Rmd' using rmarkdown
--- finished re-building 'data-flags.Rmd'

--- re-building 'memory-and-parallelization.Rmd' using rmarkdown
--- finished re-building 'memory-and-parallelization.Rmd'

--- re-building 'metadata-and-data-units.Rmd' using rmarkdown
--- finished re-building 'metadata-and-data-units.Rmd'

--- re-building 'sapfluxnetr-quick-guide.Rmd' using rmarkdown
Quitting from lines 259-261 (sapfluxnetr-quick-guide.Rmd) 
Error: processing vignette 'sapfluxnetr-quick-guide.Rmd' failed with diagnostics:
Invalid unit
--- failed re-building 'sapfluxnetr-quick-guide.Rmd'

--- re-building 'sfn-data-classes.Rmd' using rmarkdown
Quitting from lines 200-208 (sfn-data-classes.Rmd) 
Error: processing vignette 'sfn-data-classes.Rmd' failed with diagnostics:
Invalid unit
--- failed re-building 'sfn-data-classes.Rmd'

SUMMARY: processing the following files failed:
  'sapfluxnetr-quick-guide.Rmd' 'sfn-data-classes.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:140:23: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/Compiler/gcc-4.9.3/local330/include/gmp-x64.h:141:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/sbrl.Rcheck/00install.out' for details.
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.
Running examples in 'scorecardModelUtils-Ex.R' failed
The error most likely occurred in:

> ### Name: scalling
> ### Title: Converting coefficients of logistic regression into scores for
> ###   scorecard building
> ### Aliases: scalling
> 
> ### ** Examples
> 
> data <- iris
> set.seed(11)
> data$Y <- sample(0:1,size=nrow(data),replace=TRUE)
> x <- c("Sepal.Length","Sepal.Width","Petal.Length","Petal.Width")
> iv_table_list <- iv_table(base = data,target = "Y",num_var_name = x,cat_var_name = "Species")
> num_cat <- num_to_cat(base = data,num_woe_table = iv_table_list$num_woe_table)
> log_model <- glm(Y ~ ., data = num_cat, family = "binomial")
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels
Calls: glm ... model.matrix -> model.matrix.default -> contrasts<-
Execution halted
Running examples in 'scriptexec-Ex.R' failed
The error most likely occurred in:

> ### Name: execute
> ### Title: Executes a script and returns the output. The stdout and stderr
> ###   are captured and returned. In case of errors, the exit code will
> ###   return in the status field.
> ### Aliases: execute
> 
> ### ** Examples
> 
> library('scriptexec')
> library('testthat')
> 
> # execute script text
> output <- scriptexec::execute('echo command1\necho command2')
> expect_equal(output$status, 0)
> expect_equal(grepl('command1', output$output), TRUE)
Error: grepl("command1", output$output) not equal to TRUE.
1 element mismatch
Execution halted
Error(s) in re-building vignettes:
--- re-building 'scriptexec.Rmd' using rmarkdown
Quitting from lines 24-62 (scriptexec.Rmd) 
Error: processing vignette 'scriptexec.Rmd' failed with diagnostics:
grepl("command1", output$output) not equal to TRUE.
1 element mismatch
--- failed re-building 'scriptexec.Rmd'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   3.5Mb
Running examples in 'secret-Ex.R' failed
The error most likely occurred in:

> ### Name: add_github_user
> ### Title: Add a user via their GitHub username.
> ### Aliases: add_github_user
> 
> ### ** Examples
> 
> vault <- file.path(tempdir(), ".vault")
> create_vault(vault)
> 
> add_github_user("hadley", vault = vault)
> list_users(vault = vault)
[1] "github-hadley"
> delete_user("github-hadley", vault = vault)
> 
> 
> 
> cleanEx()
Error: connections left open:
	file (textConnection)
Execution halted
Running examples in 'seedy-Ex.R' failed
The error most likely occurred in:

> ### 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
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/selac.Rcheck/00install.out' for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Error(s) in re-building vignettes:
--- re-building 'Introduction.Rmd' using rmarkdown
trying URL 'https://pure.strath.ac.uk/portal/files/43595106/Figure_2.zip'
Quitting from lines 38-41 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open URL 'https://pure.strath.ac.uk/portal/files/43595106/Figure_2.zip'
--- failed re-building 'Introduction.Rmd'

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

Error: Vignette re-building failed.
Execution halted
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.
installed size is 94.0Mb
  sub-directories of 1Mb or more:
    doc     11.2Mb
    gdal     3.9Mb
    libs    70.0Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    www   7.3Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    www   7.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Running 'testthat.R' [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 # 3 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
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   2.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   2.5Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tthread/tinythread.h:632:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tbb_stddef.h:470:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/atomic.h:29:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:42:14: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:43:35: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:75:21: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:102:10: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:80:37: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
  d:/RCompile/CRANpkg/lib/3.6/RcppParallel/include/tbb/tick_count.h:127:30: warning: ISO C++ 1998 does not support 'long long' [-Wlong-long]
See 'd:/Rcompile/CRANpkg/local/3.6/skm.Rcheck/00install.out' for details.
Running 'testthat.R' [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
Running 'testthat.R' [18s]
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: 286 SKIPPED: 0 FAILED: 1
  1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJob.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [19s]
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: 286 SKIPPED: 0 FAILED: 1
  1. Failure: parseJob() doesn't deviate from historical behavior (@test_parseJob.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.4Mb
Found the following significant warnings:
  Warning: package 'Rcpp' was built under R version 3.7.0
See 'd:/Rcompile/CRANpkg/local/3.6/snipEM.Rcheck/00install.out' for details.
Running examples in 'SNPknock-Ex.R' failed
The error most likely occurred in:

> ### Name: SNPknock.fp.loadFit
> ### Title: Load the parameter estimates obtained by fastPHASE
> ### Aliases: SNPknock.fp.loadFit
> 
> ### ** Examples
> 
> # Specify the location of the fastPHASE output files containing the parameter estimates.
> # Example files can be found in the package installation directory.
> r_file = system.file("extdata", "genotypes_rhat.txt", package = "SNPknock")
> alpha_file = system.file("extdata", "genotypes_alphahat.txt", package = "SNPknock")
> theta_file = system.file("extdata", "genotypes_thetahat.txt", package = "SNPknock")
> char_file = system.file("extdata", "genotypes_origchars", package = "SNPknock")
> 
> # Read the parameter files and build the HMM
> hmm = SNPknock.fp.loadFit(r_file, alpha_file, theta_file, char_file)
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	lines (textConnection)
	lines (textConnection)
	lines (textConnection)
	lines (textConnection)
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.2Mb
    libs   2.1Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Running examples in 'spa-Ex.R' failed
The error most likely occurred in:

> ### 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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.7Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    R      5.1Mb
    doc    4.9Mb
    help   5.1Mb
    libs   1.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Output for data("spinalCord", package = "specmine"):
  Warning message:
  In fun(libname, pkgname) :
    mzR has been built against a different Rcpp version (1.0.0)
  than is installed on your system (1.0.1). This might lead to errors
  when loading mzR. If you encounter such issues, please send a report,
  including the output of sessionInfo() to the Bioc support forum at 
  https://support.bioconductor.org/. For details see also
  https://github.com/sneumann/mzR/wiki/mzR-Rcpp-compiler-linker-issue.
Running 'testthat.R' [2s]
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
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   2.0Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
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.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    include   9.0Mb
Error(s) in re-building vignettes:
--- re-building 'stmVignette.Rnw' using Sweave
stm v1.3.3 (2018-1-26) successfully loaded. See ?stm for help. 
 Papers, resources, and other materials at structuraltopicmodel.com
Warning in load(url("http://goo.gl/VPdxlS")) :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine sichere in eine nicht sichere Verbindung.'

Error: processing vignette 'stmVignette.Rnw' failed with diagnostics:
 chunk 7 
Error in load(url("http://goo.gl/VPdxlS")) : cannot open the connection

--- failed re-building 'stmVignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/STraTUS.Rcheck/00install.out' for details.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("stringdist")
  Loading required package: stringdist
  Warning: stack imbalance in 'vapply', 83 then 84
  -- 1. Failure: Elementary tests on seq_distmatrix (@testSeqDist.R#61)  ---------
  seq_distmatrix(...) not equal to matrix(...).
  2/4 mismatches (average diff: 2)
  [1] 2 - 0 ==  2
  [3] 0 - 2 == -2
  
  Warning: stack imbalance in '{', 71 then 72
  -- 2. Failure: elementary seq_sim test (@testStringsim.R#62)  ------------------
  seq_sim(list(1:3, 2:4), list(1:3)) not equal to stringsim(c("abc", "bcd"), "abc").
  1/2 mismatches
  [1] 0.333 - 1 == -0.667
  
  Warning: stack imbalance in '{', 71 then 72
  == testthat results  ===========================================================
  OK: 415 SKIPPED: 1 FAILED: 2
  1. Failure: Elementary tests on seq_distmatrix (@testSeqDist.R#61) 
  2. Failure: elementary seq_sim test (@testStringsim.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  Keine Instanzen verfgbar.
  -- 1. Failure: child process is terminated in Windows (@test-termination.R#33)  
  `child_id` has length 0, not length 1.
  
  -- 2. Error: child process is terminated in Windows (@test-termination.R#34)  --
  `pid` must be a single integer value
  1: expect_true(process_exists(child_id)) at testthat/test-termination.R:34
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: process_exists(child_id)
  5: isTRUE(.Call("C_process_exists", as.integer(x)))
  
  == testthat results  ===========================================================
  OK: 58 SKIPPED: 3 FAILED: 2
  1. Failure: child process is terminated in Windows (@test-termination.R#33) 
  2. Error: child process is terminated in Windows (@test-termination.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  Keine Instanzen verfgbar.
  -- 1. Failure: child process is terminated in Windows (@test-termination.R#33)  
  `child_id` has length 0, not length 1.
  
  -- 2. Error: child process is terminated in Windows (@test-termination.R#34)  --
  `pid` must be a single integer value
  1: expect_true(process_exists(child_id)) at testthat/test-termination.R:34
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: process_exists(child_id)
  5: isTRUE(.Call("C_process_exists", as.integer(x)))
  
  == testthat results  ===========================================================
  OK: 58 SKIPPED: 3 FAILED: 2
  1. Failure: child process is terminated in Windows (@test-termination.R#33) 
  2. Error: child process is terminated in Windows (@test-termination.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.7Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
dlgMessage.tcltkGUI: no visible global function definition for 'alarm'
dlgMessage.tcltkGUI: no visible global function definition for
  'bringToTop'
Undefined global functions or variables:
  alarm bringToTop
Consider adding
  importFrom("grDevices", "bringToTop")
  importFrom("utils", "alarm")
to your NAMESPACE file.
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_close', possibly from 'close' (Fortran)
    Object: 'mi10unix.o'
  Found '_gfortran_st_open', possibly from 'open' (Fortran)
    Object: 'mi10unix.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable 'iset' in DATA statement at (1)
  Warning: GNU Extension: Variable 'iset' at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
Found the following additional notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/SWATmodel.Rcheck/00install.out' for details.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(tbltools)
  > 
  > test_check("tbltools")
  -- 1. Failure: filter_data, arrange_data (@test-tbl.R#60)  ---------------------
  nrow(filter_data(d, d$abc == "a")) not equal to 34.
  1/1 mismatches
  [1] 30 - 34 == -4
  
  == testthat results  ===========================================================
  OK: 99 SKIPPED: 0 FAILED: 1
  1. Failure: filter_data, arrange_data (@test-tbl.R#60) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   1.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs      13.3Mb
    tessdata  14.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.5Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.1Mb
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.01    0.00    2.24 
> 
> 
> 
> cleanEx()

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

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11835 (sockconn)
Execution halted
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.01    0.00    2.13 
> 
> 
> 
> cleanEx()

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

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11876 (sockconn)
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    rmarkdown   1.3Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Running examples in 'tm.plugin.lexisnexis-Ex.R' failed
The error most likely occurred in:

> ### Name: LexisNexisSource
> ### Title: LexisNexis Source
> ### Aliases: LexisNexisSource getElem.LexisNexisSource eoi.LexisNexisSource
> 
> ### ** Examples
> 
>     library(tm)
Loading required package: NLP
>     file <- system.file("texts", "lexisnexis_test_en.html",
+                         package = "tm.plugin.lexisnexis")
>     corpus <- Corpus(LexisNexisSource(file))
> 
>     # See the contents of the documents
>     inspect(corpus)
<<VCorpus>>
Metadata:  corpus specific: 0, document level (indexed): 0
Content:  documents: 2

[[1]]
<<PlainTextDocument>>
Metadata:  17
Content:  chars: 94

[[2]]
<<PlainTextDocument>>
Metadata:  17
Content:  chars: 66

> 
>     # See meta-data associated with first article
>     meta(corpus[[1]])
  author       : By PAPER AUTHOR
  datetimestamp: 1991-12-19
  description  : character(0)
  heading      : Heading One
  id           : SomeNewsp199112191
  language     : en
  origin       : Some Newspaper
  intro        : character(0)
  section      : Section 5; Part 2; Page 16; Column 2; National Desk
  subject      : character(0)
  coverage     : character(0)
  company      : character(0)
  stocksymbol  : character(0)
  industry     : character(0)
  type         : character(0)
  wordcount    : 584
  rights       : Copyright 1991 My Company
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:tm', 'package:NLP'

Error: connections left open:
	as.character(tree) (textConnection)
Execution halted
Packages suggested but not available for checking:
  'Rcampdf', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Package unavailable to check Rd xrefs: 'Rpoppler'
Error(s) in re-building vignettes:
--- re-building 'topicmodels.Rnw' using Sweave
Warning: package 'corpus.JSS.papers' is not available (for R Under development)

Error: processing vignette 'topicmodels.Rnw' failed with diagnostics:
 chunk 6 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called 'corpus.JSS.papers'

--- failed re-building 'topicmodels.Rnw'

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/topologyGSA.Rcheck/00install.out' for details.
Package in Depends field not imported from: 'lgtdl'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ci.plot: no visible global function definition for 'gaussian'
ci.plot: no visible global function definition for 'qnorm'
ci.plot: no visible global function definition for 'plot'
ci.plot: no visible global function definition for 'lines'
cst.fit.ff: no visible global function definition for 'pnorm'
cstfit.1: no visible global function definition for 'var'
gof.test.boots.pf: no visible binding for global variable 'sd'
gof.test.int.1.ff: no visible global function definition for 'quantile'
gof.test.int.1.ff: no visible global function definition for 'var'
gof.test.int.ff: no visible global function definition for 'pnorm'
gofTest: no visible binding for global variable 'sd'
plotGof: no visible global function definition for 'plot'
plotGof : <anonymous>: no visible global function definition for
  'lines'
plotGof: no visible global function definition for 'lines'
sig.test.int.1.ff: no visible global function definition for 'quantile'
sig.test.int.1.ff: no visible global function definition for 'var'
sig.test.int.ff: no visible global function definition for 'pnorm'
test.boots.1: no visible binding for global variable 'sd'
tpr: no visible global function definition for 'poisson'
tpr: no visible global function definition for 'glm.fit'
tpr: no visible global function definition for 'coef'
tpr: no visible global function definition for 'approx'
Undefined global functions or variables:
  approx coef gaussian glm.fit lines plot pnorm poisson qnorm quantile
  sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "coef", "gaussian", "glm.fit", "pnorm",
             "poisson", "qnorm", "quantile", "sd", "var")
to your NAMESPACE file.
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    data      2.1Mb
    doc       2.7Mb
    extdata   8.4Mb
Running examples in 'treatSens-Ex.R' failed
The error most likely occurred in:

> ### Name: treatSens.BART
> ### Title: Dual-Parameter Sensitivity Analysis Using BART
> ### Aliases: treatSens.BART
> 
> ### ** Examples
> 
> N <- 250                      # number of observations
> 
> zetay <- 0.5                  # coefficient on U in the outcome model
> zetaz <- 0.5                  # coefficient on U in the treatment model
> betaz <- c(0.75, -0.5,  0.25) # coefficients of X in the treatment model
> betay <- c(0.5,   1.0, -1.5)  # coefficients of X in the outcome model
> tau   <- 0.25                 # treatment effect
> 
> set.seed(725)
> X <- matrix(rnorm(3 * N), N)  # covariates
> 
> U  <- rbinom(N, 1, 0.5)                        # unmeasured confounder
> ps <- pnorm(X %*% betaz + zetaz * (U - 0.5)) # propensity score
> Z  <- rbinom(N, 1, ps)                         # treatment variable
> epsilon <- rnorm(N, 0.0, 2.0)                  # error term
> 
> Y0 <- X %*% betay + zetay * (U - 0.5) + epsilon       # potential outcome(Z=0)
> Y1 <- X %*% betay + zetay * (U - 0.5) + tau + epsilon # potential outcome(Z=1)
> Y  <- Y0 * (1 - Z) + Y1 * Z                             # realization of potential outcome
> 
> # sensitivity analysis
> out.bin <- treatSens.BART(Y ~ Z + X, nsim = 3, nthin = 2, nburn = 0,
+                           spy.range = c(0, 4), spz.range = c(-2 , 2), grid.dim = c(5, 3),
+                           standardize = FALSE, verbose = TRUE)
Warning in model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored
Warning in model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored
Binary U with binomial distribution is assumed.
"ATE" option is selected. Sensitivity analysis is performed with the default Weights for the average treatment effect.
Weight trimming is applied.  The maximum size of weights is set to 25 , which is 10 % of the size of the inferential group.
Computing final grid...
Running examples in 'TreeSim-Ex.R' failed
The error most likely occurred in:

> ### Name: sim.bd.age
> ### Title: sim.bd.age: Simulating birth-death trees of a fixed age.
> ### Aliases: sim.bd.age
> 
> ### ** Examples
> 
> age<-2
> lambda <- 2.0
> mu <- 0.5
> frac <-0.6
> numbsim<-3
> 
> ##
> # Simulating trees with time age since the origin:
> 
> sim.bd.age(age,numbsim,lambda,mu,mrca=FALSE,complete=TRUE)
[[1]]

Phylogenetic tree with 117 tips and 116 internal nodes.

Tip labels:
	t51, t46, t102, t11, t8, t87, ...

Rooted; includes branch lengths.

[[2]]
[1] 0

[[3]]
[1] 0

> sim.bd.age(age,numbsim,lambda,mu,frac,mrca=FALSE,complete=FALSE)
Warning in max(oldnodes) :
  no non-missing arguments to max; returning -Inf
Error in integer(max(oldnodes)) : vector size cannot be infinite
Calls: sim.bd.age ... drop.extinct -> .drop.tip -> collapse.singles -> integer
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    4.7Mb
    libs   1.5Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/tth.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/UCSCXenaTools.Rcheck/00install.out' for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs        4.2Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    8.3Mb
Running 'test_unifDAG.R' [7s]
Running the tests in 'tests/test_unifDAG.R' failed.
Complete output:
  > library(unifDAG)
  > 
  > my.wgtMatrix <- function(g, transpose = TRUE) {
  +   res <- as(g, "matrix") # from 'graph' package, now reliable (we hope)
  +   if (transpose) ## default!
  +     t(res) else res
  + }
  > 
  > ## exact
  > set.seed(123)
  > n <- 2
  > reps <- 100
  > res <- matrix(0, reps, 3)
  > for (i in 1:reps) {
  +     gAM <- unifDAG(n)
  +     wm <- my.wgtMatrix(gAM)
  +     if (wm[1,2] != 0) {
  +         res[i,1] <- 1
  +     } else {
  +           if (wm[2,1] != 0) {
  +               res[i,2] <- 1
  +           } else {
  +                 res[i,3] <- 1
  +             }
  +       }
  + }
  > if (!all(round(colMeans(res), 2) == c(0.41, 0.31, 0.28))) {
  +     stop("test_unifDAG: Saved result could not be reproduced (unifDAG).")
  + }
  Error: test_unifDAG: Saved result could not be reproduced (unifDAG).
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.6Mb
    libs   1.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/uroot.Rcheck/00install.out' for details.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
File 'uuid/libs/i386/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'
File 'uuid/libs/x64/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("vanddraabe")
  Loading required package: vanddraabe
  -- 1. Failure: the correct mobility values are returned (@test-BoundWaterEnviron
  Mobility(Bvalues, occupancy) not equal to `mobility.answer`.
  14/14 mismatches (average diff: 0.0382)
  [1] 0.224 - 0.225 == -0.00168
  [2] 0.373 - 0.375 == -0.00280
  [3] 0.471 - 0.474 == -0.00354
  [4] 0.621 - 0.626 == -0.00467
  [5] 0.706 - 0.676 ==  0.03025
  [6] 0.824 - 0.876 == -0.05229
  [7] 0.993 - 0.948 ==  0.04521
  [8] 1.006 - 1.013 == -0.00756
  [9] 1.242 - 1.126 ==  0.11578
  ...
  
  -- 2. Failure: counting AtomTypes works (@test-utilities.R#102)  ---------------
  getAtomTypeCounts(atom.types) not equal to `ATCounts.answer`.
  56/167 mismatches (average diff: 5.09)
  [4]  0 - 1 == -1
  [9]  0 - 8 == -8
  [11] 0 - 7 == -7
  [14] 7 - 1 ==  6
  [15] 1 - 0 ==  1
  [18] 0 - 1 == -1
  [21] 0 - 1 == -1
  [23] 0 - 4 == -4
  [31] 1 - 0 ==  1
  ...
  
  == testthat results  ===========================================================
  OK: 63 SKIPPED: 0 FAILED: 2
  1. Failure: the correct mobility values are returned (@test-BoundWaterEnvironments.R#71) 
  2. Failure: counting AtomTypes works (@test-utilities.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 78.6Mb
  sub-directories of 1Mb or more:
    gdal   3.8Mb
    libs  68.7Mb
    proj   5.0Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    doc    1.2Mb
    help   2.8Mb
    libs   1.3Mb
Running examples in 'virtualspecies-Ex.R' failed
The error most likely occurred in:

> ### Name: generateRandomSp
> ### Title: Generate a random virtual species distribution from
> ###   environmental variables
> ### Aliases: generateRandomSp
> 
> ### ** Examples
> 
> # Create an example stack with six environmental variables
> a <- matrix(rep(dnorm(1:100, 50, sd = 25)), 
+             nrow = 100, ncol = 100, byrow = TRUE)
> env <- stack(raster(a * dnorm(1:100, 50, sd = 25)),
+              raster(a * 1:100),
+              raster(a * logisticFun(1:100, alpha = 10, beta = 70)),
+              raster(t(a)),
+              raster(exp(a)),
+              raster(log(a)))
> names(env) <- paste("Var", 1:6, sep = "")   
> 
> # More than 6 variables: by default a PCA approach will be used
> generateRandomSp(env)
 - Perfoming the pca

 - Defining the response of the species along PCA axes

 - Calculating suitability values

 - Converting into Presence - Absence

   --- Determing species.prevalence automatically according to alpha and beta


Virtual species generated from 6 variables:
 Var1, Var2, Var3, Var4, Var5, Var6

- Approach used: Response to axes of a PCA
- Axes:  1, 2 ;  81.71 % explained by these axes
- Responses to axes:
   .Axis 1  [min=-3.52; max=3.55] : dnorm (mean=1.399218; sd=2.969177)
   .Axis 2  [min=-1.74; max=3.75] : dnorm (mean=0.2190712; sd=1.881691)
- Environmental suitability was rescaled between 0 and 1

- Converted into presence-absence:
   .Method = probability
   .alpha (slope)           = -0.1
   .beta  (inflexion point) = 0.128128128128128
   .species prevalence      = 0.914> 
> # Manually choosing a response approach
> generateRandomSp(env, approach = "response")
 - Determining species' response to predictor variables

Error in seq.default(cur.rast@data@min, cur.rast@data@max, length = 1000) : 
  'from' must be a finite number
Calls: generateRandomSp -> sample -> seq -> seq.default
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc           4.2Mb
    docjs         1.4Mb
    htmlwidgets   3.9Mb
File 'waffect/libs/i386/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'
File 'waffect/libs/x64/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   7.6Mb
Error(s) in re-building vignettes:
--- re-building 'vignette.Rnw' using Sweave
There are  2000 missing values for 05054000 or 49.78 percent of the data.
The maximum block of missing 05054000 data is 12 days long.
Filled in 2000 values for 05054000
Request failed [400]. Retrying in 1 seconds...
Request failed [400]. Retrying in 1 seconds...

Error: processing vignette 'vignette.Rnw' failed with diagnostics:
 chunk 15 
Error in getWebServiceData(url, encoding = "gzip") : 
  HTTP Status 400 - invalid pathInfo: pathInfo=[null]

--- failed re-building 'vignette.Rnw'

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

Error: Vignette re-building failed.
Execution halted
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    client   8.9Mb
    doc      1.0Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.6Mb
Bundesliga.Mannschaft: no visible global function definition for 'data'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible global function definition for 'data'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible global function definition for 'data'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
sens.spec: no visible global function definition for 'na.omit'
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
.__A__.1 : <anonymous>: no visible binding for global variable '.hwnd'
Undefined global functions or variables:
  .hwnd
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.5Mb
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data  11.1Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/XGR.Rcheck/00install.out' for details.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
Running examples in 'Xmisc-Ex.R' failed
The error most likely occurred in:

> ### Name: dfsplit
> ### Title: Split data.frame given one leveled column
> ### Aliases: dfsplit
> 
> ### ** Examples
> 
> x <- read.table(textConnection("
+ chr1  0   100
+ chr2  100 200
+ chr10 200 300
+ "),col.names=c('chr','start','end'))
> 
> ## compare the results by base::split and dfsplit
> split(x,f=x[,'chr'])
$chr1
   chr start end
1 chr1     0 100

$chr10
    chr start end
3 chr10   200 300

$chr2
   chr start end
2 chr2   100 200

> ## $chr1
> ##    chr start end
> ## 1 chr1     0 100
> 
> ## $chr10
> ##     chr start end
> ## 3 chr10   200 300
> 
> ## $chr2
> ##    chr start end
> ## 2 chr2   100 200
> 
> dfsplit(x,'chr',c('chr1','chr2','chr10'))
$chr1
   chr start end
1 chr1     0 100

$chr2
   chr start end
2 chr2   100 200

$chr10
    chr start end
3 chr10   200 300

> ## $chr1
> ##    chr start end
> ## 1 chr1     0 100
> 
> ## $chr2
> ##    chr start end
> ## 2 chr2   100 200
> 
> ## $chr10
> ##     chr start end
> ## 3 chr10   200 300
> 
> 
> 
> cleanEx()
Error: connections left open:
	"\nchr1  0   100\nchr2  100 200\nchr10 200 300\n" (textConnection)
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
File 'xml2/libs/i386/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'
File 'xml2/libs/x64/xml2.dll':
  Found non-API calls to R: 'R_GetConnection', 'R_WriteConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Error(s) in re-building vignettes:
--- re-building 'zoomgrid-vignette.Rmd' using rmarkdown
pandoc.exe: Could not fetch https://latex.codecogs.com/gif.latex?f%28x_1%2C%20x_2%29%20%3D%202%20A%20+%20%5Csum_%7Bi%3D1%7D%5E2%20%5Cleft%28%20x_i%5E2%20-%20A%20%5Ccos%282%20%5Cpi%20x_i%29%20%5Cright%29
HttpExceptionRequest Request {
  host                 = "latex.codecogs.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/gif.latex"
  queryString          = "?f%28x_1%2C%20x_2%29%20%3D%202%20A%20+%20%5Csum_%7Bi%3D1%7D%5E2%20%5Cleft%28%20x_i%5E2%20-%20A%20%5Ccos%282%20%5Cpi%20x_i%29%20%5Cright%29"
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (ConnectionFailure Network.Socket.sendBuf: failed (Unknown error))
Error: processing vignette 'zoomgrid-vignette.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
--- failed re-building 'zoomgrid-vignette.Rmd'

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ABHgenotypeR-vignette.Rmd’ using rmarkdown
Quitting from lines 70-72 (ABHgenotypeR-vignette.Rmd) 
Error: processing vignette 'ABHgenotypeR-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ABHgenotypeR-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines 78-85 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 43-49 (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’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ASDABarPlot
> ### Title: barplot for ASDA objects
> ### Aliases: ASDABarPlot
> 
> ### ** Examples
> 
>     # Generate and ASDA object with your data, e.g.
>     # Prepare training and test set
>     # This is a very small data set, I advise you to try it on something with more
>     # variables, e.g. something from this source: http://www.cs.ucr.edu/~eamonn/time_series_data/
>     # or possibly run this on the Gaussian data example from the ASDA function
>     train <- c(1:40,51:90,101:140)
>     Xtrain <- iris[train,1:4]
>     nX <- normalize(Xtrain)
>     Xtrain <- nX$Xc
>     Ytrain <- iris[train,5]
>     Xtest <- iris[-train,1:4]
>     Xtest <- normalizetest(Xtest,nX)
>     Ytest <- iris[-train,5]
>     # Run the method
>     resIris <- ASDA(Xtrain,Ytrain)
[1] "Om not specified, using default diag(p)."
[1] "gam not specified, using default value 1e-3"
[1] "lam not specified, using default value 1e-6"
[1] "q not specified, default is the max number K-1, where K is number of classes in Yt"
[1] "method not specified, using default SDAAP. You can choose from: SDAP, SDAAP or SDAD"
> 
>     # Look at the barplots of the DVs
>     ASDABarPlot(resIris)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ASDABarPlot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ACDm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: acf_acd
> ### Title: Autocorrelation function plots for ACD models
> ### Aliases: acf_acd
> 
> ### ** Examples
> 
> fitModel <- acdFit(adjDurData)

ACD model estimation by (Quasi) Maximum Likelihood 

Call:
  acdFit(durations = adjDurData) 

Model:
  ACD(1, 1)

Distribution:
  exponential

N: 34767

Parameter estimate:
         Coef      SE PV robustSE
omega  0.0127 0.00132  0  0.00125
alpha1 0.0587 0.00277  0  0.00236
beta1  0.9295 0.00359  0  0.00306


The fixed/unfree mean distribution parameter: 
 lambda: 1

QML robust correlations:
        omega alpha1  beta1
omega   1.000  0.442 -0.762
alpha1  0.442  1.000 -0.902
beta1  -0.762 -0.902  1.000


Goodness of fit:
                      value
LogLikelihood -33300.775975
AIC            66607.551949
BIC            66632.921221
MSE                1.798696

Convergence: 0 

Number of log-likelihood function evaluations: 114 

Estimation time: 0.3395 secs 

Description: Estimated at 2019-03-29 17:14:59 by user hornik

> acf_acd(fitModel, conf_level = 0.95, max = 50, min = 1)
Error in Summary.unit(c(8, 8), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: acf_acd ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘ACSNMineR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: represent_enrichment
> ### Title: Graphic representation of enrichment
> ### Aliases: represent_enrichment
> 
> ### ** Examples
> 
> represent_enrichment(enrichment = enrichment_test,scale = "reverselog",
+                     sample_name = "test",plot = "bar")
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 ‘ACSN-vignette.Rmd’ using rmarkdown
Quitting from lines 155-164 (ACSN-vignette.Rmd) 
Error: processing vignette 'ACSN-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ACSN-vignette.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.adaptivegpca
> ### Title: Plot an adaptivegpca object
> ### Aliases: plot.adaptivegpca
> 
> ### ** Examples
> 
> data(AntibioticSmall)
> out.agpca = adaptivegpca(AntibioticSmall$X, AntibioticSmall$Q, k = 2)
> plot(out.agpca)
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 ‘adaptive_gpca_vignette.Rmd’ using rmarkdown
Quitting from lines 180-181 (adaptive_gpca_vignette.Rmd) 
Error: processing vignette 'adaptive_gpca_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘adaptive_gpca_vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hybridtoy
> ### Title: Toy hybrid dataset
> ### Aliases: hybridtoy
> 
> ### ** Examples
> 
> data(hybridtoy)
> x <- hybridtoy
> pca1 <- dudi.pca(tab(x), scannf=FALSE, scale=FALSE)
> s.class(pca1$li, pop(x))
> 
> if(require(ggplot2)) {
+ p <- ggplot(pca1$li, aes(x=Axis1)) +
+     geom_density(aes(fill=pop(x)), alpha=.4, adjust=1) +
+     geom_point(aes(y=0, color=pop(x)), pch="|", size=10, alpha=.5)
+ p
+ }
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 ‘admixturegraph.Rmd’ using rmarkdown
Loading required package: optimbase
Loading required package: Matrix
Loading required package: optimsimplex
Quitting from lines 196-197 (admixturegraph.Rmd) 
Error: processing vignette 'admixturegraph.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘admixturegraph.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.ADMM
> ### Title: Plot ADMM object
> ### Aliases: plot.ADMM
> 
> ### ** Examples
> 
> # generate data from a sparse matrix
> # first compute covariance matrix
> S = matrix(0.7, nrow = 5, ncol = 5)
> for (i in 1:5){
+  for (j in 1:5){
+    S[i, j] = S[i, j]^abs(i - j)
+  }
+  }
> 
> # generate 100 x 5 matrix with rows drawn from iid N_p(0, S)
> set.seed(123)
> Z = matrix(rnorm(100*5), nrow = 100, ncol = 5)
> out = eigen(S, symmetric = TRUE)
> S.sqrt = out$vectors %*% diag(out$values^0.5)
> S.sqrt = S.sqrt %*% t(out$vectors)
> X = Z %*% S.sqrt
> 
> # produce line graph for ADMMsigma
> plot(ADMMsigma(X), type = 'line')
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
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 ‘advclust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biploting
> ### Title: Biploting Fuzzy Cluster Result
> ### Aliases: biploting
> 
> ### ** Examples
> 
> fuzzy.CM(iris[,1:4],K=3,m=2,max.iteration=100,threshold=1e-5,RandomNumber=1234)->cl1

Membership initialiazed randomly


 iteration:	 1
 iteration:	 2
 iteration:	 3
 iteration:	 4
 iteration:	 5
 iteration:	 6
 iteration:	 7
 iteration:	 8
 iteration:	 9
 iteration:	 10
 iteration:	 11
 iteration:	 12
 iteration:	 13
 iteration:	 14
 iteration:	 15
 iteration:	 16
 iteration:	 17
 iteration:	 18
 iteration:	 19
 iteration:	 20
 iteration:	 21
 iteration:	 22
 iteration:	 23
 iteration:	 24
 iteration:	 25
 iteration:	 26
 iteration:	 27
 iteration:	 28
Finish :)
> biploting(cl1,iris[,1:4])

Scale default:TrueError in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: biploting ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advclust.Rmd’ using rmarkdown
Quitting from lines 65-66 (advclust.Rmd) 
Error: processing vignette 'advclust.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘advclust.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iplot_abundance
> ### Title: Plot of the Relative Abundance of the Pollen Types
> ### Aliases: iplot_abundance
> 
> ### ** Examples
> 
> data("munich")
> iplot_abundance (munich, interpolation = FALSE, export.plot = FALSE)
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 ‘afex-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: afex_plot
> ### Title: m-way Plot with Error Bars and Raw Data
> ### Aliases: afex_plot afex_plot.afex_aov afex_plot.mixed afex_plot.merMod
> ###   afex_plot.default interaction_plot oneway_plot
> 
> ### ** Examples
> 
> # note: use library("ggplot") to avoid "ggplot2::" in the following
> 
> ##################################################################
> ##                2-factor Within-Subject Design                ##
> ##################################################################
> 
> data(md_12.1)
> aw <- aov_ez("id", "rt", md_12.1, within = c("angle", "noise"))
> 
> ##---------------------------------------------------------------
> ##                    Basic Interaction Plots                   -
> ##---------------------------------------------------------------
> 
> afex_plot(aw, x = "angle", trace = "noise") 
Warning: Panel(s) show within-subjects factors, but not within-subjects error bars.
For within-subjects error bars use: error = "within"
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 ‘AFM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RoughnessByLengthScale
> ### Title: Calculate the roughness of the sample against length scale
> ### Aliases: RoughnessByLengthScale RoughnessByLengthScale,AFMImage-method
> 
> ### ** Examples
> 
> library(AFM)
> library(ggplot2)
> 
> data("AFMImageOfNormallyDistributedHeights")
> oneAFMImage<-AFMImageOfNormallyDistributedHeights
> AFMImagePSDAnalysis<-AFMImagePSDAnalysis()
> data<-RoughnessByLengthScale(oneAFMImage, AFMImagePSDAnalysis)
> r<-roughness<-filename<-NULL
> p1 <- ggplot(data, aes(x=r, y=roughness, colour= basename(filename)))
> p1 <- p1 + geom_point()
> p1 <- p1 + geom_line()
> p1 <- p1 + ylab("roughness (nm)")
> p1 <- p1 + xlab("lengthscale (nm)")
> p1
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 ‘afmToolkit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: afmBaselineCorrection
> ### Title: Performs a baseline correction to an AFM F-z curve
> ### Aliases: afmBaselineCorrection
> 
> ### ** Examples
> 
> AFMcurve <- afmReadJPK("force-save-JPK-2h.txt.gz", path = path.package("afmToolkit"))
JPK file force-save-JPK-2h.txt.gz loaded. 2 headers found.
> ZPointApp <- 6.43e-6
> ZPointRet <- 6.45e-6
> AFMcurve <- afmBaselineCorrection(AFMcurve,ZPointApp = ZPointApp,ZPointRet = ZPointRet)
> plot(AFMcurve)
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 ‘my-vignette.Rmd’ using rmarkdown
Quitting from lines 147-160 (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
Running examples in ‘aimPlot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aimPlot
> ### Title: Pie Like Plot for Completeness
> ### Aliases: aimPlot
> 
> ### ** Examples
> 
> 
> # basic usage
> library("aimPlot")
> aimPlot(data = RegData, title = "Plot title")
Warning: Ignoring unknown aesthetics: ymin, ymax
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 ‘aire.zmvm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: idw360
> ### Title: Inverse Distance Weighting with Directional Data
> ### Aliases: idw360
> 
> ### ** Examples
> 
> library("sp")
> library("ggplot2")
> 
> ## Could be wind direction values in degrees
> values <- c(55, 355)
> 
> ## Location of sensors. First column x/longitud, second y/latitude
> locations <- data.frame(lon = c(1, 2), lat = c(1, 2))
> coordinates(locations) <- ~lon+lat
> 
> ## The grid for which to extrapolate values
> grid <- data.frame(lon = c(1, 2, 1, 2), lat = c(1, 2, 2, 1))
> coordinates(grid) <- ~lon+lat
> 
> ## Perform the inverse distance weighted interpolation
> res <- idw360(values, locations, grid)
> head(res)
  pred
1   55
2  355
3   25
4   25
> 
> df <- cbind(res, as.data.frame(grid))
> ## The wind direction compass starts where the 90 degree mark is located
> ggplot(df, aes(lon, lat)) +
+   geom_point() +
+   geom_spoke(aes(angle = ((90 - pred) %% 360) * pi / 180),
+              radius = 1,
+              arrow=arrow(length = unit(0.2,"cm")))
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 ‘ALA4R.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: maps
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
Quitting from lines 488-490 (ALA4R.Rmd) 
Error: processing vignette 'ALA4R.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ALA4R.Rmd’

SUMMARY: processing the following file failed:
  ‘ALA4R.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DEFAULT_COLORS
> ### Title: Default colors
> ### Aliases: DEFAULT_COLORS DNA_COLORS IG_COLORS TR_COLORS
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # IG_COLORS as an isotype color set for ggplot
> isotype <- c("IgG", "IgM", "IgM", "IgA")
> db <- data.frame(x=1:4, y=1:4, iso=isotype)
> g1 <- ggplot(db, aes(x=x, y=y, color=iso)) + 
+     scale_color_manual(name="Isotype", values=IG_COLORS) +
+     geom_point(size=10)
> plot(g1)
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 ‘alfred.Rmd’ using rmarkdown
Quitting from lines 43-46 (alfred.Rmd) 
Error: processing vignette 'alfred.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘alfred.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Quitting from lines 78-80 (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
Error(s) in re-building vignettes:
  ...
--- re-building ‘ameco_dataset.Rmd’ using rmarkdown
Quitting from lines 45-55 (ameco_dataset.Rmd) 
Error: processing vignette 'ameco_dataset.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ameco_dataset.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
Quitting from lines 360-360 (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 ‘aMNLFA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aMNLFA.itemplots
> ### Title: aMNLFA item plotting function
> ### Aliases: aMNLFA.itemplots
> ### Keywords: MNLFA
> 
> ### ** Examples
> 
>  wd <- tempdir()
>  first<-paste0(system.file(package='aMNLFA'),"/examplefiles")
>  the.list <- list.files(first,full.names=TRUE)
>  file.copy(the.list,wd,overwrite=TRUE)
 [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[16] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[31] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[46] TRUE TRUE TRUE TRUE TRUE TRUE
>  ob <- aMNLFA::aMNLFA.object(dir = wd, 
+  mrdata = xstudy, 
+  indicators = paste0("BIN_", 1:12),
+  catindicators = paste0("BIN_", 1:12), 
+  meanimpact = c("AGE", "GENDER", "STUDY"), 
+  varimpact = c("AGE", "GENDER", "STUDY"), 
+  measinvar = c("AGE", "GENDER", "STUDY"),
+  factors = c("GENDER", "STUDY"),
+  ID = "ID",
+  thresholds = FALSE)
>  
>  aMNLFA.itemplots(ob)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: aMNLFA.itemplots ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘AmpliconDuo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AmpliconDuo-package
> ### Title: Statistical Analysis Of Amplicon Data Of The Same Sample To
> ###   Identify Artefacts
> ### Aliases: AmpliconDuo-package AmpliconDuo
> ### Keywords: package
> 
> ### ** Examples
> 
> 
> ## load test amplicon frequency data ampliconfreqs and vector with sample names site.f
> data(ampliconfreqs)
> data(site.f)
> 
> ## generating ampliconduo data frames 
> ## depending on the size if the data sets, may take some time
> ampliconduoset <- ampliconduo(ampliconfreqs[,1:4], sample.names = site.f[1:2])
..> 
> ## plot amplicon read numbers of sample A  vs. amplicon read numbers of sample B,
> ## indicating amplicons with significant deviations in their occurence across samples
> plotAmpliconduo.set(ampliconduoset, nrow = 3)
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
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: plotAmpliconduo.set ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘p1_getting_started.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: 'amt'

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

    filter

Warning: `data_frame()` is deprecated, use `tibble()`.
This warning is displayed once per session.
.t missing, creating `track_xy`.
Quitting from lines 256-258 (p1_getting_started.Rmd) 
Error: processing vignette 'p1_getting_started.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘p1_getting_started.Rmd’

--- re-building ‘p4_SSF.Rmd’ using rmarkdown

Attaching package: 'lubridate'

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

    date

Loading required package: sp

Attaching package: 'amt'

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

    select

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

    bbox

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

    filter

Warning in random_steps.steps_xy(., n = 15) :
  Step-lengths or turning angles contained NA, which were removed.
Warning in random_steps.steps_xy(., n = 15) :
  Step-lengths or turning angles contained NA, which were removed.
--- finished re-building ‘p4_SSF.Rmd’

SUMMARY: processing the following file failed:
  ‘p1_getting_started.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bivarPlots
> ### Title: Bi-Variate Plot
> ### Aliases: bivarPlots
> 
> ### ** Examples
> 
> bivarPlots(dataset = iris, select_var_name_1 = "Sepal.Length",
+  select_var_name_2 = "Sepal.Width")
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:
  analyzeFMRI.c:948:3: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  analyzeFMRI.c:975:5: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/AnalyzeFMRI.Rcheck/00install.out’ for details.
Running examples in ‘anchoredDistr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotMAD
> ### Title: Plot the data contained in MADproject object slots.
> ### Aliases: plotMAD plotMAD,MADproject,ANY-method
> ###   plotMAD,MADproject,character-method
> 
> ### ** Examples
> 
> data(pumping)
> plotMAD(pumping, "realizations")
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 ‘anchoredDistr.Rmd’ using rmarkdown
Quitting from lines 85-86 (anchoredDistr.Rmd) 
Error: processing vignette 'anchoredDistr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘anchoredDistr.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_plot_from_simulation
> ### Title: Create a plot from a creel survey simulation
> ### Aliases: create_plot_from_simulation
> 
> ### ** Examples
> 
> 
> start_time <- 0 
> wait_time <- 8 
> n_anglers <- 50 
> n_sites <- 1
> sampling_prob <- wait_time/12
> mean_catch_rate <- 10
> 
> tmp <- conduct_multiple_surveys(91, start_time, wait_time, n_anglers, n_sites, sampling_prob, 
+                                 mean_catch_rate, fishing_day_length = 12, mean_trip_length = 4)
> 
> create_plot_from_simulation(tmp, "catch")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: create_plot_from_simulation ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘creel_survey_simulation.Rmd’ using rmarkdown
Quitting from lines 62-74 (creel_survey_simulation.Rmd) 
Error: processing vignette 'creel_survey_simulation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘creel_survey_simulation.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_anomalies
> ### Title: Visualize the anomalies in one or multiple time series
> ### Aliases: plot_anomalies
> 
> ### ** 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)
> 
> data(tidyverse_cran_downloads)
> 
> #### SINGLE TIME SERIES ####
> tidyverse_cran_downloads %>%
+     filter(package == "tidyquant") %>%
+     ungroup() %>%
+     time_decompose(count, method = "stl") %>%
+     anomalize(remainder, method = "iqr") %>%
+     time_recompose() %>%
+     plot_anomalies(time_recomposed = TRUE)
Warning: Detecting old grouped_df format, replacing `vars` attribute by `groups`
frequency = 7 days
trend = 91 days
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 ‘anomalize_methods.Rmd’ using rmarkdown
Warning: Detecting old grouped_df format, replacing `vars` attribute by `groups`
Quitting from lines 87-110 (anomalize_methods.Rmd) 
Error: processing vignette 'anomalize_methods.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘anomalize_methods.Rmd’

--- re-building ‘anomalize_quick_start_guide.Rmd’ using rmarkdown
Warning: Detecting old grouped_df format, replacing `vars` attribute by `groups`
Warning: Detecting old grouped_df format, replacing `vars` attribute by `groups`
Quitting from lines 97-99 (anomalize_quick_start_guide.Rmd) 
Error: processing vignette 'anomalize_quick_start_guide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘anomalize_quick_start_guide.Rmd’

SUMMARY: processing the following files failed:
  ‘anomalize_methods.Rmd’ ‘anomalize_quick_start_guide.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anomaly_series
> ### Title: A technique for detecting anomalous segments based on CAPA
> ###   (Collective And Point Anomaly) by Fisch et al.
> ### Aliases: anomaly_series
> 
> ### ** Examples
> 
> library(anomaly)
> set.seed(2018)
> # Generate data typically following a normal distribution with mean 0 and variance 1. 
> # Then introduce 3 anomaly windows and 4 point outliers.
> x  = rnorm(5000)
> x[401:500]   = rnorm(100,4,1)
> x[1601:1800] = rnorm(200,0,0.01)
> x[3201:3500] = rnorm(300,0,10)
> x[c(1000,2000,3000,4000)] = rnorm(4,0,100)
> inferred_anomalies = anomaly_series(x)
> plot(inferred_anomalies)
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 ‘ANOM.Rnw’ using knitr
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

Quitting from lines 67-72 (ANOM.Rnw) 
Error: processing vignette 'ANOM.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ANOM.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(anonymizer)
  > 
  > test_check("anonymizer")
  ── 1. Failure: Produces the correct output. (@test-anonymize.R#5)  ─────────────
  anonymize("a", .seed = 1) not equal to "ed879445e47969394b3f8eb818501976bed22b9ab0e7f7c5fdf2a96df0aec80e".
  1/1 mismatches
  x[1]: "6ae80dd07643618a5ea6ac83b506fd367d81f86e5f5650a42045ca7ebe516602"
  y[1]: "ed879445e47969394b3f8eb818501976bed22b9ab0e7f7c5fdf2a96df0aec80e"
  
  ── 2. Failure: Produces the correct output. (@test-salt.R#6)  ──────────────────
  salt("a", .seed = 1, .n_chars = 1) not equal to "gag".
  1/1 mismatches
  x[1]: "yay"
  y[1]: "gag"
  
  ── 3. Failure: Produces the correct output. (@test-salt.R#7)  ──────────────────
  salt("a", .seed = 2, .n_chars = 1) not equal to "eae".
  1/1 mismatches
  x[1]: "uau"
  y[1]: "eae"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 12 SKIPPED: 1 FAILED: 3
  1. Failure: Produces the correct output. (@test-anonymize.R#5) 
  2. Failure: Produces the correct output. (@test-salt.R#6) 
  3. Failure: Produces the correct output. (@test-salt.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘ArchaeoPhases-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MultiDatesPlot
> ### Title: Plot of the endpoints of credible intervals or HPD intervals of
> ###   a series of dates
> ### Aliases: MultiDatesPlot
> ### Keywords: credible interval highest posterior density regions
> 
> ### ** Examples
> 
>   data(Events)
>   MultiDatesPlot(Events, c(2,4,3), level = 0.95, intervals ="CI", title = "Plot of CI intervals")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: MultiDatesPlot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GroupsOfDates.Rmd’ using rmarkdown
Loading required package: coda
Loading required package: hdrcde
This is hdrcde 3.3
--- finished re-building ‘GroupsOfDates.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Loading required package: coda
Loading required package: hdrcde
This is hdrcde 3.3
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘SeriesOfDates.Rmd’ using rmarkdown
Loading required package: coda
Loading required package: hdrcde
This is hdrcde 3.3
Quitting from lines 39-41 (SeriesOfDates.Rmd) 
Error: processing vignette 'SeriesOfDates.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘SeriesOfDates.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘arena2r-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_box
> ### Title: Box Plot
> ### Aliases: plot_box
> 
> ### ** Examples
> 
> library(arena2r)
> 
> plot_box(arena_results, "Entity 1.NumberOut")
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 ‘arena2r-vignette.Rmd’ using rmarkdown
Quitting from lines 79-84 (arena2r-vignette.Rmd) 
Error: processing vignette 'arena2r-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘arena2r-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘arena2r-vignette.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Q.AR1
> ### Title: Precision matrix for an AR1 process
> ### Aliases: Q.AR1 r.AR1
> 
> ### ** Examples
> 
> require("ggplot2")
Loading required package: ggplot2
> # simulate AR1 GMRF
> obs <- r.AR1(100, M=30, sigma=1, rho=.98)
> # resulting matrix is n x M
> dim(obs)
[1] 100  30
> # subtract off the first time point to more easily observe correlation
> obs_adj <- obs - obs[,1]
> # move objects to a data frame
> ar1_df <- data.frame(obs=c(t(obs_adj)), realization=rep(1:100, each=30),
+                      time=rep(1:30, 100))
> # plot each realization
> ggplot(data=ar1_df, aes(time, obs, group=realization, color=realization)) +
+     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> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘art-contrasts.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: car
Loading required package: carData

Attaching package: 'car'

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

    recode

Quitting from lines 94-106 (art-contrasts.Rmd) 
Error: processing vignette 'art-contrasts.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘art-contrasts.Rmd’

--- re-building ‘art-effect-size.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: carData

Attaching package: 'car'

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

    Recode

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

    recode

Quitting from lines 168-179 (art-effect-size.Rmd) 
Error: processing vignette 'art-effect-size.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘art-effect-size.Rmd’

SUMMARY: processing the following files failed:
  ‘art-contrasts.Rmd’ ‘art-effect-size.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘adaptive_shrinkage.Rmd’ using rmarkdown
Quitting from lines 101-125 (adaptive_shrinkage.Rmd) 
Error: processing vignette 'adaptive_shrinkage.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘adaptive_shrinkage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘AssetCorr_vignette.Rmd’ using rmarkdown
Quitting from lines 80-85 (AssetCorr_vignette.Rmd) 
Error: processing vignette 'AssetCorr_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘AssetCorr_vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: accuracy.plot
> ### Title: Make a boxplot (ggplot2 style) of assignment accuracy from
> ###   cross-validation results
> ### Aliases: accuracy.plot
> 
> ### ** Examples
> 
> Your_df <- read.table(system.file("extdata/Rate.txt", package="assignPOP"), header=TRUE)
> accuracy.plot(Your_df, pop="all")
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 ‘asVPC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VPC.graph
> ### Title: calculate percentiles of original data using bin-related weight
> ###   percentiles of simulated data with corresponding confidence interval
> ### Aliases: VPC.graph
> 
> ### ** Examples
> 
> data(origdata)
> data(simdata)
> VPC.graph(origdata,simdata,10,100)
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 ‘ATR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rotate
> ### Title: Change the class of a 'party' object.
> ### Aliases: rotate
> ### Keywords: tree
> 
> ### ** Examples
> 
> 
>   data("airquality", package = "datasets")
>   m <- ctree(Wind ~ . , data = airquality)
>   plot(rotate(m), main = "TREE", tnex = 1.5)
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
Running ‘regtest.R’ [2s/2s]
Running the tests in ‘tests/regtest.R’ failed.
Complete output:
  > 
  > library("ATR")
  Loading required package: grid
  Loading required package: partykit
  Loading required package: libcoin
  Loading required package: mvtnorm
  > library("partykit")
  > 
  > ctrl <- ctree_control(maxsurrogate = 3)
  > 
  > ### AirQuality: Standard example
  > data("airquality", package = "datasets")
  > tree <- rotate(ctree(Wind ~ . , data = airquality, 
  +                                  control = ctrl))
  > #pdf("tmp.pdf", width = 12, height = 10)
  > plot(tree, main = "Standard example")
  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
Found the following significant warnings:
  pa.c:247:2: warning: initialization of ‘struct audio_instance * (*)(struct SEXPREC *, float,  int)’ from incompatible pointer type ‘void * (*)(struct SEXPREC *, float,  int)’ [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Running examples in ‘auditor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.modelAudit
> ### Title: Model diagnostic plots
> ### Aliases: plot.modelAudit plot.modelFit plot.modelPerformance
> ###   plot.modelResiduals plot.observationInfluence
> 
> ### ** Examples
> 
> library(car)
Loading required package: carData
> lm_model <- lm(prestige~education + women + income, data = Prestige)
> lm_au <- audit(lm_model, data = Prestige, y = Prestige$prestige)
> plot(lm_au)
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
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/augmentedRCBD.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘autoimage.Rmd’ using rmarkdown
--- finished re-building ‘autoimage.Rmd’

--- re-building ‘ggplot2-comparison.Rmd’ using rmarkdown
Quitting from lines 61-64 (ggplot2-comparison.Rmd) 
Error: processing vignette 'ggplot2-comparison.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ggplot2-comparison.Rmd’

SUMMARY: processing the following file failed:
  ‘ggplot2-comparison.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Quitting from lines 248-266 (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 ‘autoplotly-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplotly
> ### Title: Automatic Visualization of Popular Statistical Results Using
> ###   'plotly.js' and 'ggplot2'
> ### Aliases: autoplotly autoplotly autoplotly-package
> 
> ### ** Examples
> 
> # Automatically generate interactive plot for results produced by `stats::prcomp`
> p <- autoplotly(prcomp(iris[c(1, 2, 3, 4)]), data = iris,
+                 colour = 'Species', label = TRUE, label.size = 3, frame = TRUE)
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: autoplotly ... unitConvert -> <Anonymous> -> convertUnit -> grid.Call
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘finding-thresholds.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 43-47 (finding-thresholds.Rmd) 
Error: processing vignette 'finding-thresholds.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘finding-thresholds.Rmd’

--- re-building ‘thresholding-image-stacks.Rmd’ using rmarkdown
--- finished re-building ‘thresholding-image-stacks.Rmd’

--- re-building ‘thresholding-images.Rmd’ using rmarkdown
--- finished re-building ‘thresholding-images.Rmd’

SUMMARY: processing the following file failed:
  ‘finding-thresholds.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BACA-package
> ### Title: A graphical tool to visualize and compare functional annotations
> ###   retrieved from DAVID knowledgebase.
> ### Aliases: BACA-package BACA
> 
> ### ** Examples
> 
>   data(result.kegg)
>  
>   bbplot.kegg <- BBplot(result.kegg, max.pval = 0.05, min.ngenes = 10, 
+                     name.com = c("Cond.1_12h","Cond.1_24h","Cond.2_12h","Cond.2_24h"), 
+                     labels = c("down", "up"), colors = c("#009E73", "red"), 
+                     title = "BBplot - KEGG", print.term = "description")
>   bbplot.kegg
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 ‘BacArena-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HeatMapFeeding
> ### Title: Function for plotting heatmap of feeding between two selected
> ###   cell models
> ### Aliases: HeatMapFeeding HeatMapFeeding,Eval-method
> 
> ### ** Examples
> 
> sim <- sihumi_test
> HeatMapFeeding(object = sim, speciesA = 1, speciesB = 2, var_nr = 78)
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 ‘BacArena-Introduction.Rmd’ using rmarkdown
Loading required package: sybil
Loading required package: Matrix
Loading required package: lattice
Loading required package: ReacTran
Loading required package: rootSolve
Loading required package: deSolve
Loading required package: shape
BacArena paper: https://doi.org/10.1371/journal.pcbi.1005544
 Tutorials: https://bacarena.github.io
 Model import from SBML: https://github.com/euba/BacArena/wiki/Model-import
 Development and help: https://github.com/euba/bacarena
Warning in simEnv(arena, time = 10) :
  If growth is limitted by maximum weight for an organism (max_weight=TRUE) it is recommended to use minimize total flux (sec_obj='mtf').
Quitting from lines 149-153 (BacArena-Introduction.Rmd) 
Error: processing vignette 'BacArena-Introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘BacArena-Introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘exampleBackShift.Rmd’ using rmarkdown
Loading required package: backShift
Loading required package: ggplot2
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.2-2 (2019-03-07) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    backsolve, forwardsolve

Loading required package: maps
See www.image.ucar.edu/~nychka/Fields for
 a vignette and other supplements. 
No id variables; using all as measure variables
Quitting from lines 257-258 (exampleBackShift.Rmd) 
Error: processing vignette 'exampleBackShift.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘exampleBackShift.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: balance.combine
> ### Title: Combine Two Sub-Plots
> ### Aliases: balance.combine
> 
> ### ** Examples
> 
> library(balance)
> data(iris)
> x <- iris[,1:4]
> sbp <- sbp.fromPBA(x)
> res <- balance(x, sbp)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: balance ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘balance.Rmd’ using rmarkdown
Quitting from lines 50-51 (balance.Rmd) 
Error: processing vignette 'balance.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘balance.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘use-ballr.Rmd’ using rmarkdown
Quitting from lines 100-116 (use-ballr.Rmd) 
Error: processing vignette 'use-ballr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘use-ballr.Rmd’

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

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

--- re-building ‘quickstart.Rmd’ using rmarkdown
Quitting from lines 127-131 (quickstart.Rmd) 
Error: processing vignette 'quickstart.Rmd' failed with diagnostics:
unexpected character '<'

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pp_check.hef
> ### Title: Posterior predictive checks for a hef object
> ### Aliases: pp_check.hef pp_check
> 
> ### ** Examples
> 
> ############################ Beta-binomial #################################
> 
> # ------------------------- Rat tumor data ------------------------------- #
> 
> rat_res <- hef(model = "beta_binom", data = rat, nrep = 50)
> 
> # Overlaid density estimates
> pp_check(rat_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 ‘bang-anova-vignette.Rmd’ using rmarkdown
--- finished re-building ‘bang-anova-vignette.Rmd’

--- re-building ‘bang-hef-vignette.Rmd’ using rmarkdown
--- finished re-building ‘bang-hef-vignette.Rmd’

--- re-building ‘bang-ppc-vignette.Rmd’ using rmarkdown
Quitting from lines 48-54 (bang-ppc-vignette.Rmd) 
Error: processing vignette 'bang-ppc-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bang-ppc-vignette.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDetectorTrace
> ### Title: Plot BANTER Detector Traces
> ### Aliases: plotDetectorTrace
> 
> ### ** Examples
> 
> data(train.data)
> # initialize BANTER model with event data
> bant.mdl <- initBanterModel(train.data$events)
> # add all detector models
> bant.mdl <- addBanterDetector(
+   bant.mdl, train.data$detectors, 
+   ntree = 50, sampsize = 1, num.cores = 1
+ )
> 
> plotDetectorTrace(bant.mdl)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotDetectorTrace ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘base2grob.Rmd’ using rmarkdown

Attaching package: 'cowplot'

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

    ggsave

The base2grob package has been deprecated. Please switch over to the ggplotify package
Saving 7 x 5 in image
Saving 7 x 5 in image
Saving 7 x 5 in image
Quitting from lines 93-97 (base2grob.Rmd) 
Error: processing vignette 'base2grob.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘base2grob.Rmd’

SUMMARY: processing the following file failed:
  ‘base2grob.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BAS-vignette.Rmd’ using rmarkdown
Warning in model.matrix.default(mt, mf, contrasts) :
  non-list contrasts argument ignored
Quitting from lines 272-278 (BAS-vignette.Rmd) 
Error: processing vignette 'BAS-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘BAS-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BatchGetSymbols-vignette.Rmd’ using rmarkdown
Quitting from lines 67-73 (BatchGetSymbols-vignette.Rmd) 
Error: processing vignette 'BatchGetSymbols-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘BatchGetSymbols-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.by.segreg.type
> ### Title: Draw a graphic showing the number of markers of each segregation
> ###   pattern.
> ### Aliases: plot.by.segreg.type
> 
> ### ** Examples
> 
> data(example.out) #Outcrossing data
> plot.by.segreg.type(example.out)
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’ [11s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bayesAB)
  > 
  > test_check("bayesAB")
  ── 1. Error: Success (@test-generics.R#46)  ────────────────────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_silent(print(plot(x))) at testthat/test-generics.R:46
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: print(plot(x))
  10: print.plotBayesTest(plot(x))
  ...
  26: pushvpgp(x)
  27: pushgrobvp(x$vp)
  28: pushgrobvp.viewport(x$vp)
  29: pushViewport(vp, recording = FALSE)
  30: lapply(vps, push.vp, recording)
  31: FUN(X[[i]], ...)
  32: push.vp.vpTree(X[[i]], ...)
  33: push.vp(vp$parent, recording)
  34: push.vp.viewport(vp$parent, recording)
  35: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 129 SKIPPED: 0 FAILED: 1
  1. Error: Success (@test-generics.R#46) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 51-53 (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
Found the following significant warnings:
  Blasso.cpp:451:53: warning: ‘*<unknown>.Blasso::icept’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/bayesCL.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘bayesdfa.Rmd’ using rmarkdown
Loading required package: Rcpp

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: StanHeaders
rstan (Version 2.18.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Quitting from lines 77-78 (bayesdfa.Rmd) 
Error: processing vignette 'bayesdfa.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bayesdfa.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bdpbinomial-vignette.Rmd’ using rmarkdown
Quitting from lines 121-123 (bdpbinomial-vignette.Rmd) 
Error: processing vignette 'bdpbinomial-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bdpbinomial-vignette.Rmd’

--- re-building ‘bdplm-vignette.Rmd’ using rmarkdown
Quitting from lines 138-140 (bdplm-vignette.Rmd) 
Error: processing vignette 'bdplm-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bdplm-vignette.Rmd’

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

--- re-building ‘bdpsurvival-vignette.Rmd’ using rmarkdown
Quitting from lines 191-193 (bdpsurvival-vignette.Rmd) 
Error: processing vignette 'bdpsurvival-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bdpsurvival-vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘bdpbinomial-vignette.Rmd’ ‘bdplm-vignette.Rmd’
  ‘bdpnormal-vignette.Rmd’ ‘bdpsurvival-vignette.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.befa
> ### Title: Plot object of class 'befa'
> ### Aliases: plot.befa
> 
> ### ** Examples
> 
> set.seed(6)
> 
> # generate fake data with 15 manifest variables and 3 factors
> Y <- simul.dedic.facmod(N = 200, dedic = rep(1:3, each = 5))
> 
> # run MCMC sampler and post process output
> # notice: 1000 MCMC iterations for illustration purposes only,
> #  increase this number to obtain reliable posterior results!
> mcmc <- befa(Y, Kmax = 5, iter = 1000)
starting MCMC sampling...
    5%
   10%
   15%
   20%
   25%
   30%
   35%
   40%
   45%
done with burn-in period
   50%
   55%
   60%
   65%
   70%
   75%
   80%
   85%
   90%
   95%
  100%
done with sampling!
> mcmc <- post.column.switch(mcmc)
> mcmc <- post.sign.switch(mcmc)
> 
> # plot results for highest posterior probability model
> plot(mcmc, what = 'hppm')
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 ‘BayesMallows-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compute_mallows
> ### Title: Preference Learning with the Mallows Rank Model
> ### Aliases: compute_mallows
> 
> ### ** Examples
> 
> # ANALYSIS OF COMPLETE RANKINGS
> # The example datasets potato_visual and potato_weighing contain complete
> # rankings of 20 items, by 12 assessors. We first analyse these using the Mallows
> # model:
> model_fit <- compute_mallows(potato_visual)
> 
> # We study the trace plot of the parameters
> assess_convergence(model_fit, parameter = "alpha")
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 ‘bayesplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MCMC-combos
> ### Title: Combination plots
> ### Aliases: MCMC-combos mcmc_combo
> 
> ### ** Examples
> 
> # some parameter draws to use for demonstration
> x <- example_mcmc_draws()
> dim(x)
[1] 250   4   4
> dimnames(x)
$Iteration
NULL

$Chain
[1] "chain:1" "chain:2" "chain:3" "chain:4"

$Parameter
[1] "alpha"   "sigma"   "beta[1]" "beta[2]"

> 
> mcmc_combo(x, pars = c("alpha", "sigma"))
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: mcmc_combo ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘Bayesrel-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotstrel.id
> ### Title: plots posterior distributions of chosen estimate and the
> ###   item-dropped cases in one plot
> ### Aliases: plotstrel.id
> 
> ### ** Examples
> 
> plotstrel.id(strel(cavalini, "lambda2", item.dropped = TRUE), "lambda2")
Picking joint bandwidth of 0.00237
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:
  mcmc.c:337:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/BayHap.Rcheck/00install.out’ for details.
Running examples in ‘BCEA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ceplane.plot
> ### Title: Cost-effectiveness plane plot
> ### Aliases: ceplane.plot
> ### Keywords: Health economic evaluation Cost Effectiveness Plane
> 
> ### ** Examples
> 
> ### create the bcea object m for the smoking cessation example
> data(Smoking)
> m <- bcea(e,c,ref=4,Kmax=500,interventions=treats)
> ### produce the plot
> ceplane.plot(m,wtp=200,graph="base")
> ### select only one comparator
> ceplane.plot(m,wtp=200,graph="base",comparator=3)
> ### or use ggplot2 instead
> if(requireNamespace("ggplot2")){
+ ceplane.plot(m,wtp=200,pos="right",ICER.size=2,graph="ggplot2")
+ }
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> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘BCellMA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aa_plot
> ### Title: Plot of average frequency of nucleotide mutations resulting in
> ###   amino acid substitution
> ### Aliases: aa_plot
> 
> ### ** Examples
> 
> data(IMGTtab7)
> Regions<-cbind(IMGTtab7$FR1_IMGT,IMGTtab7$CDR1_IMGT)
> allRegions_matrix<-aa_dist(Regions)
> data(Klassen)
> aa_plot(allRegions_matrix, "Amino acid Distribution", "right", Klassen)
Warning: Removed 386 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: aa_plot ... 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
Warning: Removed 342 rows containing missing values (geom_point).
Quitting from lines 134-137 (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 ‘bde-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BrVitale
> ### Title: Class '"BrVitale"'
> ### Aliases: BrVitale BrVitale-class
> ### Keywords: classes
> 
> ### ** Examples
> 
> # create the model 
> model <- brVitale(dataPoints = tuna.r, m = 25, M = 25/2)
> 
> 
> # examples of usual functions
> density(model,0.5)
[1] 0.638699
> 
> distribution(model,0.5,discreteApproximation=FALSE)
[1] 0.8564028
>  
> # graphical representation
> hist(tuna.r,freq=FALSE,main="Tuna Data")
> lines(model, col="red",lwd=2)
> 
> # graphical representation using ggplot2 
> graph <- gplot(model,show=TRUE,includePoints=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: gplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bdlp.Rmd’ using rmarkdown
Loading required namespace: RSQLite
Warning: call dbDisconnect() when finished working with a connection
Quitting from lines 197-211 (bdlp.Rmd) 
Error: processing vignette 'bdlp.Rmd' failed with diagnostics:
miller2012.R:7:208: unexpected '{'
6:  
7: miller2012 <- function(setnr = NULL, seedinfo = list(100, "3.6.0", c("Mersenne-Twister", "Inversion", "Rejection", metaseedinfo = list(100, "3.6.0", c("Mersenne-Twister", "Inversion", "Rejecti
                                                                                                                                                                                                                  ^
--- failed re-building ‘bdlp.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bdscale.Rmd’ using rmarkdown
Quitting from lines 52-53 (bdscale.Rmd) 
Error: processing vignette 'bdscale.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bdscale.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cluster_events
> ### Title: Clustering with trimming
> ### Aliases: cluster_events bp_kmeans bp_clara bp_dbscan bp_mclust
> ###   bp_density_cut
> 
> ### ** Examples
> 
> library(beadplexr)
> 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)
> 
> data("lplex")
> 
> lplex[[1]] %>%
+   # Speed things up a bit by selecting one fourth of the events.
+   # Probably not something you'd usually do
+   dplyr::sample_frac(0.25) %>%
+   bp_kmeans(.parameter = c("FSC-A", "SSC-A"),
+             .column_name = "population", .trim = 0.1, .k = 2) %>%
+   ggplot() +
+   aes(x = `FSC-A`, y = `SSC-A`, colour = population) +
+   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 ‘cba_macsplex_example.Rmd’ using rmarkdown
Quitting from lines 31-38 (cba_macsplex_example.Rmd) 
Error: processing vignette 'cba_macsplex_example.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cba_macsplex_example.Rmd’

--- re-building ‘legendplex-analysis.Rmd’ using rmarkdown
Quitting from lines 75-77 (legendplex-analysis.Rmd) 
Error: processing vignette 'legendplex-analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘legendplex-analysis.Rmd’

SUMMARY: processing the following files failed:
  ‘cba_macsplex_example.Rmd’ ‘legendplex-analysis.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nnc
> ### Title: Numbers Needed for Change
> ### Aliases: nnc nnt print.nnc
> ### Keywords: utilities
> 
> ### ** Examples
> 
> 
> ### Simple example
> behaviorchange::nnc(d=.4, cer=.3);
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 ‘belg1.Rmd’ using rmarkdown
Quitting from lines 48-60 (belg1.Rmd) 
Error: processing vignette 'belg1.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘belg1.Rmd’

SUMMARY: processing the following file failed:
  ‘belg1.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.bench_mark
> ### Title: Autoplot method for bench_mark objects
> ### Aliases: autoplot.bench_mark plot.bench_mark
> 
> ### ** Examples
> 
> dat <- data.frame(x = runif(10000, 1, 1000), y=runif(10000, 1, 1000))
> 
> res <- bench::mark(
+   dat[dat$x > 500, ],
+   dat[which(dat$x > 500), ],
+   subset(dat, x > 500))
> 
> if (require(ggplot2)) {
+ 
+   # Beeswarm plot
+   autoplot(res)
+ 
+   # ridge (joyplot)
+   autoplot(res, "ridge")
+ 
+   # If you want to have the plots ordered by execution time you can do so by
+   # ordering factor levels in the expressions.
+   if (require(dplyr) && require(forcats)) {
+ 
+     res %>%
+       mutate(expression = forcats::fct_reorder(expression, min, .desc = TRUE)) %>%
+       as_bench_mark() %>%
+       autoplot("violin")
+   }
+ }
Loading required package: ggplot2
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
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 ‘benchr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: benchmark
> ### Title: High Precise Measurement of R Expressions Execution Time
> ### Aliases: benchmark
> 
> ### ** Examples
> 
> ## Measure the time it takes to dispatch a simple function call
> ## compared to simply evaluating the constant NULL
> f <- function() NULL
> res <- benchmark(NULL, f(), times = 1000L)
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
> 
> ## Print results:
> print(res)
Benchmark summary:
Time units : nanoseconds 
 expr n.eval min lw.qu median   mean up.qu     max   total relative
 NULL   1000   6    20     25   30.3    31    1220   30300      1.0
  f()   1000 358   484    554 1810.0   653 1210000 1810000     22.2
> 
> ## Plot results
> boxplot(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 ‘benthos.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 335-342 (benthos.Rmd) 
Error: processing vignette 'benthos.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘benthos.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: authorProdOverTime
> ### Title: Top-Authors' Productivity over the Time
> ### Aliases: authorProdOverTime
> 
> ### ** Examples
> 
> data(scientometrics)
> res <- authorProdOverTime(scientometrics, k=10)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: authorProdOverTime ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bibliometrix-vignette.Rmd’ using rmarkdown
Quitting from lines 385-386 (bibliometrix-vignette.Rmd) 
Error: processing vignette 'bibliometrix-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bibliometrix-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘calibration.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 25-34 (calibration.Rmd) 
Error: processing vignette 'calibration.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘calibration.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bife_introduction.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 89-143 (bife_introduction.Rmd) 
Error: processing vignette 'bife_introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bife_introduction.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘analysis.Rmd’ using rmarkdown
Quitting from lines 126-128 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘analysis.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: asPlotlyText
> ### Title: Plotly text
> ### Aliases: asPlotlyText
> 
> ### ** Examples
> 
> set.seed(1)
> 
> X <- big_attachExtdata()
> svd <- big_SVD(X, big_scale(), k = 10)
> 
> p <- plot(svd, type = "scores")
> 
> pop <- rep(c("POP1", "POP2", "POP3"), c(143, 167, 207))
> df <- data.frame(Population = pop, Index = 1:517)
> 
> plot(p2 <- p + ggplot2::aes(text = asPlotlyText(df)))
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 ‘BinarybalancedCut-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Binary_threshold
> ### Title: This Supports the datascientist to determine the optimal
> ###   threshold for binary classifier problem by visuallizing the
> ###   sensitivity, specificity and accurarcy of the given model
> ### Aliases: Binary_threshold
> 
> ### ** Examples
> 
> set.seed(100);disease <- sample(c("yes","no"), 1000, replace=TRUE);
> Probabilities<-sample(seq(0,1,by=0.01),1000,replace=TRUE);
> Binary_threshold(Probabilities,disease)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: Binary_threshold ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘binneR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotChromFromFile
> ### Title: plotChromFromFile
> ### Aliases: plotChromFromFile
> 
> ### ** Examples
> 
> plotChromFromFile(list.files(system.file('mzML',package = 'binneR'),
+                             full.names=TRUE),scans = c(6,18))
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 ‘binsreg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binsreg
> ### Title: Data-driven Binscatter Estimation with Robust Inference
> ###   Procedures and Plots
> ### Aliases: binsreg
> 
> ### ** Examples
> 
>  x <- runif(500); y <- sin(x)+rnorm(500)
>  ## Binned scatterplot
>  binsreg(y,x)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: binsreg ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘biogas_quick_start.Rnw’ using knitr
Quitting from lines 263-268 (biogas_quick_start.Rnw) 
Error: processing vignette 'biogas_quick_start.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘biogas_quick_start.Rnw’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.criterion_distribution
> ### Title: Plot criterion distribution
> ### Aliases: plot.criterion_distribution
> 
> ### ** Examples
> 
> target_feature <- create_feature_target(10, 375, 15, 600) 
> example_result <- distr_crit(target = target_feature[,1], 
+                              feature = target_feature[,2])
> plot(example_result)
> 
> # a ggplot2 plot
> library(ggplot2)
> ggplot_distr <- function(x) {
+ b <- data.frame(cbind(x=as.numeric(rownames(attr(x, "plot_data"))), 
+                       attr(x, "plot_data")))
+ d1 <- cbind(b[,c(1,2)], attr(x, "nice_name"))
+ d2 <- cbind(b[,c(1,3)], "Probability")
+ colnames(d1) <- c("x", "y", "panel")
+ colnames(d2) <- c("x", "y", "panel")
+ d <- rbind(d1, d2)
+ p <- ggplot(data = d, mapping = aes(x = x, y = y)) + 
+   facet_grid(panel~., scale="free") + 
+   geom_freqpoly(data= d2, aes(color=y), stat = "identity") + 
+   scale_fill_brewer(palette = "Set1") + 
+   geom_point(data=d1, aes(size=y), stat = "identity") + 
+   guides(color = "none") + 
+   guides(size = "none") + 
+   xlab("Number of cases with feature=1 and target=1") + ylab("")
+ p
+ }
> ggplot_distr(example_result)
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 ‘overview.Rmd’ using rmarkdown
Loading required package: slam
Quitting from lines 102-131 (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 ‘Biograph-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Lexis.lines
> ### Title: Draws Lexis diagram with lifelines for selected subjects
> ### Aliases: Lexis.lines
> 
> ### ** Examples
> 
> #  Example 1: Employment careers
>   data(GLHS) 
>   z<- Parameters (GLHS)
[1] ". . . . Running function Parameters . . . . "
[1] "Exploring types of transitions"
>   GLHS.yr <- date_b(Bdata=GLHS,selectday=1,format.out="year")
>   D <- Biograph.long (GLHS.yr)
[1] . . . . .  Creating long format  . . . . . .
[1] . . . . .  running reshape  . . . . . 
[1]  . . . . Sort data in long format  . . . . 
[1]  . . . . Adjust long format for survival package etc . . .  
>   tit5 <- "Employment careers for a selection of subjects. GLHS"
>   subjects <- c(1,78,120,208)
>   z <- Lexis.lines (Bdata=GLHS.yr,Dlong=D$Depisode,subjectsID = subjects,title = tit5)
[1] "Producing long format for ggplot2. Patience please."
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: Lexis.lines ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘bioinactivation-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fit_dynamic_inactivation
> ### Title: Fitting of Dynamic Inactivation Models
> ### Aliases: fit_dynamic_inactivation
> 
> ### ** Examples
> 
> ## EXAMPLE 1 ------
> 
> data(dynamic_inactivation)  # The example data set is used.
> 
> get_model_data()  # Retrieve the valid model keys.
[1] "Bigelow"   "Mafart"    "Geeraerd"  "Peleg"     "Arrhenius"
> 
> simulation_model <- "Peleg"  # Peleg's model will be used
> 
> model_data <- get_model_data(simulation_model)
> model_data$parameters  # Set the model parameters
[1] "k_b"       "temp_crit" "n"        
> 
> dummy_temp <- data.frame(time = c(0, 1.25, 2.25, 4.6),
+                          temperature = c(70, 105, 105, 70))  # Dummy temp. profile
> 
> ## Set known parameters and initial points/bounds for unknown ones
> 
> known_params = c(temp_crit = 100)
> 
> starting_points <- c(n = 1, k_b = 0.25, N0 = 1e+05)
> upper_bounds <- c(n = 2, k_b = 1, N0 = Inf)
> lower_bounds <- c(n = 0, k_b = 0, N0 = 1e4)
> 
> dynamic_fit <- fit_dynamic_inactivation(dynamic_inactivation, simulation_model,
+                                         dummy_temp, starting_points,
+                                         upper_bounds, lower_bounds,
+                                         known_params)
> 
> plot(dynamic_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
Error(s) in re-building vignettes:
  ...
--- re-building ‘inactivation.Rmd’ using rmarkdown
Quitting from lines 69-74 (inactivation.Rmd) 
Error: processing vignette 'inactivation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘inactivation.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: inactivation_OED
> ### Title: Optimum Experimental Design of Microbial Inactivation
> ### Aliases: inactivation_OED
> 
> ### ** Examples
> 
> ## Definition of input variables
> 
> parms_fix <- c(temp_ref = 57.5)
> parms <- c(delta_ref = 3.9,
+            z = 4.2,
+            p = 1,
+            N0 = 1e6
+            )
> 
> temp_profile <- data.frame(time = c(0, 60), temperature = c(30, 60))
> 
> n_points <- 5
> 
> ## OED with local optimization
> 
> set.seed(191210)
> 
> local_OED <- inactivation_OED("Mafart", parms, temp_profile, parms_fix,
+                       n_points, criteria = "E-mod", sensvar = "logN",
+                       optim_algorithm = "local")
> 
> print(local_OED$optim_times)
[1]  8.006242 15.241762 18.737011 29.041776 50.342996
> plot(local_OED)
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_bioOED.Rmd’ using rmarkdown
Quitting from lines 303-304 (vignette_bioOED.Rmd) 
Error: processing vignette 'vignette_bioOED.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette_bioOED.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_enrichment_summaries
> ### Title: Plotting Prognostic Enrichment Estimates
> ### Aliases: plot_enrichment_summaries
> 
> ### ** Examples
> 
> 
> data(dcaData)
> # one marker
> analysis.single.marker <- enrichment_analysis(Cancer ~ Marker1,
+ data=dcaData,
+ reduction.under.treatment=0.3,
+ cost.screening=100, cost.keeping=1000)
Warning in enrichment_analysis(Cancer ~ Marker1, data = dcaData, reduction.under.treatment = 0.3,  :
  2 bootstrap replications had zero events above a specified biomarker threshold and were re-sampled.
> plot_enrichment_summaries(analysis.single.marker)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_enrichment_summaries ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘bioplots-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: heatmap.overlaps
> ### Title: Plot heatmat
> ### Aliases: heatmap.overlaps
> 
> ### ** Examples
> 
> mat <- matrix(rnbinom(135, size = 10, prob = 0.2), nrow = 15, ncol = 9)
> colnames(mat) <- paste0("Treat", 1:9)
> rownames(mat) <- c("a", "b", "c", "d", "ab", "ac", "ad", "bc", "bd", "cd",
+                    "abc", "abd", "acd", "bcd", "abcd")
> head(mat)
   Treat1 Treat2 Treat3 Treat4 Treat5 Treat6 Treat7 Treat8 Treat9
a      38     39     39     30     60     35     48     29     36
b      58     46     24     27     80     40     36     64     63
c      23     30     60     35     40     34     57     23     63
d      51     21     38     45     28     54     64     36     59
ab     29     47     49     44     41     23     59     47     38
ac     29     52     38     28     67     54     52     47     21
> 
> heatmap.overlaps(mat)
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> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘bioRad-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.ppi
> ### Title: Plot a plan position indicator ('ppi')
> ### Aliases: plot.ppi
> 
> ### ** Examples
> 
> # load an example scan:
> data(example_scan)
> # print to screen the available scan parameters:
> summary(example_scan)
                  Polar scan (class scan)

     parameters:  VRADH DBZH ZDR RHOHV PHIDP 
elevation angle:  0.5 deg
           dims:  480 bins x 360 rays
> # make ppi for the scan
> ppi <- project_as_ppi(example_scan)
> # plot the first scan parameter, which in this case is "VRADH":
> plot(ppi)
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 ‘bioset-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: models_linear
> ### Title: Linear model functions.
> ### Aliases: models_linear fit_linear plot_linear interpolate_linear
> 
> ### ** Examples
> 
> # generate data
> x <- c(1, 3, 4, 7)
> y_known <- c(3.5, 6.5, 8, 12.5)  # x is known for these values
> y_unknown <- c(5, 9.5, 11)       # we will calculate x for those
> 
> model <- fit_linear(x = x, y = y_known)
> model

Call:
stats::lm(formula = y ~ x)

Coefficients:
(Intercept)            x  
        2.0          1.5  

> 
> plot_linear(x = x, y = y_known)
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 ‘BioStatR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_qqplot
> ### Title: Graphique des quantiles (qqplot) et droite interquartile
> ### Aliases: gg_qqplot
> ### Keywords: univar
> 
> ### ** Examples
> 
> glycine.blanche<-subset(Mesures,subset=(Mesures$espece=="glycine blanche"))
> gg_qqplot(glycine.blanche,"taille")
1st quartile :  -0.674489750196082 
3rd quartile :  0.674489750196082 
Intercept :  14.6 
Slope :  3.37292004710024 
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 ‘bisect_vignette.Rmd’ using rmarkdown
Quitting from lines 69-101 (bisect_vignette.Rmd) 
Error: processing vignette 'bisect_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bisect_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BIS.Rmd’ using rmarkdown
Parsed with column specification:
cols(
  .default = col_character()
)
See spec(...) for full column specifications.
Parsed with column specification:
cols(
  .default = col_double(),
  FREQ = col_character(),
  Frequency = col_character(),
  REF_AREA = col_character(),
  `Reference area` = col_character(),
  `Time Period` = col_character()
)
See spec(...) for full column specifications.

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: 'zoo'

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

    as.Date, as.Date.numeric

Quitting from lines 61-79 (BIS.Rmd) 
Error: processing vignette 'BIS.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘BIS.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro.Rmd’ using knitr
Quitting from lines 72-75 (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’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: blandr.display.and.draw
> ### Title: Bland-Altman display and draw for R
> ### Aliases: blandr.display.and.draw
> 
> ### ** Examples
> 
> # Generates two random measurements
> measurement1 <- rnorm(100)
> measurement2 <- rnorm(100)
> 
> # Generates a plot, with no optional arguments
> blandr.display.and.draw( measurement1 , measurement2 )
Number of comparisons:  100 
Maximum value for average measures:  1.413359 
Minimum value for average measures:  -1.495408 
Maximum value for difference in measures:  3.055592 
Minimum value for difference in measures:  -2.71775 

Bias:  0.1466954 
Standard deviation of bias:  1.313775 

Standard error of bias:  0.1313775 
Standard error for limits of agreement:  0.2252705 

Bias:  0.1466954 
Bias- upper 95% CI:  0.407377 
Bias- lower 95% CI:  -0.1139861 

Upper limit of agreement:  2.721695 
Upper LOA- upper 95% CI:  3.168681 
Upper LOA- lower 95% CI:  2.274709 

Lower limit of agreement:  -2.428304 
Lower LOA- upper 95% CI:  -1.981318 
Lower LOA- lower 95% CI:  -2.87529 

Derived measures:  
Mean of differences/means:  115.563 
Point estimate of bias as proportion of lowest average:  -9.809724 
Point estimate of bias as proportion of highest average 10.37921 
Spread of data between lower and upper LoAs:  5.149999 
Bias as proportion of LoA spread:  2.848456 

Bias: 
 0.1466954  ( -0.1139861  to  0.407377 ) 
ULoA: 
 2.721695  ( 2.274709  to  3.168681 ) 
LLoA: 
 -2.428304  ( -2.87529  to  -1.981318 ) 

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 knitr
Quitting from lines 113-114 (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 ‘blastula-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_ggplot
> ### Title: Helper function for adding an ggplot
> ### Aliases: add_ggplot
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> # Create a ggplot plot
> plot <-
+   ggplot(
+     data = mtcars,
+     aes(x = disp, y = hp,
+         color = wt, size = mpg)) +
+   geom_point()
> 
> # Create an HTML fragment that
> # contains an the ggplot as an
> # embedded plot
> plot_html <-
+   add_ggplot(
+     plot_object = plot,
+     height = 5,
+     width = 7)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: add_ggplot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘blorr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: blr_decile_capture_rate
> ### Title: Event rate by decile
> ### Aliases: blr_decile_capture_rate
> 
> ### ** Examples
> 
> model <- glm(honcomp ~ female + read + science, data = hsb2,
+              family = binomial(link = 'logit'))
> gt <- blr_gains_table(model)
> blr_decile_capture_rate(gt)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: blr_decile_capture_rate ... 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 89-91 (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 ‘testthat.R’ [168s/178s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BMSC)
  Loading required package: Rcpp
  > 
  > test_check("BMSC")
  ── 1. Failure: A message is returned if some rows are missing (@test_missingValu
  `BMSC:::handleMissingData(data, formula, yUncertainty)$data` produced unexpected messages.
  Expected match: 7 rows \\(9.33% of the data\\) were excluded due to missing values.
  Actual values:
  * 8 rows (10.67% of the data) were excluded due to missing values.
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 61 SKIPPED: 1 FAILED: 1
  1. Failure: A message is returned if some rows are missing (@test_missingValuesHandling.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bodenmiller.Rmd’ using rmarkdown
Quitting from lines 53-59 (bodenmiller.Rmd) 
Error: processing vignette 'bodenmiller.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bodenmiller.Rmd’

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

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

Attaching package: 'bomrang'

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

    filter

Loading required package: maps
Quitting from lines 1180-1223 (bomrang.Rmd) 
Error: processing vignette 'bomrang.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bomrang.Rmd’

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

Attaching package: 'bomrang'

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

    filter

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bootnet
> ### Title: Bootstrapped network estimation
> ### Aliases: bootnet
> 
> ### ** Examples
> 
> # BFI Extraversion data from psych package:
> library("psych")

Attaching package: ‘psych’

The following objects are masked from ‘package:ggplot2’:

    %+%, alpha

> data(bfi)
> bfiSub <- bfi[,1:25]
> 
> # Estimate network:
> Network <- estimateNetwork(bfiSub, default = "EBICglasso")
Estimating Network. Using package::function:
  - qgraph::EBICglasso for EBIC model selection
    - using glasso::glasso
  - qgraph::cor_auto for correlation computation
    - using lavaan::lavCor
Variables detected as ordinal: A1; A2; A3; A4; A5; C1; C2; C3; C4; C5; E1; E2; E3; E4; E5; N1; N2; N3; N4; N5; O1; O2; O3; O4; O5
Warning in EBICglassoCore(S = S, n = n, gamma = gamma, penalize.diagonal = penalize.diagonal,  :
  A dense regularized network was selected (lambda < 0.1 * lambda.max). Recent work indicates a possible drop in specificity. Interpret the presence of the smallest edges with care. Setting threshold = TRUE will enforce high specificity, at the cost of sensitivity.
> 
> # Centrality indices:
> library("qgraph")
> centralityPlot(Network)
Note: z-scores are shown on x-axis rather than raw centrality indices.
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: centralityPlot ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘bossMaps-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: asinh_trans
> ### Title: Create an axis transform using the Inverse hyperbolic sine
> ###   transformation
> ### Aliases: asinh_trans
> 
> ### ** Examples
> 
>   
>  library(ggplot2)
>  ggplot(data.frame(x=seq(-1000,1000,len=200)), aes(x=x,y=x))+
+  geom_line(size=1)+
+  scale_x_continuous(trans = 'asinh',breaks=c(-1000,-100,10,-1,0,1,10,100,1000))
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 ‘bossMaps.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

Attaching package: 'raster'

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

    extract

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

    select

Quitting from lines 82-83 (bossMaps.Rmd) 
Error: processing vignette 'bossMaps.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bossMaps.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘PlottingGuide.Rnw’ using knitr_notangle
Warning in final.x[i] <- rect.x[selected.arcs] :
  number of items to replace is not a multiple of replacement length
Warning in final.y[i] <- rect.y[selected.arcs] :
  number of items to replace is not a multiple of replacement length
Warning in final.x[i] <- rect.x[selected.arcs] :
  number of items to replace is not a multiple of replacement length
Warning in final.y[i] <- rect.y[selected.arcs] :
  number of items to replace is not a multiple of replacement length
Warning in final.x[i] <- rect.x[selected.arcs] :
  number of items to replace is not a multiple of replacement length
Warning in final.y[i] <- rect.y[selected.arcs] :
  number of items to replace is not a multiple of replacement length
Warning in final.x[i] <- rect.x[selected.arcs] :
  number of items to replace is not a multiple of replacement length
Warning in final.y[i] <- rect.y[selected.arcs] :
  number of items to replace is not a multiple of replacement length
Warning in cor.test.default(x = x, y = y, alternative = alternative, method = method,  :
  Cannot compute exact p-value with ties
Quitting from lines 484-544 (PlottingGuide.Rnw) 
Error: processing vignette 'PlottingGuide.Rnw' failed with diagnostics:
no string supplied for 'strwidth/height' unit
--- failed re-building ‘PlottingGuide.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘BradleyTerryScalable.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


Attaching package: 'dplyr'

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

    as_data_frame, groups, union

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 234-275 (BradleyTerryScalable.Rmd) 
Error: processing vignette 'BradleyTerryScalable.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘BradleyTerryScalable.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: formatResponseMap
> ### Title: Format Response and Error Maps
> ### Aliases: formatResponseMap formatDifferenceMap
> ### Keywords: aplot
> 
> ### ** Examples
> 
> data(es8olatmz,package="braidrm")
> rmap <- responseMap(act~conc1+conc2,es8olatmz)
> formatResponseMap(rmap,xl="Olaparib",yl="TMZ",zl="Survival")
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 ‘BrailleR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VI.ggplot
> ### Title: VI for graphs created using ggplot2
> ### Aliases: VI.ggplot print.VIgraph
> 
> ### ** Examples
> 
> if(require(ggplot2)){
+ g = ggplot(economics_long, aes(date, value01, colour = variable))
+ g = g + geom_line() + ggtitle('dummy title')
+ VI(g)
+ g
+ }
Loading required package: ggplot2

Attaching package: ‘ggplot2’

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

    xlab, ylab

Warning: Detecting old grouped_df format, replacing `vars` attribute by `groups`
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 ‘BrailleRHistory.rmd’ using rmarkdown
--- finished re-building ‘BrailleRHistory.rmd’

--- re-building ‘Ex1histograms.rmd’ using rmarkdown
--- finished re-building ‘Ex1histograms.rmd’

--- re-building ‘Ex2BasicNumerical.rmd’ using rmarkdown
--- finished re-building ‘Ex2BasicNumerical.rmd’

--- re-building ‘Ex3UnivariateDescription.rmd’ using rmarkdown
--- finished re-building ‘Ex3UnivariateDescription.rmd’

--- re-building ‘Ex4SingleResponseOneGroupingFactor.rmd’ using rmarkdown
--- finished re-building ‘Ex4SingleResponseOneGroupingFactor.rmd’

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

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

--- re-building ‘qplot.Rmd’ using rmarkdown
Quitting from lines 26-30 (qplot.Rmd) 
Error: processing vignette 'qplot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘qplot.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_brmap
> ### Title: Get Brazilian maps from different geographic levels
> ### Aliases: get_brmap
> ### Keywords: IBGE geographic levels shapefile spatial
> 
> ### ** Examples
> 
> ## Retrieving the map from the State of Rio de Janeiro
> rio_map <- get_brmap(geo = "State",
+                      geo.filter = list(State = 33),
+                      class = "sf")
> plot_brmap(rio_map)
Regions defined for each Polygons
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 ‘breakDown-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: broken.glm
> ### Title: Breaking Down of Model Predictions for glm models
> ### Aliases: broken.glm
> 
> ### ** Examples
> 
> # example for wine data
> wine$qualityb <- factor(wine$quality > 5.5, labels = c("bad", "good"))
> modelg <- glm(qualityb~fixed.acidity + volatile.acidity + citric.acid +
+               residual.sugar + chlorides + free.sulfur.dioxide +
+               total.sulfur.dioxide + density + pH + sulphates + alcohol,
+     data=wine, family = "binomial")
> new_observation <- wine[1,]
> br <- broken(modelg, new_observation)
> logit <- function(x) exp(x)/(1+exp(x))
> plot(br, logit)
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 ‘data_formats.Rmd’ using rmarkdown
Quitting from lines 51-55 (data_formats.Rmd) 
Error: processing vignette 'data_formats.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘data_formats.Rmd’

--- re-building ‘methods_and_concepts.Rmd’ using rmarkdown
Quitting from lines 55-77 (methods_and_concepts.Rmd) 
Error: processing vignette 'methods_and_concepts.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘methods_and_concepts.Rmd’

SUMMARY: processing the following files failed:
  ‘data_formats.Rmd’ ‘methods_and_concepts.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stan_fit
> ### Title: Bayesian Stan fit to 13C Breath Data
> ### Aliases: stan_fit
> 
> ### ** Examples
> 
> library(breathtestcore)
> suppressPackageStartupMessages(library(dplyr))
> d = breathtestcore::simulate_breathtest_data(n_records = 3) # default 3 records
> data = breathtestcore::cleanup_data(d$data)
> # Use more than 80 iterations and 4 chains for serious fits
> fit = stan_fit(data, chains = 1, iter = 80)
> plot(fit) # calls plot.breathtestfit
Warning in if (is.null(data$xmin) & is.null(data$xmax) & class(params$width) !=  :
  the condition has length > 1 and only the first element will be used
Warning in if (is.null(data$ymin) & is.null(data$ymax) & class(params$height) !=  :
  the condition has length > 1 and only the first element will be used
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 ‘BreedingSchemeLanguage-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: defineSpecies
> ### Title: Define and create species
> ### Aliases: defineSpecies
> 
> ### ** Examples
> 
> if (exists("simEnv")){
+ rm(list=names(simEnv), envir=simEnv)
+ rm(simEnv)
+ }
> simEnv <- defineSpecies(nSim=2, nChr=5, lengthChr=100, effPopSize=20, nMarkers=100, nQTL=10)
> initializePopulation(nInd=50) # popID 0 created
> phenotype()
> select(nSelect=20) # popID 1 selected out of popID 0
> cross() # popID 2 created
> phenotype(nRep=2)
> select(nSelect=5) # popID 3 selected out of popID 2
> cross() # popID 4 created
> plotData()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotData ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_to_BSL.Rmd’ using rmarkdown
Quitting from lines 113-114 (Intro_to_BSL.Rmd) 
Error: processing vignette 'Intro_to_BSL.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Intro_to_BSL.Rmd’

--- re-building ‘Load_existing_data.Rmd’ using rmarkdown
Loading required package: snowfall
Loading required package: snow
Loading required package: Rcpp
Quitting from lines 78-83 (Load_existing_data.Rmd) 
Error: processing vignette 'Load_existing_data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Load_existing_data.Rmd’

--- re-building ‘Optimize_parameter_vector.Rmd’ using rmarkdown
Loading required package: snowfall
Loading required package: snow
Loading required package: Rcpp
--- finished re-building ‘Optimize_parameter_vector.Rmd’

--- re-building ‘Within_family_selection.Rmd’ using rmarkdown
Loading required package: snowfall
Loading required package: snow
Loading required package: Rcpp
Quitting from lines 66-74 (Within_family_selection.Rmd) 
Error: processing vignette 'Within_family_selection.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Within_family_selection.Rmd’

SUMMARY: processing the following files failed:
  ‘Intro_to_BSL.Rmd’ ‘Load_existing_data.Rmd’
  ‘Within_family_selection.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘the_bridgedist_basics.Rmd’ using rmarkdown
Quitting from lines 33-45 (the_bridgedist_basics.Rmd) 
Error: processing vignette 'the_bridgedist_basics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘the_bridgedist_basics.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: theme_karl
> ### Title: Karl's ggplot2 theme
> ### Aliases: theme_karl karl_theme
> 
> ### ** Examples
> 
> library(ggplot2)
> mtcars$cyl <- factor(mtcars$cyl)
> ggplot(mtcars, aes(y=mpg, x=disp, color=cyl)) +
+     geom_point() + theme_karl()
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 ‘broom_mixed_intro.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

Registered S3 methods overwritten by 'broom.mixed':
  method         from 
  augment.lme    broom
  augment.merMod broom
  glance.lme     broom
  glance.merMod  broom
  glance.stanreg broom
  tidy.brmsfit   broom
  tidy.gamlss    broom
  tidy.lme       broom
  tidy.merMod    broom
  tidy.rjags     broom
  tidy.stanfit   broom
  tidy.stanreg   broom
Loading required package: brms
Loading required package: Rcpp
Loading 'brms' package (version 2.8.0). Useful instructions
can be found by typing help('brms'). A more detailed introduction
to the package is available through vignette('brms_overview').
Loading required package: dotwhisker
Loading required package: ggplot2
Quitting from lines 68-82 (broom_mixed_intro.rmd) 
Error: processing vignette 'broom_mixed_intro.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘broom_mixed_intro.rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [29s/34s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  ── 1. Error: tidy.htest/oneway.test (@test-stats-htest.R#14)  ──────────────────
  object 'extra' not found
  1: oneway.test(extra ~ group, data = sleep) at testthat/test-stats-htest.R:14
  2: eval(m, parent.frame())
  3: eval(m, parent.frame())
  4: stats::model.frame(formula = extra ~ group, data = sleep)
  5: model.frame.default(formula = extra ~ group, data = sleep)
  6: eval(predvars, data, env)
  7: eval(predvars, data, env)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 976 SKIPPED: 2 FAILED: 1
  1. Error: tidy.htest/oneway.test (@test-stats-htest.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘adding-tidiers.Rmd’ using rmarkdown
--- finished re-building ‘adding-tidiers.Rmd’

--- re-building ‘available-methods.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

Joining, by = "class"
Joining, by = "class"
--- finished re-building ‘available-methods.Rmd’

--- re-building ‘bootstrapping.Rmd’ using rmarkdown
Quitting from lines 28-32 (bootstrapping.Rmd) 
Error: processing vignette 'bootstrapping.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bootstrapping.Rmd’

--- re-building ‘broom.Rmd’ using rmarkdown
Warning in wilcox.test.default(x = c(3.215, 3.44, 3.46, 3.57, 3.19, 3.15,  :
  cannot compute exact p-value with ties
--- finished re-building ‘broom.Rmd’

--- re-building ‘broom_and_dplyr.Rmd’ using rmarkdown
Quitting from lines 34-40 (broom_and_dplyr.Rmd) 
Error: processing vignette 'broom_and_dplyr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘broom_and_dplyr.Rmd’

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

--- re-building ‘kmeans.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 22-47 (kmeans.Rmd) 
Error: processing vignette 'kmeans.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘kmeans.Rmd’

SUMMARY: processing the following files failed:
  ‘bootstrapping.Rmd’ ‘broom_and_dplyr.Rmd’ ‘kmeans.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘benchmarks.Rmd’ using rmarkdown
Quitting from lines 52-61 (benchmarks.Rmd) 
Error: processing vignette 'benchmarks.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘benchmarks.Rmd’

--- re-building ‘brotli-2015-09-22.pdf.asis’ using asis
--- finished re-building ‘brotli-2015-09-22.pdf.asis’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dtavg
> ### Title: Average of the Student t Distribution
> ### Aliases: dtavg ptavg
> ### Keywords: distribution
> 
> ### ** Examples
> 
> x=seq(from=-10, to=10, length.out=100)
> ggplot2::qplot(x, ptavg(x, df=3, hi=3), 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 ‘brt.rmd’ using rmarkdown
Quitting from lines 47-57 (brt.rmd) 
Error: processing vignette 'brt.rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘brt.rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘usage.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 67-71 (usage.Rmd) 
Error: processing vignette 'usage.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘usage.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘bssm.Rmd’ using rmarkdown
Quitting from lines 263-268 (bssm.Rmd) 
Error: processing vignette 'bssm.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bssm.Rmd’

--- re-building ‘growth_model.Rmd’ using rmarkdown
Quitting from lines 150-157 (growth_model.Rmd) 
Error: processing vignette 'growth_model.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘growth_model.Rmd’

SUMMARY: processing the following files failed:
  ‘bssm.Rmd’ ‘growth_model.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bayesian_changepoint_groove_detection.Rmd’ using rmarkdown
Quitting from lines 23-43 (Bayesian_changepoint_groove_detection.Rmd) 
Error: processing vignette 'Bayesian_changepoint_groove_detection.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Bayesian_changepoint_groove_detection.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: delete
> ### Title: Remove series or years from an fhx object.
> ### Aliases: delete
> 
> ### ** Examples
> 
> data(lgr2)
> plot(delete(lgr2, s = 'LGR46'))
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 127-128 (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 ‘C443-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: emp_eq
> ### Title: Check empirical equivalences between predictors
> ### Aliases: emp_eq
> 
> ### ** Examples
> 
> require(MASS)
Loading required package: MASS
> emp_eq(data = Pima.tr, X = c("npreg", "glu", "bp", "skin", "bmi", "ped", "age"))
$cp
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:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/C50.Rcheck/00install.out’ for details.
Running examples in ‘C50-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.C5.0
> ### Title: Plot a decision tree
> ### Aliases: plot.C5.0
> ### Keywords: models
> 
> ### ** Examples
> 
> 
> mod1 <- C5.0(Species ~ ., data = iris)
> plot(mod1)
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 ‘C5.0.Rmd’ using rmarkdown
Quitting from lines 61-62 (C5.0.Rmd) 
Error: processing vignette 'C5.0.Rmd' failed with diagnostics:
no string supplied for 'strwidth/height' unit
--- failed re-building ‘C5.0.Rmd’

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

SUMMARY: processing the following file failed:
  ‘C5.0.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘CA3variants-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.CA3variants
> ### Title: Graphical display resulting from 'CAvariants3'
> ### Aliases: plot.CA3variants
> ### Keywords: graphical display interactive plot interactive biplot
> 
> ### ** Examples
> 
> data(happy)
> ris.ca3<-CA3variants(happy,p=2,q=2,r=2, ca3type = "CA3") 
> plot(ris.ca3)
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: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘caffsim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: caffPlot
> ### Title: Create concentration-time curve after single dose of caffeine
> ### Aliases: caffPlot
> 
> ### ** Examples
> 
> caffPlot(caffConcTime(Weight = 20, Dose = 200, N = 20))
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 ‘CAinterprTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: caCluster
> ### Title: Clustering row/column categories on the basis of Correspondence
> ###   Analysis coordinates from a space of user-defined dimensionality.
> ### Aliases: caCluster
> ### Keywords: caCluster
> 
> ### ** Examples
> 
> data(brand_coffee)
> 
> #displays a dendrogram of row AND column categories
> res <- caCluster(brand_coffee, opt.part=FALSE)
> 
> #displays a dendrogram for row AND column categories; the clustering is based on the CA 
> #coordinates from a full high-dimensional space. Rectangles indicating the clusters defined by 
> #the optimal partition method (see Details). A silhouette plot, a scatterplot, and a CA 
> #scatterplot with indication of cluster membership are also produced (see Details). 
> #The cluster membership is stored in the object 'res'.
> res <- caCluster(brand_coffee, opt.part=TRUE)
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: caCluster ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Adapting_Algorithm_for_CAISEr.Rmd’ using rmarkdown
Quitting from lines 273-289 (Adapting_Algorithm_for_CAISEr.Rmd) 
Error: processing vignette 'Adapting_Algorithm_for_CAISEr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Adapting_Algorithm_for_CAISEr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CaliCo-introduction.Rmd’ using rmarkdown
Quitting from lines 57-77 (CaliCo-introduction.Rmd) 
Error: processing vignette 'CaliCo-introduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CaliCo-introduction.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotGlobalSens
> ### Title: Plot results of GlobalSens function
> ### Aliases: PlotGlobalSens
> 
> ### ** Examples
> 
> ## IASA model
> 
> ## Parameters and intial conditions.
> data(dogs)
> dogs_iasa <- GetDataIASA(dogs,
+                          destination.label = "Pinhais",
+                          total.estimate = 50444)
> 
> # Solve for point estimates.
> solve_iasa_pt <- SolveIASA(pars = dogs_iasa$pars,
+                           init = dogs_iasa$init,
+                           time = 0:15,
+                           alpha.owned = TRUE,
+                           method = 'rk4')
> 
> ## Set ranges 10 % greater and lesser than the
> ## point estimates.
> rg_solve_iasa <- SetRanges(pars = dogs_iasa$pars)
> 
> ## Calculate golobal sensitivity of combined parameters.
> ## To calculate global sensitivity to each parameter, set
> ## all as FALSE.
> glob_all_solve_iasa <- CalculateGlobalSens(
+   model.out = solve_iasa_pt,
+   ranges = rg_solve_iasa, 
+   sensv = "n2", all = TRUE)
> PlotGlobalSens(glob_all_solve_iasa)
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 ‘caret-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: safs_initial
> ### Title: Ancillary simulated annealing functions
> ### Aliases: safs_initial safs_perturb safs_prob caretSA rfSA treebagSA
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> selected_vars <- safs_initial(vars = 10 , prob = 0.2)
> selected_vars
[1] 4 7 9
> 
> ###
> 
> safs_perturb(selected_vars, vars = 10, number = 1)
[1] 1 4 7 9
> 
> ###
> 
> safs_prob(old = .8, new = .9, iteration = 1)
[1] 0.8824969
> safs_prob(old = .5, new = .6, iteration = 1)
[1] 0.8187308
> 
> grid <- expand.grid(old = c(4, 3.5),
+                     new = c(4.5, 4, 3.5) + 1,
+                     iter = 1:40)
> grid <- subset(grid, old < new)
> 
> grid$prob <- apply(grid, 1,
+                    function(x)
+                      safs_prob(new = x["new"],
+                                old= x["old"],
+                                iteration = x["iter"]))
> 
> grid$Difference <- factor(grid$new - grid$old)
> grid$Group <- factor(paste("Current Value", grid$old))
> 
> ggplot(grid, aes(x = iter, y = prob, color = Difference)) +
+   geom_line() + facet_wrap(~Group) + theme_bw() +
+   ylab("Probability") + xlab("Iteration")
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 ‘caret.Rmd’ using rmarkdown
Quitting from lines 184-185 (caret.Rmd) 
Error: processing vignette 'caret.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘caret.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: groupedBar
> ### Title: Grouped bar chart
> ### Aliases: groupedBar groupedBar.default groupedBar.formula
> ### Keywords: bar grouped plot
> 
> ### ** Examples
> 
> 
> 
> groupedBar(states03$Region)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: groupedBar ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘cartools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: speedplot
> ### Title: A scatter plot of traffic data.
> ### Aliases: speedplot
> 
> ### ** Examples
> 
> speedplot(QUKtdayX)
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 ‘CAST-intro.Rmd’ using rmarkdown
CAST                   package:CAST                    R Documentation

'_c_a_r_e_t' _A_p_p_l_i_c_a_t_i_o_n_s _f_o_r _S_p_a_t_i_a_l-_T_e_m_p_o_r_a_l _M_o_d_e_l_s

_D_e_s_c_r_i_p_t_i_o_n:

     Supporting functionality to run 'caret' with spatial or
     spatial-temporal data. 'caret' is a frequently used package for
     model training and prediction using machine learning. This package
     includes functions to improve spatial-temporal modelling tasks
     using 'caret'. It prepares data for Leave-Location-Out and
     Leave-Time-Out cross-validation which are target-oriented
     validation strategies for spatial-temporal models. To decrease
     overfitting and improve model performances, the package implements
     a forward feature selection that selects suitable predictor
     variables in view to their contribution to the target-oriented
     performance.

_D_e_t_a_i_l_s:

     'caret' Applications for Spatio-Temporal models

_A_u_t_h_o_r(_s):

     Hanna Meyer, Christoph Reudenbach, Marvin Ludwig, Thomas Nauss
     _Maintainer:_ Hanna Meyer <email: hanna.meyer@geo.uni-marburg.de>



Attaching package: 'lubridate'

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

    date

Quitting from lines 83-90 (CAST-intro.Rmd) 
Error: processing vignette 'CAST-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CAST-intro.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: catenary
> ### Title: Creates a catenary object
> ### Aliases: catenary catenary catenary-package
> 
> ### ** Examples
> 
> cat1 <- catenary()
> plot(cat1)
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 ‘fit_cat.Rmd’ using rmarkdown

Attaching package: 'catenary'

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

    show

── 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()
Warning: `data_frame()` is deprecated, use `tibble()`.
This warning is displayed once per session.
Quitting from lines 20-30 (fit_cat.Rmd) 
Error: processing vignette 'fit_cat.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘fit_cat.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cate-vignette.Rnw’ using knitr
Quitting from lines 153-156 (cate-vignette.Rnw) 
Error: processing vignette 'cate-vignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cate-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘cate-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  catnet_rexport.cpp:202:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:206:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:213:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:216:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:217:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:232:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:231:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/catnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  MLEEstimator.cpp:81:17: warning: catching polymorphic type ‘class std::domain_error’ by value [-Wcatch-value=]
  MLEEstimator.cpp:127:17: warning: catching polymorphic type ‘class std::domain_error’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/catSurv.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘CausalImpact.Rmd’ using rmarkdown
Loading required package: bsts
Loading required package: BoomSpikeSlab
Loading required package: Boom
Loading required package: MASS

Attaching package: 'Boom'

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

    rWishart

Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: xts
Quitting from lines 147-149 (CausalImpact.Rmd) 
Error: processing vignette 'CausalImpact.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CausalImpact.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: BinaryPredictor
> ### Title: Univariate analysis for binary classification.
> ### Aliases: BinaryPredictor BinaryPredictor.factor BinaryPredictor.numeric
> ###   BinaryPredictor.data.frame BinaryPredictor.default
> ###   plot.BinaryPredictor print.BinaryPredictorList
> 
> ### ** Examples
> 
> library(ggplot2)
> data(diamonds)
> # set a dependent variable that is TRUE when the price is above $5000
> dv <- diamonds$price > 5000
> 
> # convert ordered to factor
> diamonds$cut <- as.factor(as.character(diamonds$cut))
> diamonds$color <- as.factor(as.character(diamonds$color))
> diamonds$clarity <- as.factor(as.character(diamonds$clarity))
> 
> # evaluate diamond cut and carats, and generate a plot for each
> bp.cut <- BinaryPredictor(diamonds$cut, dv)
> plot(bp.cut)
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 ‘CAvariants-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.CAvariants
> ### Title: Main plot function
> ### Aliases: plot.CAvariants
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(asbestos)
> resasbestos<-CAvariants(asbestos, catype = "CA", firstaxis = 1, lastaxis = 2) 
> plot(resasbestos, plottype = "classic", plot3d = TRUE)
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: plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘CB2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_count_distribution
> ### Title: A function to plot read count distribution.
> ### Aliases: plot_count_distribution
> 
> ### ** Examples
> 
> library(CB2)
> data(Evers_CRISPRn_RT112)
> cpm <- get_CPM(Evers_CRISPRn_RT112$count)
> plot_count_distribution(cpm, Evers_CRISPRn_RT112$design)
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 ‘cb2-tutorial.Rmd’ using rmarkdown
>RAB_3
CTGTAGAAGCTACATCGGCT
>RAB_4
AGCACATACACGAGCGGAAA
>RAB_5
TACCCGTTCAAGTCATCCGC
@BASE1-1
TATTTATTTTGCTACTTAATAATTGGGACTGTGCCCAGCGCGGCGGCAAGAAAAAAATGAAGATTATAATGTGTAATTTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
@BASE1-2
TATTTATTTTGCTACTTAATAATTGGGACTCAACTATTGCTGATCATCCTAAAAAAATGAAGATTATAATGTGTAATTTA
+
IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII
Detects the length of guided RNA is 20
25 gRNAs were found from the gRNA_Reference library.
All 688 were proceed!
Detects the length of guided RNA is 20
25 gRNAs were found from the gRNA_Reference library.
All 608 were proceed!
Detects the length of guided RNA is 20
25 gRNAs were found from the gRNA_Reference library.
All 703 were proceed!
Detects the length of guided RNA is 20
25 gRNAs were found from the gRNA_Reference library.
All 659 were proceed!
Quitting from lines 109-110 (cb2-tutorial.Rmd) 
Error: processing vignette 'cb2-tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cb2-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘cb2-tutorial.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Plot_ALIGE
> ### Title: Plot_ALIGE
> ### Aliases: Plot_ALIGE
> 
> ### ** Examples
> 
> data(igm)
> igm$hs=ifelse(igm$HEDUC=="HS",1,0)
> igm$col=ifelse(igm$HEDUC=="COL",1,0)
> formla=lcfincome~lfincome
> xformla=~hs+col
> tvals=seq(quantile(igm$lfincome,probs = 0.1),quantile(igm$lfincome,probs = 0.9),length.out = 10)
> h=1.2
> data=igm
> cl=1
> B=7
> ALIGE=localIGE(formla=formla, xformla=xformla, data=data,tvals=tvals,h=h,cl=cl)
> sd_ALIGE=sdF(B,formla=formla, xformla=xformla, data=data,tvals=tvals,h=h)
> Plot_ALIGE(tvals,ALIGE,sd_ALIGE,xlab="t",ylab="ALIGE",ylim=c(0,1))
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 examples in ‘cdom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: spectra
> ### Title: CDOM absorption data.
> ### Aliases: spectra
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(ggplot2)
> library(tidyr)
> data("spectra")
> 
> spectra <- gather(spectra, sample, absorption, -wavelength)
> 
> ggplot(spectra, aes(x = wavelength, y = absorption, group = sample)) +
+  geom_line(size = 0.1)
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 examples in ‘cellWise-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DDC
> ### Title: Detect Deviating Cells
> ### Aliases: DDC
> 
> ### ** Examples
> 
> library(MASS); set.seed(12345)
> n <- 50; d <- 20
> A <- matrix(0.9, d, d); diag(A) = 1
> x <- mvrnorm(n, rep(0,d), A)
> x[sample(1:(n * d), 50, FALSE)] <- NA
> x[sample(1:(n * d), 50, FALSE)] <- 10
> x[sample(1:(n * d), 50, FALSE)] <- -10
> x <- cbind(1:n, x)
> DDCx <- DDC(x)
 
 The input data has 50 rows and 21 columns.
 
 The data contained 1 columns that were identical to the case number
 (number of the row).
 Their column names are:
 
[1] X1
 
 These columns will be ignored in the analysis.
 We continue with the remaining 20 columns:
 
 [1] X2  X3  X4  X5  X6  X7  X8  X9  X10 X11 X12 X13 X14 X15 X16 X17 X18 X19 X20
[20] X21
 
 The final data set we will analyze has 50 rows and 20 columns.
 
> cellMap(DDCx$remX, DDCx$stdResid,
+ columnlabels = 1:d, rowlabels = 1:n)
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 ‘DDC_examples.Rmd’ using knitr
Quitting from lines 50-70 (DDC_examples.Rmd) 
Error: processing vignette 'DDC_examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DDC_examples.Rmd’

--- re-building ‘MacroPCA_examples.Rmd’ using knitr
Quitting from lines 53-57 (MacroPCA_examples.Rmd) 
Error: processing vignette 'MacroPCA_examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MacroPCA_examples.Rmd’

--- re-building ‘Wrap_examples.Rmd’ using knitr
bushfire              package:robustbase               R Documentation

_C_a_m_p_b_e_l_l _B_u_s_h_f_i_r_e _D_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     This data set was used by Campbell (1984) to locate bushfire
     scars.  The dataset contains satelite measurements on five
     frequency bands, corresponding to each of 38 pixels.

_U_s_a_g_e:

     data(bushfire, package="robustbase")
     
_F_o_r_m_a_t:

     A data frame with 38 observations on 5 variables.

_S_o_u_r_c_e:

     Maronna, R.A. and Yohai, V.J. (1995) The Behavoiur of the
     Stahel-Donoho Robust Multivariate Estimator.  _Journal of the
     American Statistical Association_ *90*, 330-341.

_E_x_a_m_p_l_e_s:

     data(bushfire)
     plot(bushfire)
     covMcd(bushfire)
     

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

SUMMARY: processing the following files failed:
  ‘DDC_examples.Rmd’ ‘MacroPCA_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Census2016.Rmd’ using rmarkdown
Quitting from lines 84-114 (Census2016.Rmd) 
Error: processing vignette 'Census2016.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Census2016.Rmd’

SUMMARY: processing the following file failed:
  ‘Census2016.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: centralplot
> ### Title: centralplot
> ### Aliases: centralplot
> 
> ### ** Examples
> 
> name <- c('a','b','c')
> distance <- c(1,2,3)
> bound <- 2.5
> centralplot("centre",name,distance,bound)
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 ‘cgmanalysis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cgmreport
> ### Title: Generate AGP
> ### Aliases: cgmreport
> 
> ### ** Examples
> 
> cgmreport(system.file("extdata","Cleaned",package = "cgmanalysis"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: cgmreport ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘CGPfunctions-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: OurConf
> ### Title: Plotting random samples of confidence intervals around the mean
> ### Aliases: OurConf
> 
> ### ** Examples
> 
> OurConf(samples = 100, n = 30, mu = 0, sigma = 1, conf.level = 0.95)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: OurConf ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using-Plot2WayANOVA.Rmd’ using rmarkdown
Quitting from lines 74-75 (Using-Plot2WayANOVA.Rmd) 
Error: processing vignette 'Using-Plot2WayANOVA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Using-Plot2WayANOVA.Rmd’

--- re-building ‘Using-PlotXTabs.Rmd’ using rmarkdown
Quitting from lines 55-67 (Using-PlotXTabs.Rmd) 
Error: processing vignette 'Using-PlotXTabs.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Using-PlotXTabs.Rmd’

--- re-building ‘Using-newggslopegraph.Rmd’ using rmarkdown
Quitting from lines 40-41 (Using-newggslopegraph.Rmd) 
Error: processing vignette 'Using-newggslopegraph.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Using-newggslopegraph.Rmd’

SUMMARY: processing the following files failed:
  ‘Using-Plot2WayANOVA.Rmd’ ‘Using-PlotXTabs.Rmd’
  ‘Using-newggslopegraph.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘NEWS.Rmd’ using rmarkdown
Quitting from lines 150-154 (NEWS.Rmd) 
Error: processing vignette 'NEWS.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘NEWS.Rmd’

--- re-building ‘ChainLadder.Rnw’ using Sweave

Welcome to ChainLadder version 0.2.9

Type vignette('ChainLadder', package='ChainLadder') to access
the overall package documentation.

See demo(package='ChainLadder') for a list of demos.

More information is available on the ChainLadder project web-site:
https://github.com/mages/ChainLadder

To suppress this message use:
suppressPackageStartupMessages(library(ChainLadder))

Loading required package: systemfit
Loading required package: Matrix
Loading required package: car
Loading required package: carData
Loading required package: lmtest
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric


Please cite the 'systemfit' package as:
Arne Henningsen and Jeff D. Hamann (2007). systemfit: A Package for Estimating Systems of Simultaneous Equations in R. Journal of Statistical Software 23(4), 1-40. http://www.jstatsoft.org/v23/i04/.

If you have questions, suggestions, or comments regarding the 'systemfit' package, please use a forum or 'tracker' at systemfit's R-Forge site:
https://r-forge.r-project.org/projects/systemfit/
--- finished re-building ‘ChainLadder.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_word
> ### Title: Plot the 2D fractal containing the chosen word
> ### Aliases: plot_word
> 
> ### ** Examples
> 
> # function with word as input, constructs the IFSP and runs the chaos game:
> # for nice results use, for example, R = 20 and orbit = 3000
> A <- plot_word(word = "copula", R = 50, orbit = 100)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plot_word ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘checkmate.Rmd’ using rmarkdown
Quitting from lines 160-171 (checkmate.Rmd) 
Error: processing vignette 'checkmate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘checkmate.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make_percentile_tab
> ### Title: calculate raw values
> ### Aliases: make_percentile_tab
> 
> ### ** Examples
> 
> ptab <- make_percentile_tab(ref = kro.ref,
+                             item = "height",
+                            perc = c(2.5,10,50,90,97.5),
+                            stack = TRUE)
Loading required namespace: reshape2
> 
> ggplot2::ggplot(ptab, ggplot2::aes(x = age, y = value, colour = variable)) +
+    ggplot2::geom_line() +
+    ggplot2::facet_wrap(~ sex, nrow = 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
Running examples in ‘chillR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: make_daily_chill_plot2
> ### Title: Plot daily climate metric accumulation throughout the year (2)
> ### Aliases: make_daily_chill_plot2
> ### Keywords: utility
> 
> ### ** Examples
> 
> 
> 
> daily<-daily_chill(stack_hourly_temps(fix_weather(
+   KA_weather[which(KA_weather$Year>2005),])),running_mean=11)
> 
> make_daily_chill_plot2(daily,metrics=c("Chill_Portions","GDH"),cumulative=TRUE,
+    startdate=300,enddate=30,focusyears=c(2009,2008))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: make_daily_chill_plot2 ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘duplicate.missing.cases.Rmd’ using rmarkdown
--- finished re-building ‘duplicate.missing.cases.Rmd’

--- re-building ‘kernel.density.Rmd’ using rmarkdown
--- finished re-building ‘kernel.density.Rmd’

--- re-building ‘pump.neighborhoods.Rmd’ using rmarkdown
--- finished re-building ‘pump.neighborhoods.Rmd’

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

--- re-building ‘tiles.polygons.Rmd’ using rmarkdown
--- finished re-building ‘tiles.polygons.Rmd’

--- re-building ‘time.series.Rmd’ using rmarkdown
--- finished re-building ‘time.series.Rmd’

--- re-building ‘unstacking.bars.Rmd’ using rmarkdown
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Quitting from lines 110-204 (unstacking.bars.Rmd) 
Error: processing vignette 'unstacking.bars.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘unstacking.bars.Rmd’

SUMMARY: processing the following file failed:
  ‘unstacking.bars.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculate_percent_change
> ### Title: Calculate the percentage change between two choroplethr
> ###   dataframes.
> ### Aliases: calculate_percent_change
> 
> ### ** Examples
> 
> # load median age estimates from 2010 and 2015
> data(df_state_age_2010)
> data(df_state_age_2015)
> 
> df_age_diff = calculate_percent_change(df_state_age_2010, df_state_age_2015)
> state_choropleth(df_age_diff, 
+     title      = "Percent Change in Median Age, 2010-2015", 
+     legend     = "Percent Change", 
+     num_colors = 0)
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 ‘chron-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale
> ### Title: Coordinates and Positions for Chronological Objects
> ### Aliases: chron_trans scale_x_chron scale_y_chron
> 
> ### ** Examples
> 
> if(require("ggplot2")) {
+     dd <- data.frame(tt = chron(1:10), value = 101:110)
+     p <- ggplot(dd, aes(tt, value)) +
+              geom_point() + scale_x_chron(format = "%m-%d")
+     print(p)
+ }
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: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CINNA.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

Quitting from lines 231-234 (CINNA.Rmd) 
Error: processing vignette 'CINNA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CINNA.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intermediate-ssm-analysis.Rmd’ using rmarkdown
Quitting from lines 46-47 (intermediate-ssm-analysis.Rmd) 
Error: processing vignette 'intermediate-ssm-analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intermediate-ssm-analysis.Rmd’

--- re-building ‘introduction-to-ssm-analysis.Rmd’ using rmarkdown
Quitting from lines 94-127 (introduction-to-ssm-analysis.Rmd) 
Error: processing vignette 'introduction-to-ssm-analysis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction-to-ssm-analysis.Rmd’

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

SUMMARY: processing the following files failed:
  ‘intermediate-ssm-analysis.Rmd’ ‘introduction-to-ssm-analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘civis_ml.Rmd’ using rmarkdown
Quitting from lines 215-216 (civis_ml.Rmd) 
Error: processing vignette 'civis_ml.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘civis_ml.Rmd’

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

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

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

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ck37r-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cvsl_plot_roc
> ### Title: Plot a ROC curve from cross-validated AUC from CV.SuperLearner
> ### Aliases: cvsl_plot_roc
> 
> ### ** Examples
> 
> 
> library(SuperLearner)
Loading required package: nnls
Super Learner
Version: 2.0-24
Package created on 2018-08-10

> library(ck37r)
> 
> data(Boston, package = "MASS")
> 
> set.seed(1, "L'Ecuyer-CMRG")
> 
> # Subset rows to speed up example computation.
> row_subset = sample(nrow(Boston), 100)
> 
> Boston = Boston[row_subset, ]
> X = subset(Boston, select = -chas)
> 
> cvsl = CV.SuperLearner(Boston$chas, X[, 1:2], family = binomial(),
+                       cvControl = list(V = 2, stratifyCV = TRUE),
+                       SL.library = c("SL.mean", "SL.glm"))
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
> cvsl_plot_roc(cvsl)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: cvsl_plot_roc ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘clhs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clhs.data.frame
> ### Title: Conditioned Latin Hypercube Sampling
> ### Aliases: clhs.data.frame clhs.Raster clhs clhs.data.frame
> ###   clhs.SpatialPointsDataFrame clhs.Raster clhs.SpatialPointsDataFrame
> 
> ### ** Examples
> 
> 
> df <- data.frame(
+   a = runif(1000), 
+   b = rnorm(1000), 
+   c = sample(LETTERS[1:5], size = 1000, replace = TRUE)
+ )
> 
> # Returning the indices of the sampled points
> res <- clhs(df, size = 50, iter = 100, progress = FALSE, simple = TRUE)
> str(res)
 int [1:50] 852 723 173 523 593 211 238 120 604 588 ...
> 
> # Returning a cLHS_result object for plotting
> res <- clhs(df, size = 50, iter = 100, progress = FALSE, simple = FALSE)
> str(res)
List of 5
 $ initial_object:'data.frame':	1000 obs. of  3 variables:
  ..$ a: num [1:1000] 0.266 0.372 0.573 0.908 0.202 ...
  ..$ b: num [1:1000] 0.0773 -0.2969 -1.1832 0.0113 0.9916 ...
  ..$ c: Factor w/ 5 levels "A","B","C","D",..: 1 3 3 2 5 1 1 5 4 2 ...
 $ index_samples : int [1:50] 831 527 395 837 719 256 337 863 176 322 ...
 $ sampled_data  :'data.frame':	50 obs. of  3 variables:
  ..$ a: num [1:50] 0.6997 0.8044 0.1549 0.0764 0.4226 ...
  ..$ b: num [1:50] -0.572 -1.01 0.661 -1.164 0.776 ...
  ..$ c: Factor w/ 5 levels "A","B","C","D",..: 2 5 3 4 3 2 4 1 1 5 ...
 $ obj           : num [1:100] 70.3 70.3 70.3 70.3 70.3 ...
 $ cost          : NULL
 - attr(*, "class")= chr [1:2] "cLHS_result" "list"
> plot(res)
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’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clhs)
  > 
  > test_check("clhs")
  ── 1. Failure: basic clhs on a data.frame works (@test-clhs-data.frame.R#15)  ──
  `res` not equal to c(188, 657, 140, 301, 817).
  5/5 mismatches (average diff: 210)
  [1]  97 - 188 == -91
  [2] 903 - 657 == 246
  [3] 539 - 140 == 399
  [4] 451 - 301 == 150
  [5] 979 - 817 == 162
  
  ── 2. Failure: DLHS method on a data.frame works (@test-method_DLHS.R#17)  ─────
  `res` not equal to c(214, 40, 702, 919, 521).
  5/5 mismatches (average diff: 211)
  [1] 412 - 214 ==  198
  [2] 170 -  40 ==  130
  [3] 196 - 702 == -506
  [4] 820 - 919 ==  -99
  [5] 641 - 521 ==  120
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 2
  1. Failure: basic clhs on a data.frame works (@test-clhs-data.frame.R#15) 
  2. Failure: DLHS method on a data.frame works (@test-method_DLHS.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro-clhs.Rmd’ using rmarkdown
Quitting from lines 66-80 (intro-clhs.Rmd) 
Error: processing vignette 'intro-clhs.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘intro-clhs.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hmPlot
> ### Title: Plots a Heatmap
> ### Aliases: hmPlot hmPlot,MarkovChain-method
> ### Keywords: methods
> 
> ### ** Examples
> 
> 
> # fitting a simple Markov chain and predicting the next click
> clickstreams <- c("User1,h,c,c,p,c,h,c,p,p,c,p,p,o",
+                "User2,i,c,i,c,c,c,d",
+                "User3,h,i,c,i,c,p,c,c,p,c,c,i,d",
+                "User4,c,c,p,c,d",
+                "User5,h,c,c,p,p,c,p,p,p,i,p,o",
+                "User6,i,h,c,c,p,p,c,p,c,d")
> csf <- tempfile()
> writeLines(clickstreams, csf)
> cls <- readClickstreams(csf, header = TRUE)
> mc <- fitMarkovChain(cls)
> hmPlot(mc)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: hmPlot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘clifro-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: windrose
> ### Title: Plot a windrose
> ### Aliases: windrose
> 
> ### ** Examples
> 
> # Create some dummy wind data with predominant south to westerly winds, and
> # occasional yet higher wind speeds from the NE (not too dissimilar to
> # Auckland).
> 
> wind_df = data.frame(wind_speeds = c(rweibull(80, 2, 4), rweibull(20, 3, 9)),
+                      wind_dirs = c(rnorm(80, 135, 55), rnorm(20, 315, 35)) %% 360,
+                      station = rep(rep(c("Station A", "Station B"), 2),
+                                    rep(c(40, 10), each = 2)))
> 
> # Plot a simple windrose using all the defaults, ignoring any facet variable
> with(wind_df, windrose(wind_speeds, wind_dirs))
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 ‘climbeR_examples.Rmd’ using rmarkdown
Quitting from lines 72-74 (climbeR_examples.Rmd) 
Error: processing vignette 'climbeR_examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘climbeR_examples.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotall
> ### Title: Visualise climate window data
> ### Aliases: plotall
> 
> ### ** Examples
> 
> 
> # Visualise a fixed climate window generated for dataframes Mass and MassClimate
> 
> data(MassOutput)
> data(Mass)
> data(MassClimate)
> 
> single <- singlewin(xvar = list(Temp = MassClimate$Temp), 
+                    cdate = MassClimate$Date, bdate = Mass$Date, 
+                    baseline = lm(Mass ~ 1, data = Mass), 
+                    range = c(72, 15), 
+                    stat = "mean", func = "lin", 
+                    type = "absolute", refday = c(20, 5), 
+                    cmissing = FALSE, cinterval = "day")
>            
> plotall(dataset = MassOutput, bestmodel = single$bestmodel, 
+        bestmodeldata = single$bestmodeldata,
+        cw1 = 0.95, cw2 = 0.5, cw3 = 0.25, title = "Mass")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotall ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced_climwin.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: gridExtra
Loading required package: Matrix
--- finished re-building ‘advanced_climwin.Rmd’

--- re-building ‘climwin.Rmd’ using rmarkdown
Loading required package: ggplot2
Loading required package: gridExtra
Loading required package: Matrix
Quitting from lines 353-356 (climwin.Rmd) 
Error: processing vignette 'climwin.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘climwin.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DRDensityPlot
> ### Title: Plot Bayes or confidence interval density contours over a grid
> ###   of points (usually dose or time)
> ### Aliases: DRDensityPlot
> ### Keywords: nonlinear hplot
> 
> ### ** Examples
> 
> 
> ## Not run: 
> ##D data(examples14)
> ##D exdat<-examples14[[32]]
> ##D 
> ##D fitout<-fitEmax(exdat$y,exdat$dose,modType=3,count=exdat$nsize,
> ##D 								msSat=(exdat$sd)^2)
> ##D 
> ##D dgrid<-seq(0,1,length=100)
> ##D seout95<-predict(fitout,dgrid,clev=0.95)
> ##D seout90<-predict(fitout,dgrid,clev=0.9)
> ##D seout80<-predict(fitout,dgrid,clev=0.8)
> ##D seout50<-predict(fitout,dgrid,clev=0.5)
> ##D 
> ##D qlev<-c(0.025,0.05,0.10,0.25)
> ##D 
> ##D qL<-cbind(seout95$ubdif,seout90$ubdif,seout80$ubdif,seout50$ubdif)
> ##D qH<-cbind(seout95$lbdif,seout90$lbdif,seout80$lbdif,seout50$lbdif)
> ##D 
> ##D DRDensityPlot(dgrid,qL,qH,qlevL=qlev,xlab='Dose',ylab='Diff with PBO')
> ##D 
> ## End(Not run)
> ## Don't show: 
> data(examples14)
> exdat<-examples14[[32]]
> 
> dgrid<-seq(0,1,length=5)
> 
> qlev<-c(0.10,0.25)
> 
> qL<-matrix(c(0.000000, 0.000000,
+ 1.181590, 1.093189,
+ 1.301505, 1.220726,
+ 1.354046, 1.273955,
+ 1.384266, 1.303586),ncol=2,byrow=TRUE)
> 
> qH<-matrix(c(0.0000000, 0.0000000,
+ 0.8083449, 0.8967468,
+ 0.9604440, 1.0412232,
+ 1.0158898, 1.0959808,
+ 1.0436238, 1.1243036),ncol=2,byrow=TRUE)
> 
> DRDensityPlot(dgrid,qL,qH,qlevL=qlev,xlab='Dose',ylab='Diff with PBO')
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: DRDensityPlot ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘ClinReport-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gg_desc_quali
> ### Title: Creates a ggplot object corresponding to a qualitative desc
> ###   object
> ### Aliases: gg_desc_quali
> 
> ### ** Examples
> 
>  ## Don't show: 
> data(data)
> 
> desc=report.quali(data=data,y="y_logistic",x1="GROUP",
+ 	x2="TIMEPOINT")
> 
> gg=ClinReport:::gg_desc_quali(desc,
+ title="Qualitative desc object with 2 explicative variables",
+ legend.label="Y levels")
> 
> 
> desc2=report.quali(data=data,y="y_logistic",x1="GROUP")
> ClinReport:::gg_desc_quali(desc2,title="Qualitative desc object with 1 explicative 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
Running examples in ‘CluMP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CluMP_view
> ### Title: Cluster profiles' (CluMP results) visualisation
> ### Aliases: CluMP_view
> ### Keywords: CluMP
> 
> ### ** Examples
> 
> dataMale <- GeneratePanel(n = 50, Param = ParamLinear, NbVisit = 10)
> dataMale$Gender <- "M"
> dataFemale <- GeneratePanel(n = 50, Param = ParamLinear, NbVisit = 10)
> dataFemale$ID <- dataFemale$ID + 50
> dataFemale$Gender <- "F"
> data <- rbind(dataMale, dataFemale)
> 
> CluMPoutput <- CluMP(formula = Y ~ Time, group = "ID", data = data, cl_numb = 3)
> title <- "Plotting clusters' representatives with error bars"
> CluMP_view(CluMPoutput, type = "all" , return_table = TRUE, title = title)
`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: <Anonymous> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘clustcurv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.clustcurv_surv
> ### Title: Visualization of 'clustcurv_surv' objects with ggplot2 graphics
> ### Aliases: autoplot.clustcurv_surv
> 
> ### ** Examples
> 
> 
> library(survival)
> library(clustcurv)
> library(condSURV)
> library(ggplot2)
> library(ggfortify)
> data(veteran)
> data(colonCS)
> 
> cl2 <- kgroups_surv(time = veteran$time, status = veteran$status,
+ fac = veteran$celltype, k = 2, algorithm = "kmeans")
> 
> autoplot(cl2)
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 ‘clusterfly-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cfly_dist
> ### Title: Static plot: Variable distribution. Draw a density plot for each
> ###   continuous variable, facetted across clustering.
> ### Aliases: cfly_dist
> ### Keywords: hplot
> 
> ### ** Examples
> 
> if (require("ggplot2")) {
+ o <- olive_example()
+ cfly_dist(o, "kmeans")
+ cfly_dist(o, "kmeans") + scale_y_continuous(limit=c(0, 2))
+ }
Loading required package: ggplot2
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 ‘clusterlab-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clusterlab
> ### Title: clusterlab
> ### Aliases: clusterlab
> 
> ### ** Examples
> 
> synthetic <- clusterlab(centers=4,r=8,sdvec=c(2.5,2.5,2.5,2.5),   
+ alphas=c(1,1,1,1),centralcluster=FALSE,   
+ numbervec=c(50,50,50,50)) # for a six cluster solution)   
***clusterlab***
mode: circle
simulating clusters...
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: clusterlab ... 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 44-46 (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 ‘using-clusternomics.Rmd’ using rmarkdown
Quitting from lines 89-93 (using-clusternomics.Rmd) 
Error: processing vignette 'using-clusternomics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-clusternomics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-clustRcompaR.Rmd’ using rmarkdown
Quitting from lines 57-60 (introduction-to-clustRcompaR.Rmd) 
Error: processing vignette 'introduction-to-clustRcompaR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction-to-clustRcompaR.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clustree
> ### Title: Plot a clustering tree
> ### Aliases: clustree clustree.matrix clustree.data.frame
> ###   clustree.SingleCellExperiment clustree.seurat
> 
> ### ** Examples
> 
> data(iris_clusts)
> clustree(iris_clusts, prefix = "K")
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 ‘clustree.Rmd’ using rmarkdown
Quitting from lines 80-81 (clustree.Rmd) 
Error: processing vignette 'clustree.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘clustree.Rmd’

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

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

--- re-building ‘create_output_matrix.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 84-86 (create_output_matrix.Rmd) 
Error: processing vignette 'create_output_matrix.Rmd' failed with diagnostics:
`heatmap_width` and `width` should not all be the absolute units.
--- failed re-building ‘create_output_matrix.Rmd’

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

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

Attaching package: 'tidyr'

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

    extract


Attaching package: 'purrr'

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

    set_names


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 53-66 (diagnostic.Rmd) 
Error: processing vignette 'diagnostic.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘diagnostic.Rmd’

--- re-building ‘pooling.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 ‘pooling.Rmd’

--- re-building ‘workflow.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:  1 failed to parse.
Warning:  1 failed to parse.
--- finished re-building ‘workflow.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bal.plot
> ### Title: Generate Univariate Balance Plots
> ### Aliases: bal.plot
> 
> ### ** Examples
> 
> library(MatchIt); data("lalonde", package = "cobalt")

Attaching package: ‘MatchIt’

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

    lalonde

> 
> #Nearest Neighbor Matching
> m.out <- matchit(treat ~ age + educ + race + 
+                  married + nodegree + re74 + re75, 
+                  data = lalonde)
> 
> bal.plot(m.out, "age", which = "both")
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 ‘cocoreg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cocoreg
> ### Title: The Common Components by Regression (CoCoReg) algorithm
> ### Aliases: cocoreg
> 
> ### ** Examples
> 
> dc <- create_syn_data_toy()
> ccr <- cocoreg(dc$data)
> 
> ggplot_dflst(dc$data, ncol=1)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: ggplot_dflst ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cocoreg-basics.Rmd’ using rmarkdown
Quitting from lines 28-35 (cocoreg-basics.Rmd) 
Error: processing vignette 'cocoreg-basics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cocoreg-basics.Rmd’

SUMMARY: processing the following file failed:
  ‘cocoreg-basics.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: likert_from_items
> ### Title: Derive a likert object from items
> ### Aliases: likert_from_items
> 
> ### ** Examples
> 
> data("bfi", package = "codebook")
> open_items <- paste0("BFIK_open_",1:4)
> graphics::plot(likert_from_items(bfi[, open_items]))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: <Anonymous> -> print.likert.bar.plot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘codingMatrices.Rnw’ using knitr
Quitting from lines 478-486 (codingMatrices.Rnw) 
Error: processing vignette 'codingMatrices.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘codingMatrices.Rnw’

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

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

--- re-building ‘Temporal_Diversity_Indices.Rmd’ using rmarkdown
Quitting from lines 108-110 (Temporal_Diversity_Indices.Rmd) 
Error: processing vignette 'Temporal_Diversity_Indices.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Temporal_Diversity_Indices.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: buildModelCI
> ### Title: buildModelCI
> ### Aliases: buildModelCI
> 
> ### ** Examples
> 
> 
> data(diamonds)
> model1 <- lm(price ~ carat + cut, data=diamonds)
> coefplot:::buildModelCI(model1)
                  Value Coefficient   HighInner    LowInner  HighOuter
cut^4          74.59427       cut^4    90.83386    58.35469   107.0734
cut.C         367.90995       cut.C   388.12410   347.69579   408.3383
cut.Q        -528.59779       cut.Q  -505.46541  -551.73018  -482.3330
cut.L        1239.80045       cut.L  1265.90049  1213.70040  1292.0005
carat        7871.08213       carat  7885.06176  7857.10251  7899.0414
(Intercept) -2701.37602 (Intercept) -2685.94495 -2716.80710 -2670.5139
              LowOuter  Model
cut^4          42.1151 model1
cut.C         327.4816 model1
cut.Q        -574.8626 model1
cut.L        1187.6004 model1
carat        7843.1229 model1
(Intercept) -2732.2382 model1
> coefplot(model1)
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 ‘coinmarketcapr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_top_5_currencies
> ### Title: To plot Top 5 Cryptocurrencies
> ### Aliases: plot_top_5_currencies
> 
> ### ** Examples
> 
> plot_top_5_currencies('EUR')
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 ‘CollapseLevels-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: displayIV
> ### Title: displayIV
> ### Aliases: displayIV
> 
> ### ** Examples
> 
> 
> # Load the German_Credit data set supplied with this package
> 
> 
> data("German_Credit")
> 
> displayIV(German_Credit,col="Credit_History",resp="Good_Bad")
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 ‘CollapseLevels.Rmd’ using rmarkdown
Quitting from lines 205-223 (CollapseLevels.Rmd) 
Error: processing vignette 'CollapseLevels.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CollapseLevels.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘collateral.Rmd’ using rmarkdown
Quitting from lines 42-48 (collateral.Rmd) 
Error: processing vignette 'collateral.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘collateral.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.colocal
> ### Title: Making scatter plots for signal proportions before and after
> ###   d-type or z-type normalization
> ### Aliases: plot.colocal
> 
> ### ** Examples
> 
> ## a simulated 3D example data.
> data("twolines")
> 
> twolines.results <- nsinc.d(data = twolines, membership = "membership",
+                             dim = 3, r.model = "r.med")
The method is 'nsinc.d'!
The input data has dimension of 3!
The input study region is 'NULL'!
The observed study region is [-0.994687642,0.991983793] X [-0.994783715,0.984829183] X [-0.25846953,0.343853326]!

 The default full r range for colocalization index of type d is [0.00550850564633427,2.03825393738339]!

The r.model = 'r.med'!
r.min = 0.722833786275035 is used!
r.max = 0.722833786275035 is used!
Because of r.min = r.max, r.count = 1 and r.adjust = 0 are used!
Bi-direction colocalization is considered!
index.d for r = 0.722833786275035 is -0.224788967716664 ;
The average coolocalization index of type d over all choosen r's is = -0.224788967716664!
> 
> plot(twolines.results)
[[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 ‘noise.Rmd’ using rmarkdown
Quitting from lines 36-40 (noise.Rmd) 
Error: processing vignette 'noise.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘noise.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CreateExampleData
> ### Title: Creates demonstration data of the colorpatch package
> ### Aliases: CreateExampleData
> 
> ### ** Examples
> 
> library(ggplot2)
> library(colorpatch)
> dat <- CreateExampleData()
> df <- ToDataFrame(dat)
> p <- ggplot(df, aes(x = x, y = y, ratio = ratio, conf = conf)) 
> p <- p + theme_colorpatch() + coord_fixed(ratio = 1)  + stat_colorpatch()
Warning: Ignoring unknown parameters: colour.fun
> plot(p)
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
Loading required package: colorpatch
Loading required package: ggplot2
Loading required package: grid
Loading required package: gridExtra
Quitting from lines 92-107 (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
Running examples in ‘colorspace-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_colour_continuous_diverging
> ### Title: HCL-Based Continuous Diverging Color Scales for ggplot2
> ### Aliases: scale_colour_continuous_diverging
> ###   scale_color_continuous_diverging scale_fill_continuous_diverging
> 
> ### ** Examples
> 
> # adapted from stackoverflow: https://stackoverflow.com/a/20127706/4975218
> 
> library("ggplot2")
> 
> # generate dataset and base plot
> set.seed(100)
> df <- data.frame(country = LETTERS, V = runif(26, -40, 40))
> df$country = factor(LETTERS, LETTERS[order(df$V)]) # reorder factors
> gg <- ggplot(df, aes(x = country, y = V, fill = V)) +
+   geom_bar(stat = "identity") +
+   labs(y = "Under/over valuation in %", x = "Country") +
+   coord_flip() + theme_minimal()
>   
> # plot with default diverging scale
> gg + scale_fill_continuous_diverging()
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 ‘colorspace.Rmd’ using rmarkdown
Quitting from lines 181-184 (colorspace.Rmd) 
Error: processing vignette 'colorspace.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘colorspace.Rmd’

--- re-building ‘hcl-colors.Rnw’ using Sweave
Loading required package: grid
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
--- finished re-building ‘hcl-colors.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Compboost
> ### Title: Compboost API
> ### Aliases: Compboost
> 
> ### ** Examples
> 
> cboost = Compboost$new(mtcars, "mpg", loss = LossQuadratic$new())
> cboost$addBaselearner("hp", "spline", BaselearnerPSpline, degree = 3,
+   n.knots = 10, penalty = 2, differences = 2)
> cboost$train(1000)
   1/1000: risk = 16
  25/1000: risk = 5.1
  50/1000: risk = 4
  75/1000: risk = 3.8
 100/1000: risk = 3.8
 125/1000: risk = 3.7
 150/1000: risk = 3.7
 175/1000: risk = 3.6
 200/1000: risk = 3.6
 225/1000: risk = 3.6
 250/1000: risk = 3.5
 275/1000: risk = 3.5
 300/1000: risk = 3.5
 325/1000: risk = 3.5
 350/1000: risk = 3.5
 375/1000: risk = 3.5
 400/1000: risk = 3.5
 425/1000: risk = 3.4
 450/1000: risk = 3.4
 475/1000: risk = 3.4
 500/1000: risk = 3.4
 525/1000: risk = 3.4
 550/1000: risk = 3.4
 575/1000: risk = 3.4
 600/1000: risk = 3.4
 625/1000: risk = 3.4
 650/1000: risk = 3.4
 675/1000: risk = 3.4
 700/1000: risk = 3.4
 725/1000: risk = 3.3
 750/1000: risk = 3.3
 775/1000: risk = 3.3
 800/1000: risk = 3.3
 825/1000: risk = 3.3
 850/1000: risk = 3.3
 875/1000: risk = 3.3
 900/1000: risk = 3.3
 925/1000: risk = 3.3
 950/1000: risk = 3.3
 975/1000: risk = 3.3
1000/1000: risk = 3.3


Train 1000 iterations in 0 Seconds.
Final risk based on the train set: 3.3

> 
> table(cboost$getSelectedBaselearner())

hp_spline 
     1000 
> cboost$plot("hp_spline")
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 ‘compboost.Rmd’ using rmarkdown
Quitting from lines 183-187 (compboost.Rmd) 
Error: processing vignette 'compboost.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘compboost.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bootcoefs
> ### Title: Bootstrap the regression coefficients for a robust linear
> ###   regression model
> ### Aliases: bootcoefs bootcoefs.complmrob bootcoefs.lmrob
> 
> ### ** Examples
> 
> data <- data.frame(lifeExp = state.x77[, "Life Exp"], USArrests[ , -3])
> mUSArr <- complmrob(lifeExp ~ ., data = data)
> bc <- bootcoefs(mUSArr, R = 200) # the number of bootstrap replicates should
>                                  # normally be higher!
> summary(bc)
Robust linear regression with compositional covariates
complmrob(formula = lifeExp ~ ., data = data)

Standard errors and derived statistics are base on 200 bootstrap replications

Coefficients:
            Estimate     bias Std. Error Pr(b<>0)   
(Intercept) 70.65261 -0.18646    1.92971  0.00498 **
Murder      -2.23318 -0.03454    0.43169  0.00498 **
Assault     -1.04628  0.04709    1.02541  0.17413   
Rape         3.27946 -0.11608    0.68111  0.00498 **
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Confidence intervals:
            Estimate   2.5 %  97.5 %
(Intercept)  70.6526 67.0257 73.9220
Murder       -2.2332 -3.1284 -1.3909
Assault      -1.0463 -2.8183  1.0016
Rape          3.2795  1.8936  4.3363

Robust residual standard error: 0.6931 
Multiple R-squared: 0.7115	Adjusted R-squared: 0.6992
> plot(bc) # for the model diagnostic plots
Warning: Ignoring unknown aesthetics: ymax
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 ‘comtradr-vignette.Rmd’ using rmarkdown
Quitting from lines 232-249 (comtradr-vignette.Rmd) 
Error: processing vignette 'comtradr-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘comtradr-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotpint
> ### Title: Plot the P-Value Function
> ### Aliases: plotpint
> 
> ### ** Examples
> 
> # Simulate random data
> 
> GroupA<-rnorm(50)
> GroupB<-rnorm(50)
> 
> RandomData<-data.frame(GroupA, GroupB)
> RandomModel<-lm(GroupA ~ GroupB, data=RandomData)
> 
> intervalsdf<-genintervals(RandomModel, "GroupB")
> 
> p<-plotpint(intervalsdf)
> 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
Running ‘testthat.R’ [50s/53s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(conflicted)
  > 
  > test_check("conflicted")
  ── 1. Failure: shimmed arguments match unshimmed (@test-shim.R#4)  ─────────────
  formals(shim_require) not equal to formals(base::require).
  Length mismatch: comparison on first 5 components
  Component "warn.conflicts": Modes: logical, name
  Component "warn.conflicts": target is logical, current is name
  
  ── 2. Failure: shimmed arguments match unshimmed (@test-shim.R#5)  ─────────────
  formals(shim_library) not equal to formals(base::library).
  Length mismatch: comparison on first 9 components
  Component "warn.conflicts": Modes: logical, name
  Component "warn.conflicts": target is logical, current is name
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 29 SKIPPED: 0 FAILED: 2
  1. Failure: shimmed arguments match unshimmed (@test-shim.R#4) 
  2. Failure: shimmed arguments match unshimmed (@test-shim.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘ConfoundedMeta-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sens_plot
> ### Title: Plots for sensitivity analyses
> ### Aliases: sens_plot
> ### Keywords: confounding, meta-analysis, sensitivity
> 
> ### ** Examples
> 
> # with variable bias and with confidence band
> sens_plot( .type="line", .q=log(1.1), .Bmin=log(1), .Bmax=log(4), .sigB=0.1,
+            .yr=log(1.3), .vyr=0.005, .t2=0.4, .vt2=0.03 )
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 ‘chamber.Rmd’ using rmarkdown
Quitting from lines 78-90 (chamber.Rmd) 
Error: processing vignette 'chamber.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘chamber.Rmd’

--- re-building ‘senate.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

--- finished re-building ‘senate.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: contourWalker
> ### Title: Contour Walker Function, Rcpp Interface to C++ Routine
> ### Aliases: contourWalker
> 
> ### ** Examples
> 
> n = 100
> x = runif(n)
> y = runif(n)
> df = expand.grid(x,y);
> colnames(df) = c("x","y")
> df$z = df$x^2 + df$y^2
> dm  = getDelaunayMesh(df$x,df$y)
> res = contourWalker(dm,as.matrix(df),levels=pretty(df$z,n=20))
> res = data.frame(res); colnames(res) = c('LID','GID','PID','x','y','z')
> res$Group = interaction(res$LID,res$GID)
> library(ggplot2)
> ggplot(res,aes(x,y,group=Group,colour=z)) + 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> ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘coopProductGame-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCoreSet
> ### Title: Plot Core Set for cooperative production linear games.
> ### Aliases: plotCoreSet
> 
> ### ** Examples
> 
> # Vector of benefits
> c <- c(68, 52)
> # Production matrix
> A <- matrix(c(4, 5, 6, 2), ncol = 2, byrow = TRUE)
> # Matrix of resources. Each row is the vector of resources of each player
> B <- matrix(c(4, 6, 60, 33, 39, 0), ncol = 3, byrow = TRUE)
> # Solution of the associated linear production game
> plotCoreSet(c, A, B)
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 ‘CoordinateCleaner-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.spatialvalid
> ### Title: Plot Method for Class Spatialvalid
> ### Aliases: plot.spatialvalid
> ### Keywords: Visualisation
> 
> ### ** Examples
> 
> 
> 
> exmpl <- data.frame(species = sample(letters, size = 250, replace = TRUE),
+                     decimallongitude = runif(250, min = 42, max = 51),
+                     decimallatitude = runif(250, min = -26, max = -11))
> 
> test <- clean_coordinates(exmpl, species = "species", 
+                           tests = c("sea", "gbif", "zeros"),
+                           verbose = FALSE)
> 
> summary(test)
    .val     .zer     .gbf .summary 
       0        0        0        0 
> plot(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 ‘CopulaDTA_Vignette.Rmd’ using rmarkdown
Quitting from lines 292-293 (CopulaDTA_Vignette.Rmd) 
Error: processing vignette 'CopulaDTA_Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CopulaDTA_Vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: corkscrew-package
> ### Title: Preprocessor for Data Modeling
> ### Aliases: corkscrew-package corkscrew
> ### Keywords: package
> 
> ### ** Examples
> 
> # using transformation 
> data(airquality)
> transformation(names(airquality)[2:4],"Ozone",airquality)
[1] "Working on variable #1"
[1] "Working on variable #2"
[1] "Working on variable #3"
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: transformation ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘corrr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: focus_if
> ### Title: Conditionally focus correlation data frame
> ### Aliases: focus_if
> 
> ### ** 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

> any_greater_than <- function(x, val) {
+   mean(abs(x), na.rm = TRUE) > val
+ }
> 
> x <- correlate(mtcars)

Correlation method: 'pearson'
Missing treated using: 'pairwise.complete.obs'

> 
> x %>% focus_if(any_greater_than, .6)
# A tibble: 6 x 6
  rowname    mpg    cyl   disp     hp     wt
  <chr>    <dbl>  <dbl>  <dbl>  <dbl>  <dbl>
1 drat     0.681 -0.700 -0.710 -0.449 -0.712
2 qsec     0.419 -0.591 -0.434 -0.708 -0.175
3 vs       0.664 -0.811 -0.710 -0.723 -0.555
4 am       0.600 -0.523 -0.591 -0.243 -0.692
5 gear     0.480 -0.493 -0.556 -0.126 -0.583
6 carb    -0.551  0.527  0.395  0.750  0.428
> x %>% focus_if(any_greater_than, .6, mirror = TRUE) %>% network_plot()
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘corrr-databases.Rmd’ using rmarkdown
Quitting from lines 49-52 (corrr-databases.Rmd) 
Error: processing vignette 'corrr-databases.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘corrr-databases.Rmd’

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

Correlation method: 'pearson'
Missing treated using: 'pairwise.complete.obs'


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 102-106 (using-corrr.Rmd) 
Error: processing vignette 'using-corrr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-corrr.Rmd’

SUMMARY: processing the following files failed:
  ‘corrr-databases.Rmd’ ‘using-corrr.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘cosinor2-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cosinor.PR
> ### Title: Percent Rhythm
> ### Aliases: cosinor.PR
> 
> ### ** Examples
> 
> fit.temperature<-cosinor.lm(Temperature~time(Time), period = 24, data = temperature_zg)
> cosinor.PR(fit.temperature)
          r Percent rhythm p-value
1 0.9838823      0.9680243       0
> 
> fit.november<-population.cosinor.lm(data = PANAS_november, time = PANAS_time,
+ period = 7)
     MESOR Amplitude Acrophase
1 1.435419 0.2662682 -5.544496
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: population.cosinor.lm ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘cosinor2.Rmd’ using rmarkdown
Loading required package: cosinor
Quitting from lines 47-48 (cosinor2.Rmd) 
Error: processing vignette 'cosinor2.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cosinor2.Rmd’

SUMMARY: processing the following file failed:
  ‘cosinor2.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggplot.cosinor.lm
> ### Title: Plot a cosinor model
> ### Aliases: ggplot.cosinor.lm
> 
> ### ** Examples
> 
> fit <- cosinor.lm(Y ~ time(time) + X + amp.acro(X), data = vitamind)
> ggplot.cosinor.lm(fit, "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
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro.Rmd’ using knitr
Quitting from lines 59-61 (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’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_fitcmp
> ### Title: plot_fitcmp
> ### Aliases: plot_fitcmp
> 
> ### ** Examples
> 
> df <- data.frame(poisson = rpois(25, 0.3), binomial = rbinom(25, 1, 0.8))
> fitcmp <- compare_fit(df, fitlist = fit_counts(df, model = "all"))
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
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
> plot_fitcmp(fitcmp)
Warning: Removed 10 rows containing missing values (position_stack).
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 ‘countytimezones.Rmd’ using rmarkdown
Loading required package: acs
Loading required package: stringr
Loading required package: XML

Attaching package: 'acs'

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

    apply


Attaching package: 'dplyr'

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

    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 111-123 (countytimezones.Rmd) 
Error: processing vignette 'countytimezones.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘countytimezones.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘coveffectsplot-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
> 
> 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

> 
> # Example 1
> 
> plotdata <- get_sample_data("forest-plot-table.csv")
> plotdata <- plotdata %>%
+   mutate(midlabel = format(round(mid,2), nsmall = 2),
+          lowerlabel = format(round(lower,2), nsmall = 2),
+          upperlabel = format(round(upper,2), nsmall = 2),
+          LABEL = paste0(midlabel, " [", lowerlabel, "-", upperlabel, "]"))
> param <- "BZD AUC"
> plotdata <-  filter(plotdata,paramname==param)
> plotdata$covname <- reorder(plotdata$covname,plotdata$upper,FUN =max)
> plotdata$label <- reorder(plotdata$label,plotdata$scen)
> covs <- c("WEIGHT","AGE")
> plotdata <-  filter(plotdata,covname%in%covs)
> forest_plot(plotdata,
+             ref_legend_text = "Reference (vertical line)",
+             area_legend_text = "Reference (vertical line)",
+             xlabel = paste("Fold Change in", param, "Relative to Reference"),
+             show_ref_area = FALSE,
+             facet_formula = "covname~.",
+             facet_scales = "free_y",
+             facet_space = "free_y",
+             show_table_facet_strip = "none",
+             table_position = "right",
+             plot_table_ratio = 4)
Error in Summary.unit(c(8.8, 8.8), na.rm = FALSE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: forest_plot ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_to_coveffectsplot.Rmd’ using rmarkdown
Quitting from lines 61-95 (introduction_to_coveffectsplot.Rmd) 
Error: processing vignette 'introduction_to_coveffectsplot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘introduction_to_coveffectsplot.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_sub
> ### Title: Add annotation underneath a plot
> ### Aliases: add_sub
> 
> ### ** Examples
> 
> p1 <- ggplot(mtcars, aes(mpg, disp)) + geom_line(colour = "blue") + background_grid(minor='none')
> ggdraw(add_sub(p1, "This is an annotation.\nAnnotations can span multiple lines."))
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 ‘coxed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: baseline.plot
> ### Title: Plot the simulated baseline functions
> ### Aliases: baseline.plot
> 
> ### ** Examples
> 
> simdata <- sim.survdata(N=1000, T=100, num.data.frames=1)
> baseline.plot(simdata$baseline)
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 ‘coxrt-vignette.Rmd’ using rmarkdown
Quitting from lines 64-85 (coxrt-vignette.Rmd) 
Error: processing vignette 'coxrt-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘coxrt-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bsplineD
> ### Title: B-spline Derivatives
> ### Aliases: bsplineD
> 
> ### ** Examples
> 
> 
> set.seed(42)
> 
> xvec <- seq(0.1, 9.9, length = 1000)
> iknots <- sort(runif(rpois(1, 3), 1, 9))
> bknots <- c(0, 10)
> 
> # basis matrix and the first and second derivatives thereof, for cubic (order =
> # 4) b-splines
> bmat  <- bsplines(xvec, iknots, bknots = bknots)
> bmat1 <- bsplineD(xvec, iknots, bknots = bknots, derivative = 1)
> bmat2 <- bsplineD(xvec, iknots, bknots = bknots, derivative = 2)
> 
> # control polygon ordinates
> theta <- runif(length(iknots) + 4L, -5, 5)
> 
> # plot data
> plot_data <-
+   dplyr::data_frame(x = xvec,
+                     Spline = as.numeric(bmat %*% theta),
+                     "First Derivative" = as.numeric(bmat1 %*% theta),
+                     "Second Derivative" = as.numeric(bmat2 %*% theta))
Warning: `data_frame()` is deprecated, use `tibble()`.
This warning is displayed once per session.
> plot_data <- tidyr::gather(plot_data, key = key, value = value, -x)
> 
> ggplot2::ggplot(plot_data) +
+ ggplot2::aes(x = x, y = value, color = key) +
+ ggplot2::geom_line() +
+ ggplot2::geom_hline(yintercept = 0) +
+ ggplot2::geom_vline(xintercept = iknots, linetype = 3)
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 ‘cpr-pkg.Rmd’ using rmarkdown
Quitting from lines 93-95 (cpr-pkg.Rmd) 
Error: processing vignette 'cpr-pkg.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cpr-pkg.Rmd’

SUMMARY: processing the following file failed:
  ‘cpr-pkg.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘cr17-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCuminc
> ### Title: Cumulative incidences curves
> ### Aliases: plotCuminc
> 
> ### ** Examples
> 
> fitC <- fitCuminc(time = LUAD$time, risk = LUAD$event, group = LUAD$gender, cens = "alive")
19 cases omitted due to missing values
> plotCuminc(ci = fitC, cens = "alive", target = 1200)
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 ‘vignette.Rmd’ using rmarkdown
Quitting from lines 117-121 (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
Error(s) in re-building vignettes:
  ...
--- re-building ‘cranly.Rmd’ using rmarkdown
Quitting from lines 62-68 (cranly.Rmd) 
Error: processing vignette 'cranly.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cranly.Rmd’

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

--- re-building ‘glms.Rmd’ using rmarkdown
Quitting from lines 58-61 (glms.Rmd) 
Error: processing vignette 'glms.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘glms.Rmd’

SUMMARY: processing the following files failed:
  ‘cranly.Rmd’ ‘glms.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Quitting from lines 74-79 (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 ‘cRegulome-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cor_joy
> ### Title: A joy plot of correlation of microRNA or tf sets
> ### Aliases: cor_joy
> 
> ### ** Examples
> 
> # locate the testset file and connect
> fl <- system.file('extdata', 'cRegulome.db', package = 'cRegulome')
> conn <- RSQLite::dbConnect(RSQLite::SQLite(), fl)
> 
> # enter a custom query with different arguments
> dat <- get_mir(conn,
+                mir = c('hsa-let-7g', 'hsa-let-7i'),
+                study = 'STES')
> 
> # make a cmicroRNA object   
> cmir <- cmicroRNA(dat)
> 
> # print object
> cor_joy(cmir)
Picking joint bandwidth of 0.0445
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’ [14s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cRegulome)
  > 
  > test_check("cRegulome")
  ── 1. Error: cor_upset works (@test-methods.plots.R#42)  ───────────────────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: cor_upset(cmir) at testthat/test-methods.plots.R:42
  2: cor_upset.cmicroRNA(cmir)
  3: upset(dat, ...)
  4: Make_base_plot(Main_bar, Matrix, Sizes, labels, mb.ratio, att.x, att.y, New_data, 
         expression, att.pos, first.col, att.color, AllQueryData, attribute.plots, legend, 
         query.legend, BoxPlots, Set_names, set.metadata, set.metadata.plots)
  5: NoAttBasePlot(legend, size_plot_height, Main_bar_plot, Matrix_plot, hratios, Size_plot, 
         query_legend, set_metadata, set_metadata_plots)
  6: grid.draw(arrangeGrob(Main_bar_plot, Matrix_plot, heights = hratios))
  7: grid.draw.gTree(arrangeGrob(Main_bar_plot, Matrix_plot, heights = hratios))
  8: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  9: drawGTree(x)
  10: grid.draw(x$children[[i]], recording = FALSE)
  ...
  29: pushvpgp(x)
  30: pushgrobvp(x$vp)
  31: pushgrobvp.viewport(x$vp)
  32: pushViewport(vp, recording = FALSE)
  33: lapply(vps, push.vp, recording)
  34: FUN(X[[i]], ...)
  35: push.vp.vpTree(X[[i]], ...)
  36: push.vp(vp$parent, recording)
  37: push.vp.viewport(vp$parent, recording)
  38: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 133 SKIPPED: 0 FAILED: 1
  1. Error: cor_upset works (@test-methods.plots.R#42) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘crmPack-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DataMixture-class
> ### Title: Class for the data with mixture sharing
> ### Aliases: DataMixture-class .DataMixture
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## decide on the dose grid:
> doseGrid <- 1:80
> 
> ## and MCMC options:
> options <- McmcOptions()
> 
> ## the classic model would be:
> model <- LogisticLogNormal(mean = c(-0.85, 1),
+                            cov = matrix(c(1, -0.5, -0.5, 1), nrow = 2),
+                            refDose = 50)
> 
> nodata <- Data(doseGrid=doseGrid)
> 
> priorSamples <- mcmc(nodata, model, options)
> plot(priorSamples, model, nodata)
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 ‘Crossover-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot
> ### Title: Plots information about the search algorithm and its process.
> ### Aliases: plot plot,CrossoverSearchResult,missing-method
> 
> ### ** Examples
> 
> 
> ## Not run: 
> ##D x <- searchCrossOverDesign(s=9, p=5, v=4, model=4)
> ##D plot(x)
> ## End(Not run)
> 
> x <- searchCrossOverDesign(s=9, p=5, v=4, model=4, n=c(50,10), jumps=c(10, 10))
> plot(x, show.jumps=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 ‘Crossover.Rnw’ using knitr
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data

Attaching package: 'TH.data'

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

    geyser

Quitting from lines 23-29 (./childs/Search.Rnw) 
Quitting from lines NA-239 (./childs/Search.Rnw) 
Error: processing vignette 'Crossover.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Crossover.Rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CrossScreening-vignette.Rnw’ using knitr
Warning in wilcox.test.default(d.lead, alternative = "greater") :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(d.lead, alternative = "greater") :
  cannot compute exact p-value with zeroes
Quitting from lines 364-367 (CrossScreening-vignette.Rnw) 
Error: processing vignette 'CrossScreening-vignette.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘CrossScreening-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘CrossScreening-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘csp.Rmd’ using rmarkdown
Warning: Removed 1776 rows containing missing values (geom_path).
Quitting from lines 48-58 (csp.Rmd) 
Error: processing vignette 'csp.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘csp.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Cubist.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘cubist.Rmd’ using rmarkdown
Quitting from lines 127-129 (cubist.Rmd) 
Error: processing vignette 'cubist.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cubist.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lay_grid
> ### Title: Use Layout object with grid graphics.
> ### Aliases: lay_grid layGrid
> 
> ### ** Examples
> 
> 
> library(ggplot2)
> 
> l1 <- lay_new(matrix(1:2, ncol = 1), heights = c(2, 3))
> l2 <- lay_new(matrix(1:2, ncol = 1), heights = c(1, 3))
> l3 <- lay_bind_col(l1, l2)
> 
> pl1 <- qplot(mpg, wt, data = mtcars)
> pl2 <- qplot(mpg, gear, data = mtcars)
> pl3 <- qplot(cyl, gear, data = mtcars)
> pl4 <- qplot(qsec, am, data = mtcars)
> 
> lay_grid(list(pl1, pl2, pl3, pl4), l3)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: lay_grid ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Roadmap.Rmd’ using rmarkdown
--- finished re-building ‘Roadmap.Rmd’

--- re-building ‘customlayout-cookbook.Rmd’ using rmarkdown
Loading required package: MASS

Attaching package: 'cowplot'

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

    ggsave

Quitting from lines 30-86 (customlayout-cookbook.Rmd) 
Error: processing vignette 'customlayout-cookbook.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘customlayout-cookbook.Rmd’

--- re-building ‘layouts-for-officer-power-point-document.Rmd’ using rmarkdown
Quitting from lines 57-66 (layouts-for-officer-power-point-document.Rmd) 
Error: processing vignette 'layouts-for-officer-power-point-document.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘layouts-for-officer-power-point-document.Rmd’

SUMMARY: processing the following files failed:
  ‘customlayout-cookbook.Rmd’
  ‘layouts-for-officer-power-point-document.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HeatStruct
> ### Title: Structure Heatmap with Missing Value Demonstration
> ### Aliases: HeatStruct
> 
> ### ** Examples
> 
> data(hqmr.data)
> # use a subset of the hqmr.data
> # notice the gold chunks which represent missing values
> subdata <- hqmr.data[1000:1200, 1:30]
> HeatStruct(subdata)
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 ‘cutpointr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cutpoint
> ### Title: Extract the cutpoints from a ROC curve generated by cutpointr
> ### Aliases: cutpoint cutpoints
> 
> ### ** Examples
> 
> oc <- cutpointr(suicide, dsi, suicide, gender)
Assuming the positive class is yes
Assuming the positive class has higher x values
> plot_cutpointr(oc, cutpoint, accuracy)
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 ‘cutpointr.Rmd’ using rmarkdown
Quitting from lines 59-60 (cutpointr.Rmd) 
Error: processing vignette 'cutpointr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cutpointr.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘how_to_test_CVs.Rmd’ using rmarkdown
Quitting from lines 108-116 (how_to_test_CVs.Rmd) 
Error: processing vignette 'how_to_test_CVs.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘how_to_test_CVs.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cvxclust
> ### Title: Convex Clustering Path via Variable Splitting Methods
> ### Aliases: cvxclust
> 
> ### ** Examples
> 
> ## Clusterpaths for Mammal Dentition
> data(mammals)
> X <- as.matrix(mammals[,-1])
> X <- t(scale(X,center=TRUE,scale=FALSE))
> n <- ncol(X)
> 
> ## Pick some weights and a sequence of regularization parameters.
> k <- 5
> phi <- 0.5
> w <- kernel_weights(X,phi)
> w <- knn_weights(w,k,n)
> gamma <- seq(0.0,43, length.out=100)
> 
> ## Perform clustering
> sol <- cvxclust(X,w,gamma)
Warning in cvxclust_ama(X, Lambda, ix - 1, M1 - 1, M2 - 1, s1, s2, w[w >  :
  The stepsize nu may be too large. Setting it to maximum of 1/n and 1/AnM.
> 
> ## Plot the cluster path
> library(ggplot2)
> svdX <- svd(X)
> pc <- svdX$u[,1:2,drop=FALSE]
> pc.df <- as.data.frame(t(pc)%*%X)
> nGamma <- sol$nGamma
> df.paths <- data.frame(x=c(),y=c(), group=c())
> for (j in 1:nGamma) {
+   pcs <- t(pc)%*%sol$U[[j]]
+   x <- pcs[1,]
+   y <- pcs[2,]
+   df <- data.frame(x=pcs[1,], y=pcs[2,], group=1:n)
+   df.paths <- rbind(df.paths,df)
+ }
> X_data <- as.data.frame(t(X)%*%pc)
> colnames(X_data) <- c("x","y")
> X_data$Name <- mammals[,1]
> data_plot <- ggplot(data=df.paths,aes(x=x,y=y))
> data_plot <- data_plot + geom_path(aes(group=group),colour='grey30',alpha=0.5)
> data_plot <- data_plot + geom_text(data=X_data,aes(x=x,y=y,label=Name),
+   position=position_jitter(h=0.125,w=0.125))
> data_plot <- data_plot + geom_point(data=X_data,aes(x=x,y=y),size=1.5)
> data_plot <- data_plot + xlab('Principal Component 1') + ylab('Principal Component 2')
> data_plot + 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
Running examples in ‘cytofan-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_fan
> ### Title: Fan plots for trend and population visualizations
> ### Aliases: geom_fan stat_fan
> 
> ### ** Examples
> 
> # reformat dataset from short-wide to tall-skinny
> EuStockMarkets_ts <- lapply(colnames(EuStockMarkets),function(id) {
+   data.frame(id=id,value=as.numeric(EuStockMarkets[,id]))
+ })
> EuStockMarkets_ts <- do.call('rbind',EuStockMarkets_ts)
> 
> # plot the distribution of the different stock markets
> ggplot(EuStockMarkets_ts,aes(x=id,y=value))+
+   geom_fan()
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 ‘cytofan_flow_cytometry.Rmd’ using rmarkdown
Quitting from lines 78-84 (cytofan_flow_cytometry.Rmd) 
Error: processing vignette 'cytofan_flow_cytometry.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘cytofan_flow_cytometry.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CytomeTree
> ### Title: Binary tree algorithm for cytometry data analysis.
> ### Aliases: CytomeTree
> 
> ### ** Examples
> 
> head(DLBCL)
  FL1 FL2 FL4 label
1 416 251 293     2
2 210  93 184     2
3 387 300 233     2
4 403 438 288     2
5 399 128 116     2
6 538 288 189     2
> 
> # number of cell event
> N <- nrow(DLBCL)
> 
> # Cell events
> cellevents <- DLBCL[, c("FL1", "FL2", "FL4")]
> 
> 
> # Manual partitioning of the set N (from FlowCAP-I)
> manual_labels <- DLBCL[, "label"]
> 
> 
> # Build the binary tree
> Tree <- CytomeTree(cellevents, minleaf = 1, t=.1)

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================================| 100%
> 
> 
> # Retreive the resulting partition of the set N
> Tree_Partition <- Tree$labels
> 
> 
> # Plot node distributions
> par(mfrow=c(1, 2))
> plot_nodes(Tree)
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_nodes ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘autogating_cytometree.Rmd’ using rmarkdown
Loading required package: Rcpp
Quitting from lines 86-88 (autogating_cytometree.Rmd) 
Error: processing vignette 'autogating_cytometree.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘autogating_cytometree.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: errorsINx
> ### Title: Simulate data for straight line regression, with "errors in x".
> ### Aliases: errorsINx
> ### Keywords: datagen
> 
> ### ** Examples
> 
> library(lattice)
> errorsINx()
              Intercept Slope
No error in x      15.3 1.483
0.4sx              18.6 1.222
0.8sx              23.6 0.833
1.2sx              26.5 0.587
1.6sx              29.2 0.381
2sx                30.4 0.281
Error in unit(0.5 * shows, "strwidth", list(sep)) : 
  no string supplied for 'strwidth/height' unit
Calls: errorsINx ... strip -> do.call -> strip.default -> paste.and.draw -> unit
Execution halted
Running examples in ‘dabestr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dabest
> ### Title: Differences between Groups with Bootstrap Confidence Intervals
> ### Aliases: dabest
> 
> ### ** Examples
> 
> # Performing unpaired (two independent groups) analysis.
> unpaired_mean_diff <- dabest(iris, Species, Petal.Width,
+                              idx = c("setosa", "versicolor"),
+                              paired = FALSE)
Warning: Some components of ... were not used: ..1
> 
> # Display the results in a user-friendly format.
> unpaired_mean_diff
DABEST (Data Analysis with Bootstrap Estimation) v0.2.0
=======================================================

Variable: Petal.Width 

Unpaired mean difference of versicolor (n=50) minus setosa (n=50)
 1.08 [95CI  1.01; 1.14]


5000 bootstrap resamples.
All confidence intervals are bias-corrected and accelerated.

> 
> # Produce an estimation plot.
> plot(unpaired_mean_diff)
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 ‘bootstrap-confidence-intervals.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 72-106 (bootstrap-confidence-intervals.Rmd) 
Error: processing vignette 'bootstrap-confidence-intervals.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘bootstrap-confidence-intervals.Rmd’

--- re-building ‘robust-statistical-visualization.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 110-166 (robust-statistical-visualization.Rmd) 
Error: processing vignette 'robust-statistical-visualization.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘robust-statistical-visualization.Rmd’

--- re-building ‘using-dabestr.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 82-83 (using-dabestr.Rmd) 
Error: processing vignette 'using-dabestr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘using-dabestr.Rmd’

SUMMARY: processing the following files failed:
  ‘bootstrap-confidence-intervals.Rmd’
  ‘robust-statistical-visualization.Rmd’ ‘using-dabestr.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: designPlotlabels
> ### Title: Plots labels on a two-way grid using 'ggplot2'
> ### Aliases: designPlotlabels
> ### Keywords: aplot hplot design
> 
> ### ** Examples
> 
> Treatments <- factor(rep(1:6, times = 5))
> RCBD.lay <- designRandomize(allocated = Treatments,
+                             recipient = list(Blocks = 5, Units = 6),
+                             nested.recipients = list(Units = "Blocks"),
+                             seed = 74111)
> designPlotlabels(RCBD.lay, labels = "Treatments", 
+                  grid.x = "Units", grid.y = "Blocks",
+                  colour.column = "Treatments", size = 5)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: designPlotlabels ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘DALEX-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: model_feature_response
> ### Title: Marginal Response for a Single Variable
> ### Aliases: model_feature_response model_feature_response.explainer
> ###   model_feature_response.default
> 
> ### ** Examples
> 
> library("DALEX")
> 
> HR_glm_model <- glm(status == "fired" ~ ., data = HR, family = "binomial")
> explainer_glm <- explain(HR_glm_model, data = HR)
> expl_glm <- model_feature_response(explainer_glm, "age", "pdp")
> head(expl_glm)
         x         y var type label
1 20.00389 0.3690356 age  pdp    lm
2 20.80378 0.3688270 age  pdp    lm
3 21.60368 0.3686184 age  pdp    lm
4 22.40357 0.3684098 age  pdp    lm
5 23.20346 0.3682013 age  pdp    lm
6 24.00336 0.3679928 age  pdp    lm
> plot(expl_glm)
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 ‘dalmatian-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: traceplots
> ### Title: Traceplots (Generic)
> ### Aliases: traceplots
> 
> ### ** Examples
> 
> 
> ## Load output from previously run model
> load(system.file("Pied_Flycatchers_1","pfresults.RData",package="dalmatian"))
> 
> ## Generate traceplots
> pftraceplots <- traceplots(pfresults)
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: traceplots ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pied-flycatchers-1.Rmd’ using rmarkdown
Quitting from lines 133-142 (pied-flycatchers-1.Rmd) 
Error: processing vignette 'pied-flycatchers-1.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pied-flycatchers-1.Rmd’

--- re-building ‘pied-flycatchers-2.Rmd’ using rmarkdown
Quitting from lines 123-138 (pied-flycatchers-2.Rmd) 
Error: processing vignette 'pied-flycatchers-2.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pied-flycatchers-2.Rmd’

--- re-building ‘weights-1-simulate.Rmd’ using rmarkdown
Quitting from lines 36-71 (weights-1-simulate.Rmd) 
Error: processing vignette 'weights-1-simulate.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘weights-1-simulate.Rmd’

SUMMARY: processing the following files failed:
  ‘pied-flycatchers-1.Rmd’ ‘pied-flycatchers-2.Rmd’
  ‘weights-1-simulate.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dams.Rmd’ using rmarkdown
Loading required package: dams
Loading required package: ggplot2
Loading required package: maps
Loading required package: mapproj
Quitting from lines 74-75 (dams.Rmd) 
Error: processing vignette 'dams.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dams.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘IntroTutorial_dartR.Rmd’ using rmarkdown
Quitting from lines 936-938 (IntroTutorial_dartR.Rmd) 
Error: processing vignette 'IntroTutorial_dartR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘IntroTutorial_dartR.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dataexplorer-intro.Rmd’ using rmarkdown
Quitting from lines 115-116 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dataexplorer-intro.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending_dataMaid.Rmd’ using rmarkdown
Quitting from lines 526-527 (extending_dataMaid.Rmd) 
Error: processing vignette 'extending_dataMaid.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘extending_dataMaid.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: box_plots
> ### Title: Box plot data
> ### Aliases: box_plots
> ### Keywords: datasets
> 
> ### ** Examples
> 
> summary(box_plots)
      left              lines               normal          right       
 Min.   :-9.76964   Min.   :-9.769575   Min.   :-9.76   Min.   :-9.760  
 1st Qu.:-2.68999   1st Qu.:-2.689993   1st Qu.:-2.68   1st Qu.:-2.680  
 Median :-0.00999   Median :-0.007132   Median : 0.00   Median : 0.000  
 Mean   :-1.17780   Mean   :-0.831733   Mean   : 0.00   Mean   : 1.174  
 3rd Qu.: 2.67007   3rd Qu.: 2.670236   3rd Qu.: 2.68   3rd Qu.: 2.680  
 Max.   : 9.75025   Max.   : 9.756001   Max.   : 9.76   Max.   : 9.760  
     split          
 Min.   :-9.769886  
 1st Qu.:-2.689989  
 Median :-0.003099  
 Mean   :-0.003060  
 3rd Qu.: 2.680000  
 Max.   : 9.760000  
> 
> ## base plot
> 
> #save current settings
> state <- par("mar", "mfrow")
> 
> par(mfrow = c(5, 2), mar=c(1,2,2,1))
> 
> nms <- names(box_plots)
> 
> for (i in 1:5){
+   nm <- nms[i]
+   hist(box_plots[[nms[i]]],
+        breaks = 100,
+        main = nm)
+   boxplot(box_plots[[nms[i]]],
+           horizontal = TRUE)
+ }
> 
> 
> #reset settings
> par(state)
> 
> ## ggplot
> if(require(ggplot2)){
+   ggplot(box_plots, aes(x=left))+
+     geom_density()
+   ggplot(box_plots, aes(x=lines))+
+     geom_density()
+   ggplot(box_plots, aes(x=normal))+
+     geom_density()
+   ggplot(box_plots, aes(x=right))+
+     geom_density()
+   ggplot(box_plots, aes(x=split))+
+     geom_density()
+ }
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘Datasaurus.Rmd’ using rmarkdown
Quitting from lines 47-55 (Datasaurus.Rmd) 
Error: processing vignette 'Datasaurus.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Datasaurus.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ClassBoxplot
> ### Title: Creates Boxplot plot for all classes
> ### Aliases: ClassBoxplot
> 
> ### ** Examples
> 
> ## Don't show: 
> data(ITS)
> #clustering only for testing
> Classification=c(rep(1,8805),rep(2,2389))
> DataVisualizations::ClassBoxplot(ITS,Classification)
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 ‘DataVisualizations.Rmd’ using rmarkdown
Quitting from lines 40-43 (DataVisualizations.Rmd) 
Error: processing vignette 'DataVisualizations.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DataVisualizations.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘daymetr-vignette.Rmd’ using rmarkdown
Sitename set to default - tmp
Quitting from lines 85-92 (daymetr-vignette.Rmd) 
Error: processing vignette 'daymetr-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘daymetr-vignette.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot
> ### Title: ggplot methods to plot dbmss objects
> ### Aliases: autoplot.envelope
> 
> ### ** Examples
> 
> data(paracou16)
> # Keep only 20% of points to run this example
> X <- as.wmppp(rthin(paracou16, 0.2))
> 
> # Plot the envelope (should be 1000 simulations, reduced to 20 to save time)
> autoplot(KdEnvelope(X, ReferenceType="Q. Rosea", NumberOfSimulations=20))
Generating 20 simulations by evaluating expression  ...
1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,  20.

Done.
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 ‘dbparser.Rmd’ using rmarkdown
Quitting from lines 90-96 (dbparser.Rmd) 
Error: processing vignette 'dbparser.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dbparser.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dbplot_bar
> ### Title: Bar plot
> ### Aliases: dbplot_bar
> 
> ### ** Examples
> 
> 
> 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

> 
> # Returns a plot of the row count per am
> mtcars %>%
+   dbplot_bar(am)
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 ‘algorithm.Rmd’ using rmarkdown
--- finished re-building ‘algorithm.Rmd’

--- re-building ‘extend.Rmd’ using rmarkdown
Quitting from lines 205-213 (extend.Rmd) 
Error: processing vignette 'extend.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘extend.Rmd’

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

Attaching package: 'ddpcr'

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

    step

Reading data files into plate... DONE (1 seconds)
Initializing plate of type `custom_thresholds`... DONE (0 seconds)
Identifying outlier droplets... DONE (0 seconds)
Classifying droplets... DONE (0 seconds)
Analysis complete
Quitting from lines 134-152 (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’

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

SUMMARY: processing the following files failed:
  ‘extend.Rmd’ ‘overview.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.dea
> ### Title: Plot for DEA models.
> ### Aliases: plot.dea
> 
> ### ** Examples
> 
> data_example <- read_data(datadea = Fortune500,
+                           dmus = 1,
+                           inputs = 2:4, 
+                           outputs = 5:6)
> result <- model_basic(data_example)
> 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 ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MultiObjectiveDecisionAnalysisinR.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

Quitting from lines 125-129 (MultiObjectiveDecisionAnalysisinR.Rmd) 
Error: processing vignette 'MultiObjectiveDecisionAnalysisinR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘MultiObjectiveDecisionAnalysisinR.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ggcorplot
> ### Title: Correlation matrix
> ### Aliases: ggcorplot
> 
> ### ** Examples
> 
> data(mtcars)
> corr.mat1<-cor.matrix(variables=d(mpg,carb,carb+rnorm(length(carb))),,
+ 	 data=mtcars,
+ 	 test=cor.test,
+ 	 method='spearman',
+ 	alternative="two.sided",exact=FALSE)
> 	
> p<-ggcorplot(corr.mat1,data = mtcars)
> print(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: print ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘degenes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: deg
> ### Title: Detection of differentially expressed genes.
> ### Aliases: deg
> 
> ### ** Examples
> 
> X1 = matrix(rnorm(2000, 0, 1), 200, 10)
> X2 = matrix(rnorm(2000, 0, 1), 200, 10)
> index = sample(1:200, 5, replace=FALSE)
> X2[index,] = X2[index,] + 5
> D = deg(X1, X2)
Fri Mar 29 20:39:01 2019
Calculation of Z
Calculation of z
Calculation of the kernel estimator
Calculation of the kernel estimator
Determination of the rejection region
Error in if (integral > single.alpha) c1 <- c : 
  missing value where TRUE/FALSE needed
Calls: deg
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ODE_parameter_inference.Rmd’ using rmarkdown
Quitting from lines 115-125 (ODE_parameter_inference.Rmd) 
Error: processing vignette 'ODE_parameter_inference.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ODE_parameter_inference.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/deisotoper.Rcheck/00install.out’ for details.
Running examples in ‘DendroSync-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sync.plot
> ### Title: Plot within- and between-group synchrony
> ### Aliases: sync.plot
> 
> ### ** Examples
> 
> ## Plot homoscedastic narrow evaluation (mNE) and unstructured model (mUN)
>  # synchronies for conifersIP data:
>  data(conifersIP)
>      
>  ##Fit the homoscedastic set of varcov models (mBE, mNE, mCS, mUN)
>  # using geographic grouping criteria (ie. Region)
>  ModHm <- dendro.varcov(TRW ~ Code, varTime = "Year", varGroup = "Region", 
+                         data = conifersIP, homoscedastic = TRUE)
[1] "Please wait. I am fitting the models now :)"
>  
>  sync.plot(sync(ModHm, modname = "mNE"))
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: sync.plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘dendroTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: glimpse_daily_data
> ### Title: glimpse_daily_data
> ### Aliases: glimpse_daily_data
> 
> ### ** Examples
> 
> data("LJ_daily_temperatures")
> glimpse_daily_data(env_data = LJ_daily_temperatures, tidy_env_data = FALSE, na.color = "white")
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 ‘Examples_daily_response.Rmd’ using rmarkdown
Quitting from lines 36-43 (Examples_daily_response.Rmd) 
Error: processing vignette 'Examples_daily_response.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Examples_daily_response.Rmd’

--- re-building ‘compare_methods_vignette.Rmd’ using rmarkdown
Quitting from lines 53-55 (compare_methods_vignette.Rmd) 
Error: processing vignette 'compare_methods_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘compare_methods_vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘Examples_daily_response.Rmd’ ‘compare_methods_vignette.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDensityClust
> ### Title: Plot densityCluster results
> ### Aliases: plotDensityClust
> 
> ### ** Examples
> 
> data(iris)
> data.dist <- dist(iris[, 1:4])
> pca <- princomp(iris[, 1:4])
> 
> # Run initial density clustering
> dens.clust <- densityClust(data.dist)
Distance cutoff calculated to 0.2767655 
> op <- par(ask = TRUE)
> 
> # Show the decision graph
> plotDensityClust(dens.clust, type = "dg")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotDensityClust ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘DepthProc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DepthCurve-class
> ### Title: DepthCurve
> ### Aliases: DepthCurve-class
> 
> ### ** Examples
> 
> library(mvtnorm)
> x <- mvrnorm(n = 100, mu = c(0, 0), Sigma = 2 * diag(2))
> y <- rmvt(n = 100, sigma = diag(2), df = 4)
> s1 <- scaleCurve(x, depth_params = list(method = "Projection"))
> s2 <- scaleCurve(y, depth_params = list(method = "Projection"), name = "Set2")
> 
> sc_list <- combineDepthCurves(s1, s2) # Add one curve to another
> 
> plot(sc_list) # Draw plot with two curves
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 ‘DescribeDisplay-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_axis
> ### Title: Geom Axis.
> ### Aliases: geom_axis
> ### Keywords: internal
> 
> ### ** Examples
> 
> library(ggplot2)
> print(ggplot(dd_example("tour2d")))
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
Running examples in ‘descriptr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dist_binom_plot
> ### Title: Visualize binomial distribution
> ### Aliases: dist_binom_plot dist_binom_prob dist_binom_perc
> 
> ### ** Examples
> 
> # visualize binomial distribution
> dist_binom_plot(10, 0.3)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: dist_binom_plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘categorical-data.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 57-59 (categorical-data.Rmd) 
Error: processing vignette 'categorical-data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘categorical-data.Rmd’

--- re-building ‘continuous-data.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 84-86 (continuous-data.Rmd) 
Error: processing vignette 'continuous-data.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘continuous-data.Rmd’

--- re-building ‘visualization.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 46-47 (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 files failed:
  ‘categorical-data.Rmd’ ‘continuous-data.Rmd’ ‘visualization.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_DistributionRuns
> ### Title: Plot Distribution of runs
> ### Aliases: plot_DistributionRuns
> 
> ### ** Examples
> 
> # getting map and ped paths
> genotypeFile <- system.file("extdata", "Kijas2016_Sheep_subset.ped", package = "detectRUNS")
> mapFile <- system.file("extdata", "Kijas2016_Sheep_subset.map", package = "detectRUNS")
> 
> # calculating runs of Homozygosity
> ## Not run: 
> ##D # skipping runs calculation
> ##D runs <- slidingRUNS.run(genotypeFile, mapFile, windowSize = 15, threshold = 0.1,  minSNP = 15,
> ##D ROHet = FALSE,  maxOppositeGenotype = 1, maxMiss = 1,  minLengthBps = 100000,  minDensity = 1/10000)
> ## End(Not run)
> # loading pre-calculated data
> runsFile <- system.file("extdata", "Kijas2016_Sheep_subset.sliding.csv", package="detectRUNS")
> runsDF <- readExternalRuns(inputFile = runsFile, program = 'detectRUNS')
Loading file from detectRUNS
> 
> plot_InbreedingChr(runs = runsDF, mapFile = mapFile, style='All')
Total genome length: 290826950
calculating Froh chromosome by chromosome
Total genome length: 290826950
calculating Froh on all genome
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_InbreedingChr ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘batch-mode.Rmd’ using rmarkdown
--- finished re-building ‘batch-mode.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 48-66 (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
Found the following significant warnings:
  GetData.c:342:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
  GetData.c:355:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/DetSel.Rcheck/00install.out’ for details.
Running ‘test-that.R’ [98s/133s]
Running the tests in ‘tests/test-that.R’ failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  --- re-building ‘new.Rnw’ using Sweave
  --- finished re-building ‘new.Rnw’
  
  --- re-building ‘new.Rnw’ using Sweave
  --- finished re-building ‘new.Rnw’
  
  --- re-building ‘new.Rnw’ using Sweave
  --- finished re-building ‘new.Rnw’
  
  --- re-building ‘test.Rmd’ using knitr
  --- finished re-building ‘test.Rmd’
  
  --- re-building ‘test.Rmd’ using knitr
  --- finished re-building ‘test.Rmd’
  
  --- re-building ‘new.Rnw’ using Sweave
  --- finished re-building ‘new.Rnw’
  
  ── 1. Error: vignettes built on install (@test-vignettes.R#118)  ───────────────
  there is no package called 'testVignettesBuilt'
  1: vignette(package = "testVignettesBuilt") at testthat/test-vignettes.R:118
  2: tools::getVignetteInfo(package, lib.loc, all)
  3: find.package(package, lib.loc)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 41 SKIPPED: 11 FAILED: 1
  1. Error: vignettes built on install (@test-vignettes.R#118) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘multistage_fundamentals.Rmd’ using rmarkdown
Computing non-mst profile_tables over an mst design, did you mean to use profile_tables_mst?
Warning: Removed 33 rows containing missing values (geom_point).
Quitting from lines 282-313 (multistage_fundamentals.Rmd) 
Error: processing vignette 'multistage_fundamentals.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘multistage_fundamentals.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Equating.Rmd’ using rmarkdown
no column `person_id` provided, automatically generating unique person id's
Quitting from lines 116-130 (Equating.Rmd) 
Error: processing vignette 'Equating.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Equating.Rmd’

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

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

--- re-building ‘data_management.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: RSQLite
--- finished re-building ‘data_management.Rmd’

--- re-building ‘dexter.Rmd’ using rmarkdown
Loading required package: RSQLite
--- finished re-building ‘dexter.Rmd’

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_generate_timeDependence
> ### Title: 95% Coverage time dependence plots for dFCM
> ### Aliases: plot_generate_timeDependence
> 
> ### ** Examples
> 
> data(DynModel_results) # Load sample model result object
> scan.length <- DynModel_results$params$ntp_per_scan
> plot_generate_timeDependence(DynModel_results$est_CI[1], scan.length, rois=c(114,134))
Loading required namespace: ggplot2
[[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 ‘dfexplore-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dfexplore-package
> ### Title: Data-frame explorer
> ### Aliases: dfexplore-package dfexplore
> ### Keywords: package
> 
> ### ** Examples
> 
> dfplot(example_df)
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 ‘test_dfplot.R’ [1s/2s]
  Running ‘test_expand_dfmatrix.R’ [1s/1s]
  Running ‘test_simulate_dataframe.R’ [1s/1s]
Running the tests in ‘tests/test_dfplot.R’ failed.
Complete output:
  > library(dfexplore)
  Loading required package: ggplot2
  > #test_dfplot
  > data(example_df)
  > dfplot(example_df)
  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 ‘DFIT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotNcdif
> ### Title: Plot the item characteristic (expected score) curve for focal
> ###   and reference groups for the iiItem along with a representation of
> ###   the focal group density.
> ### Aliases: PlotNcdif
> 
> ### ** Examples
> 
> 
> data(dichotomousItemParameters)
> # # Non Uniform - != guess DIF item close to focal distribution
> PlotNcdif(iiItem = 46, itemParameters = dichotomousItemParameters, irtModel = "3pl",
+           plotDensity = FALSE, main = "Item 46 Non uniform and different guessing DIF. 3PL")
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 ‘Dforest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DF_easy
> ### Title: Simple pre-defined pipeline for Decision forest
> ### Aliases: DF_easy
> 
> ### ** Examples
> 
>   # data(demo_simple)
>   X = iris[,1:4]
>   Y = iris[,5]
>   names(Y)=rownames(X)
> 
>   random_seq=sample(nrow(X))
>   split_rate=3
>   split_sample = suppressWarnings(split(random_seq,1:split_rate))
>   Train_X = X[-random_seq[split_sample[[1]]],]
>   Train_Y = Y[-random_seq[split_sample[[1]]]]
>   Test_X = X[random_seq[split_sample[[1]]],]
>   Test_Y = Y[random_seq[split_sample[[1]]]]
> 
>   Result = DF_easy(Train_X, Train_Y, Test_X, Test_Y)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: DF_easy ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DGCA_basic.Rmd’ using rmarkdown

Classifying the differential correlation calls.
Calculating permutation number 1.
Calculating permutation number 2.
Calculating permutation number 3.
Calculating permutation number 4.
Calculating permutation number 5.
Calculating empirical p-values using the permutation sample statistics.
Sorting the combination of the actual and permuted test statistics.
Finding the proportion of each actual test statistic greater than the permuted test statistics.
Calculating qvalues from the empirical p-values.
Classifying the differential correlation calls.
Quitting from lines 65-67 (DGCA_basic.Rmd) 
Error: processing vignette 'DGCA_basic.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DGCA_basic.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: 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-patched-gcc/Work/PKGS/dggridR.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘dggridR.Rmd’ using rmarkdown
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: ggplot2
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

Quitting from lines 16-44 (dggridR.Rmd) 
Error: processing vignette 'dggridR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dggridR.Rmd’

--- re-building ‘dggrid_v62_manual.pdf.asis’ using asis
--- finished re-building ‘dggrid_v62_manual.pdf.asis’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: diagis
> ### Title: Auxiliary functions and diagnostic plots for importance sampling
> ### Aliases: diagis diagis-package
> 
> ### ** Examples
> 
> # simple importance sampling example
> # true distribution is a standard normal:
> p <- function(x) dnorm(x)
> # proposal distribution is normal with sd s
> q <- function(x, s) dnorm(x, 0, s)
> 
> # IS weights have finite variance only if s^2 > 1/2
> # variance is s/(2-1/s^2)^(3/2)
> 
> #optimal case
> set.seed(42)
> s_opt <- sqrt(2)
> x_opt <- rnorm(1000, sd = s_opt)
> w_opt <- p(x_opt) / q(x_opt, s_opt) 
> weighted_mean(x_opt, w_opt)
[1] -0.01223051
> weighted_var(x_opt, w_opt)
[1] 0.9954861
> s_inf <- 0.25
> x_inf <- rnorm(1000, sd = s_inf)
> w_inf <- p(x_inf) / q(x_inf, s_inf)
> weighted_mean(x_inf, w_inf) #!!
[1] 0.1281881
> weighted_var(x_inf, w_inf) #!!
[1] 0.2531165
> # diagnostic plots
> weight_plot(w_inf)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: weight_plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘diagis.Rmd’ using rmarkdown
Quitting from lines 73-74 (diagis.Rmd) 
Error: processing vignette 'diagis.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘diagis.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: graphs
> ### Title: Graphical Displays
> ### Aliases: graphs graph_cdf graph_delta_area graph_heatmap graph_tracking
> ###   graph_all
> 
> ### ** Examples
> 
> # Consensus clustering for 3 algorithms
> library(ggplot2)
> suppressWarnings(RNGversion("3.5.0"))
> set.seed(911)
> x <- matrix(rnorm(80), ncol = 10)
> CC1 <- consensus_cluster(x, nk = 2:4, reps = 3,
+ algorithms = c("hc", "pam", "km"), progress = FALSE)
> 
> # Plot CDF
> p <- graph_cdf(CC1)
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: graph_cdf ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘dief-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dief
> ### Title: Tools for Computing Diefficiency Metrics
> ### Aliases: dief
> ### Keywords: package
> 
> ### ** Examples
> 
> # This example uses the answer traces provided in the package.  
> # These traces record the answers produced by three approaches "Selective", 
> # "Not Adaptive", "Random"  when executing the test "Q9.sparql"
> data(traces)
> 	
> # Plot answer traces for test "Q9.sparql"
> plotAnswerTrace(traces, "Q9.sparql")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: plotAnswerTrace ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘dielectric-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AgPalik
> ### Title: AgPalik
> ### Aliases: AgPalik
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(AgPalik)
> str(AgPalik$raw())
'data.frame':	241 obs. of  4 variables:
 $ wavelength: num  0.155 0.207 0.248 0.275 0.31 ...
 $ epsilon   : cplx  1+0i 1+0i 1+0i ...
 $ real      : num  1 1 1 1 1.01 ...
 $ imag      : num  5.84e-06 1.68e-05 3.04e-05 4.42e-05 7.16e-05 ...
> AgPalik$comment
$source
[1] "Silver in the visible, Palik"

$units
[1] "nanometres"

> demo(AgPalik)


	demo(AgPalik)
	---- ~~~~~~~

> library(dielectric)

> library(ggplot2)

> data(AgPalik)

> AgPalik$set_span(200, 800)

> raw <- dielectric2plot(AgPalik$raw())

> silver <- AgPalik$predict(n=300, all.knots=TRUE, df=200)

> d <- dielectric2plot(silver)

> ggplot(d, aes(wavelength, value)) + geom_path() +
+   facet_grid(variable~., scales="free") +
+   geom_point(data=raw)
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: demo ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Running examples in ‘diffeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MAD
> ### Title: Mean Absolute Deviation (MAD)
> ### Aliases: MAD
> ### Keywords: spatial
> 
> ### ** Examples
> 
> old.par <- par(no.readonly = TRUE)
> grid1 <- raster(system.file("external/GRID1_INT.rst", package="diffeR"))
> grid2 <- raster(system.file("external/GRID2_INT.rst", package="diffeR"))
> strata <- raster(system.file("external/strata_int.rst", package="diffeR"))
> MAD(grid1, grid2, strata, eval="original")
[1] "The mean of grid1 is less than the mean of grid2"
  Resolution Quantity Strata Element Total
1          1      2.5      0       1   3.5
> MAD(grid1, grid2, strata, eval="multiple")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: MAD ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘dimRed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_R_NX
> ### Title: plot_R_NX
> ### Aliases: plot_R_NX
> 
> ### ** Examples
> 
> 
> ## define which methods to apply
> embed_methods <- c("Isomap", "PCA")
> ## load test data set
> data_set <- loadDataSet("3D S Curve", n = 200)
> ## apply dimensionality reduction
> data_emb <- lapply(embed_methods, function(x) embed(data_set, x))
2019-03-29 20:44:04: Isomap START
2019-03-29 20:44:04: constructing knn graph
2019-03-29 20:44:04: calculating geodesic distances
2019-03-29 20:44:04: Classical Scaling
> names(data_emb) <- embed_methods
> ## plot the R_NX curves:
> plot_R_NX(data_emb) +
+     ggplot2::theme(legend.title = ggplot2::element_blank(),
+                    legend.position = c(0.5, 0.1),
+                    legend.justification = c(0.5, 0.1))
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 ‘dint-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_date_xx
> ### Title: ggplot2 Scales For date_xx Objects
> ### Aliases: scale_date_xx scale_x_date_yq scale_y_date_yq scale_x_date_ym
> ###   scale_y_date_ym scale_x_date_yw scale_y_date_yw
> 
> ### ** Examples
> 
> if (require("ggplot2", quietly = TRUE)){
+ 
+ dd <- data.frame(date = seq(date_yq(2016, 1), date_yq(2018, 1)), V1 = 1:9)
+ p <- ggplot(dd, aes(x = date, y = V1)) +
+   geom_point()
+ 
+ p  # automatically uses the proper scale
+ p + scale_x_date_yq("quarters with default spacing")
+ p + scale_x_date_yq(breaks = date_yq_breaks(3))
+ 
+ 
+ # Different ways to specify breaks and labels
+ p <- ggplot(
+   data.frame(date = seq(date_yq(2012, 4), date_yq(2018, 4)), V1 = 1:25),
+   aes(x = date, y = V1)
+ ) +
+   geom_point()
+ 
+ p + scale_x_date_yq(labels = waiver()) + ggtitle("auto Labels")
+ p + scale_x_date_yq(labels = NULL) + ggtitle("no Labels")
+ p + scale_x_date_yq(labels = LETTERS[1:4]) + ggtitle("manual Labels")
+ p + scale_x_date_yq(labels = format_yq_iso) + ggtitle("function Labels")
+ 
+ p + scale_x_date_yq(breaks = waiver()) + ggtitle("auto breaks")
+ p + scale_x_date_yq(breaks = NULL) + ggtitle("no breaks")
+ p + scale_x_date_yq(breaks = date_yq(2013, 2:3) ) + ggtitle("manual breaks")
+ p + scale_x_date_yq(breaks = date_yq_breaks(1) ) + ggtitle("function breaks")
+ }
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/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dint)
  > 
  > test_check("dint")
  ── 1. Error: scale_date_xx works as expected (@test_scale_date_xx.R#17)  ───────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_silent(print(ggplot2::ggplot(tdf, ggplot2::aes(x = yq, y = vals)))) at testthat/test_scale_date_xx.R:17
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: print(ggplot2::ggplot(tdf, ggplot2::aes(x = yq, y = vals)))
  10: print.ggplot(ggplot2::ggplot(tdf, ggplot2::aes(x = yq, y = vals)))
  ...
  15: preDraw(x)
  16: preDraw.gTree(x)
  17: pushvpgp(x)
  18: pushgrobvp(x$vp)
  19: pushgrobvp.viewport(x$vp)
  20: pushViewport(vp, recording = FALSE)
  21: lapply(vps, push.vp, recording)
  22: FUN(X[[i]], ...)
  23: push.vp.viewport(X[[i]], ...)
  24: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1239 SKIPPED: 2 FAILED: 1
  1. Error: scale_date_xx works as expected (@test_scale_date_xx.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dint.Rmd’ using rmarkdown
Quitting from lines 254-287 (dint.Rmd) 
Error: processing vignette 'dint.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dint.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DirectEffects.Rmd’ using rmarkdown
Quitting from lines 150-165 (DirectEffects.Rmd) 
Error: processing vignette 'DirectEffects.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DirectEffects.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: direct.label
> ### Title: Direct labels for color decoding
> ### Aliases: direct.label directlabels
> 
> ### ** Examples
> 
> if(require(ggplot2)){
+   ## Add direct labels to a ggplot2 scatterplot, making sure that each
+   ## label is close to its point cloud, and doesn't overlap points or
+   ## other labels.
+   scatter <- qplot(jitter(hwy),jitter(cty),data=mpg,colour=class,
+                    main="Fuel efficiency depends on car size")
+   print(direct.label(scatter))
+ }
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: print ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘disclapmix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.disclapmixfit
> ### Title: Plot a disclapmixfit
> ### Aliases: plot.disclapmixfit
> ### Keywords: plot
> 
> ### ** Examples
> 
> 
> data(danes)
> db <- as.matrix(danes[rep(1:nrow(danes), danes$n), 1:(ncol(danes)-1)])
> fit <- disclapmix(db, clusters = 4L)
> plot(fit)
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
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 77-78 (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 ‘mixtures.Rmd’ using rmarkdown
--- finished re-building ‘mixtures.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotDisco
> ### Title: plots log2FC of the corresponding genes against each other
> ### Aliases: plotDisco
> 
> ### ** Examples
> 
> library(tmod)
For tmod user guide, type `tmodUserGuide()'
> data(tmod)
> data(orthologs)
> ds <- disco.score(orthologs)
> plotDisco(orthologs, ds, tmod$MODULES2GENES[["LI.M1.0"]])
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 ‘disto-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.disto
> ### Title: Plot a disto object
> ### Aliases: plot.disto
> 
> ### ** Examples
> 
> temp <- stats::dist(iris[,1:4])
> dio  <- disto(objectname = "temp")
> plot(dio, type = "heatmap")
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_disto.Rmd’ using rmarkdown
Quitting from lines 42-72 (vignette_disto.Rmd) 
Error: processing vignette 'vignette_disto.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘vignette_disto.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_dist
> ### Title: Plot predicted bamlss distribution families with ggplot2
> ### Aliases: plot_dist
> 
> ### ** Examples
> 
> # Generating data
> data_fam <- model_fam_data(fam_name = "BE")
> # Fit model
> library("gamlss")
Loading required package: splines
Loading required package: gamlss.data

Attaching package: ‘gamlss.data’

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

    sleep

Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
 **********   GAMLSS Version 5.1-3  ********** 
For more on GAMLSS look at http://www.gamlss.org/
Type gamlssNews() to see new features/changes/bug fixes.

> beta_model <- gamlss(BE ~ norm2 + binomial1,
+   data = data_fam, family = BE())
GAMLSS-RS iteration 1: Global Deviance = -1003.068 
GAMLSS-RS iteration 2: Global Deviance = -1016.132 
GAMLSS-RS iteration 3: Global Deviance = -1016.132 
> # Get 3 predictions
> pred_df <- data_fam[sample(1:nrow(data_fam), 3), c("norm2", "binomial1")]
> param_preds <- preds(beta_model, pred_df)
> # Create pdf, cdf plots
> plot_dist(beta_model, param_preds, rug = 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
Running examples in ‘DLMtool-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: matlenlim
> ### Title: Size limit management procedures
> ### Aliases: matlenlim matlenlim2 minlenLopt1 slotlim
> 
> ### ** Examples
> 
> matlenlim(1, DLMtool::Atlantic_mackerel, plot=TRUE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: matlenlim ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dlstats.Rmd’ using rmarkdown
Quitting from lines 46-53 (dlstats.Rmd) 
Error: processing vignette 'dlstats.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dlstats.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Xd
> ### Title: Model prediction function from data.frame
> ### Aliases: Xd
> 
> ### ** Examples
> 
> # Generate a data.frame and corresponding prediction function
> timesD <- seq(0, 2*pi, 0.5)
> mydata <- data.frame(name = "A", time = timesD, value = sin(timesD), 
+                      row.names = paste0("par", 1:length(timesD)))
> x <- Xd(mydata)
> 
> # Evaluate the prediction function at different time points
> times <- seq(0, 2*pi, 0.01)
> pouter <- structure(mydata$value, names = rownames(mydata))
> prediction <- x(times, pouter)
> plot(prediction)
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 ‘dMod.Rmd’ using rmarkdown
Loading required package: cOde

Attaching package: 'dMod'

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

    profile


Attaching package: 'dplyr'

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

    combine

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

    filter, lag

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

    intersect, setdiff, setequal, union

jakstat_8ccb23dc.c:6:15: warning: ISO C forbids zero-size array ‘forc’ [-Wpedantic]
 static double forc[0];
               ^~~~
jakstat_8ccb23dc.c:7:15: warning: ISO C forbids zero-size array ‘cons’ [-Wpedantic]
 static double cons[0];
               ^~~~
jakstat_8ccb23dc.c:8:15: warning: ‘range’ defined but not used [-Wunused-variable]
 static double range[2];
               ^~~~~
jakstat_8ccb23dc.c:7:15: warning: ‘cons’ defined but not used [-Wunused-variable]
 static double cons[0];
               ^~~~
jakstat_8ccb23dc_s.c:6:15: warning: ISO C forbids zero-size array ‘forc’ [-Wpedantic]
 static double forc[0];
               ^~~~
jakstat_8ccb23dc_s.c:7:15: warning: ISO C forbids zero-size array ‘cons’ [-Wpedantic]
 static double cons[0];
               ^~~~
jakstat_8ccb23dc_s.c:8:15: warning: ‘range’ defined but not used [-Wunused-variable]
 static double range[2];
               ^~~~~
jakstat_8ccb23dc_s.c:7:15: warning: ‘cons’ defined but not used [-Wunused-variable]
 static double cons[0];
               ^~~~
Quitting from lines 74-84 (dMod.Rmd) 
Error: processing vignette 'dMod.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dMod.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘linest-lsmeans.Rnw’ using knitr
Quitting from lines 329-333 (linest-lsmeans.Rnw) 
Error: processing vignette 'linest-lsmeans.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘linest-lsmeans.Rnw’

--- re-building ‘doBy.Rnw’ using Sweave
Warning in dir.create("figures") : ‘figures’ already exists
--- finished re-building ‘doBy.Rnw’

SUMMARY: processing the following file failed:
  ‘linest-lsmeans.Rnw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: put_gap
> ### Title: Insert a gap or whitespace in a document.
> ### Aliases: put_gap
> 
> ### ** Examples
> 
> put_gap()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: put_gap ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(docxtools)
  > 
  > test_check("docxtools")
  ── 1. Error: put_gap() attributes match expectations (@test_put.R#40)  ─────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: put_gap() at testthat/test_put.R:40
  2: print(p)
  3: print.ggplot(p)
  4: grid.draw(gtable)
  5: grid.draw.gTree(gtable)
  6: recordGraphics(drawGTree(x), list(x = x), getNamespace("grid"))
  7: drawGTree(x)
  8: preDraw(x)
  9: preDraw.gTree(x)
  10: pushvpgp(x)
  11: pushgrobvp(x$vp)
  12: pushgrobvp.viewport(x$vp)
  13: pushViewport(vp, recording = FALSE)
  14: lapply(vps, push.vp, recording)
  15: FUN(X[[i]], ...)
  16: push.vp.viewport(X[[i]], ...)
  17: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Error: put_gap() attributes match expectations (@test_put.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘doremi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.doremi
> ### Title: S3 method to plot DOREMI objects
> ### Aliases: plot.doremi
> 
> ### ** Examples
> 
> mydata <- generate.panel.remi(nind = 2,
+                            dampingtime = 10,
+                            amplitude = c(5,10),
+                            nexc = 2,
+                            duration = 20,
+                            deltatf = 2,
+                            tmax = 200,
+                            minspacing = 0,
+                            internoise = 0.2,
+                            intranoise = 0.1)
> myresult <- remi(data = mydata,
+                  id = "id",
+                  input = "excitation",
+                  time = "time",
+                  signal = "dampedsignal",
+                  embedding = 5)
> plot(myresult)
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-to-doremi.Rmd’ using rmarkdown
Quitting from lines 41-68 (Introduction-to-doremi.Rmd) 
Error: processing vignette 'Introduction-to-doremi.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Introduction-to-doremi.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_brackets
> ### Title: Add Labelled Brackets to Group Predictors in a Dot-and-Whisker
> ###   Plot
> ### Aliases: add_brackets
> 
> ### ** Examples
> 
> library(broom)
> 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(mtcars)
> m1 <- lm(mpg ~ wt + cyl + disp, data = mtcars)
> two_brackets <- list(c("Engine", "Cylinder", "Displacement"),
+                      c("Not Engine", "Intercept", "Weight"))
> 
> {dwplot(m1, show_intercept = TRUE) %>%
+        relabel_predictors("(Intercept)" = "Intercept",
+                           wt = "Weight",
+                           cyl = "Cylinder",
+                           disp = "Displacement") +
+        theme_bw() + xlab("Coefficient") + ylab("") +
+        theme(legend.position="none") +
+        geom_vline(xintercept = 0, colour = "grey50", linetype = 2)} %>%
+    add_brackets(two_brackets)
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 ‘dotwhisker-vignette.Rmd’ using rmarkdown
Loading required package: ggplot2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 23-33 (dotwhisker-vignette.Rmd) 
Error: processing vignette 'dotwhisker-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dotwhisker-vignette.Rmd’

--- re-building ‘kl2007_examples.Rmd’ using rmarkdown

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

Loading required package: ggplot2
Quitting from lines 73-92 (kl2007_examples.Rmd) 
Error: processing vignette 'kl2007_examples.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘kl2007_examples.Rmd’

SUMMARY: processing the following files failed:
  ‘dotwhisker-vignette.Rmd’ ‘kl2007_examples.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dpcr_density_table
> ### Title: Calculate Density of Multiple dPCR runs
> ### Aliases: dpcr_density_table
> ### Keywords: dplot hplot
> 
> ### ** Examples
> 
> dens <- dpcr_density_table(six_panels)
> 
> # create plot using ggplot2
> library(ggplot2)
> 
> ggplot(dens[["Experiment2.2"]], aes(x = x, y = y)) + 
+   geom_line() + 
+   geom_area(aes(fill = !(conf_up | conf_low))) +
+   scale_y_continuous("Density") +
+   scale_fill_discrete("0.95 CI")
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 284-293 (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
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/dpglasso.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘compatibility.Rmd’ using rmarkdown
--- finished re-building ‘compatibility.Rmd’

--- re-building ‘dplyr.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

`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 224-237 (dplyr.Rmd) 
Error: processing vignette 'dplyr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dplyr.Rmd’

--- re-building ‘programming.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 ‘programming.Rmd’

--- re-building ‘two-table.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 ‘two-table.Rmd’

--- re-building ‘window-functions.Rmd’ using rmarkdown
--- finished re-building ‘window-functions.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running examples in ‘dr4pl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dr4pl
> ### Title: Fitting 4 Parameter Logistic (4PL) models to dose-response data.
> ### Aliases: dr4pl dr4pl-package dr4pl.formula dr4pl.data.frame
> ###   dr4pl.default
> 
> ### ** Examples
> 
>   ##Assign method.init = "logistic" to use logistic method of estimation.
>   ##default method
>   a <- dr4pl(dose = sample_data_1$Dose,
+              response = sample_data_1$Response,
+              method.init = "logistic")
>   plot(a)
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous x-axis
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 ‘walk_through_in_R.Rmd’ using rmarkdown
Quitting from lines 33-38 (walk_through_in_R.Rmd) 
Error: processing vignette 'walk_through_in_R.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘walk_through_in_R.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: visW
> ### Title: Plot the estimates for the latent factors
> ### Aliases: visW
> 
> ### ** Examples
> 
> data("toydata")
> data("stanfit")
> codafit <- coda.obj(stanfit) ## convert to mcmc.list
> W.res <- visW(codafit, Y = toydata$Y.simul$Y, D = toydata$wlu$D,
+ chain = 1, factors = c(1, 2))
> 
> ## plot the results
> 
> data <- data.frame(time = rep(1:9, 2), W.res$res.W)
> ggplot2::ggplot() +
+   ggplot2::geom_step(data = data, ggplot2::aes(x = time, y = Estimation, colour = Factor)) +
+   ggplot2::geom_step(data = data, ggplot2::aes(x = time, y = Lower.est, colour = Factor),
+   linetype = "longdash") +
+   ggplot2::geom_step(data = data, ggplot2::aes(x = time, y = Upper.est, colour = Factor),
+   linetype = "longdash")
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 ‘DataSimulationandProjection.Rmd’ using rmarkdown
--- finished re-building ‘DataSimulationandProjection.Rmd’

--- re-building ‘DimensionReduction.Rmd’ using rmarkdown
Quitting from lines 68-78 (DimensionReduction.Rmd) 
Error: processing vignette 'DimensionReduction.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DimensionReduction.Rmd’

--- re-building ‘DrBats.Rmd’ using rmarkdown
Quitting from lines 163-169 (DrBats.Rmd) 
Error: processing vignette 'DrBats.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DrBats.Rmd’

--- re-building ‘ModelEvaluation.Rmd’ using rmarkdown
Quitting from lines 57-62 (ModelEvaluation.Rmd) 
Error: processing vignette 'ModelEvaluation.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ModelEvaluation.Rmd’

--- re-building ‘ModelFit.Rmd’ using rmarkdown
Quitting from lines 75-81 (ModelFit.Rmd) 
Error: processing vignette 'ModelFit.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ModelFit.Rmd’

SUMMARY: processing the following files failed:
  ‘DimensionReduction.Rmd’ ‘DrBats.Rmd’ ‘ModelEvaluation.Rmd’
  ‘ModelFit.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.scluminex
> ### Title: Plot method for the scluminex class
> ### Aliases: plot.scluminex
> 
> ### ** Examples
> 
> # Load data and estimate models
> data(ecdata)
> data(mfidata)
> 
> dat <- mfidata[mfidata$plate=="plate_1" & mfidata$analyte=="FGF",]
> 
> sdf <- data_selection(dat, ecdata)[[1]]
> sdf_luminex <- scluminex("plate_1",sdf$standard, sdf$background,
+ "SSl4", bkg="ignore", fmfi="mfi", verbose=FALSE)
> 
> # Plot standard curves
> plot(sdf_luminex, "sc")
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 ‘drLumi.rnw’ using knitr
Quitting from lines 405-410 (drLumi.rnw) 
Error: processing vignette 'drLumi.rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘drLumi.rnw’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘userGuide.Rmd’ using rmarkdown
Quitting from lines 159-163 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘userGuide.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DSAIDE)
  Loading required package: shiny
  Welcome to the DSAIDE package. Type dsaidemenu() to get started.
  > 
  > test_check("DSAIDE")
  ── 1. Error: generate_plots returns a plot (@test-generate_plots.R#8)  ─────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_is(DSAIDE::generate_plots(result), "ggplot") at testthat/test-generate_plots.R:8
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: DSAIDE::generate_plots(result)
  5: graphics::plot(pfinal)
  6: plot.ggplot(pfinal)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 1
  1. Error: generate_plots returns a plot (@test-generate_plots.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DSAIRM)
  Loading required package: shiny
  Welcome to the DSAIRM package. Type dsairmmenu() to get started.
  > 
  > test_check("DSAIRM")
  ── 1. Error: generate_plots returns a plot (@test-generate_plots.R#8)  ─────────
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: expect_is(DSAIRM::generate_plots(result), "ggplot") at testthat/test-generate_plots.R:8
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: DSAIRM::generate_plots(result)
  5: graphics::plot(pfinal)
  6: plot.ggplot(pfinal)
  7: ggplot_gtable(data)
  8: ggplot_gtable.ggplot_built(data)
  9: build_guides(plot$scales, plot$layers, plot$mapping, position, theme, plot$guides, 
         plot$labels)
  10: guides_gengrob(gdefs, theme)
  ...
  20: pushvpgp(x)
  21: pushgrobvp(x$vp)
  22: pushgrobvp.viewport(x$vp)
  23: pushViewport(vp, recording = FALSE)
  24: lapply(vps, push.vp, recording)
  25: FUN(X[[i]], ...)
  26: push.vp.vpTree(X[[i]], ...)
  27: push.vp(vp$parent, recording)
  28: push.vp.viewport(vp$parent, recording)
  29: grid.Call.graphics(C_setviewport, vp, TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 15 SKIPPED: 0 FAILED: 1
  1. Error: generate_plots returns a plot (@test-generate_plots.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘dsa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: daily_sim
> ### Title: Create a simple, exemplary, seasonal, daily time series
> ### Aliases: daily_sim
> 
> ### ** Examples
> 
> time_series <- daily_sim(n=4, year_effect=3)
> xtsplot(time_series[,1], font="sans") # Plot of the time series
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 ‘dslabs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ds_theme_set
> ### Title: dslabs theme set
> ### Aliases: ds_theme_set
> 
> ### ** Examples
> 
> library(ggplot2)
> ds_theme_set()
> qplot(hp, mpg, data=mtcars, color=am, facets=gear~cyl, 
+ main="Scatterplots of MPG vs. Horsepower", 
+ xlab="Horsepower", ylab="Miles per Gallon")
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 ‘dslice.Rnw’ using Sweave
Loading required package: Rcpp
Loading required package: ggplot2
Loading required package: scales
Error: processing vignette 'dslice.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dslice.Rnw’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rtDescriptives
> ### Title: Descriptives of reaction time data
> ### Aliases: rtDescriptives
> 
> ### ** Examples
> 
> tt <- seq(0, 5, .01)
> pars <- matrix(.5, 5, 2)
> pars[1, ] <- 1
> pars[2, ] <- c(0, 2)
> dat <- simData(n = 3e3, pars = pars, tt = tt, pdfND = dbeta(tt, 10, 30))
> x <- rtDescriptives(data = dat)
  Condition Response Pairs 
  Prop                Counts
      lower     upper lower upper
1 0.4993333 0.5006667   749   751
2 0.1453333 0.8546667   218  1282
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: rtDescriptives ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running ‘testthat.R’ [6s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(DstarM)
  > 
  > test_check("DstarM")
  ── 1. Failure: rtDescriptives works (@test-simulate.R#113)  ────────────────────
  print(rtDescriptives) threw an error.
  Message: VECTOR_ELT() can only be applied to a 'list', not a 'double'
  Class:   simpleError/error/condition
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 23 SKIPPED: 1 FAILED: 1
  1. Failure: rtDescriptives works (@test-simulate.R#113) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘parallelization-considerations.Rmd’ using rmarkdown
--- finished re-building ‘parallelization-considerations.Rmd’

--- re-building ‘timing-experiments.Rmd’ using rmarkdown
Quitting from lines 160-173 (timing-experiments.Rmd) 
Error: processing vignette 'timing-experiments.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘timing-experiments.Rmd’

--- re-building ‘dtwclust.Rnw’ using knitr_notangle
Quitting from lines 1689-1691 (dtwclust.Rnw) 
Error: processing vignette 'dtwclust.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dtwclust.Rnw’

SUMMARY: processing the following files failed:
  ‘timing-experiments.Rmd’ ‘dtwclust.Rnw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DVHmetrics-package
> ### Title: Analyze Dose-Volume Histograms and Check Constraints
> ### Aliases: DVHmetrics-package DVHmetrics
> ### Keywords: package
> 
> ### ** Examples
> 
> showDVH(dataMZ[[1]])
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: showDVH ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘DVHmetrics.Rnw’ using knitr
Warning in getVolume(pm$valRefNum, type = "absolute", unitRef = pm$unitRef,  :
  max dose is less than requested dose
Warning in getVolume(pm$valRefNum, type = "absolute", unitRef = pm$unitRef,  :
  max dose is less than requested dose
Warning in getVolume(pm$valRefNum, type = "absolute", unitRef = pm$unitRef,  :
  max dose is less than requested dose
Warning in getVolume(pm$valRefNum, type = "absolute", unitRef = pm$unitRef,  :
  max dose is less than requested dose
Quitting from lines 411-412 (DVHmetrics.Rnw) 
Error: processing vignette 'DVHmetrics.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘DVHmetrics.Rnw’

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

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

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

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 110-117 (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
Error(s) in re-building vignettes:
  ...
--- re-building ‘TutorialdynRB.Rmd’ using rmarkdown
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-4
'nperm' >= set of all permutations: complete enumeration.
Set of permutations < 'minperm'. Generating entire set.
Quitting from lines 134-143 (TutorialdynRB.Rmd) 
Error: processing vignette 'TutorialdynRB.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘TutorialdynRB.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘dynsim-overview.Rnw’ using knitr

Lagging invest by 1 time units.

Quitting from lines 263-267 (dynsim-overview.Rnw) 
Error: processing vignette 'dynsim-overview.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘dynsim-overview.Rnw’

SUMMARY: processing the following file failed:
  ‘dynsim-overview.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘functionality.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 94-110 (functionality.Rmd) 
Error: processing vignette 'functionality.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘functionality.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dzexpm
> ### Title: The estimation and prediction function for the skewed spatial
> ###   processes
> ### Aliases: dzexpm
> 
> ### ** Examples
> 
>   real<- as.matrix(do.call(cbind, MaxTemp03))
>   n_ful<- nrow(real)
>   y_ful<- real[,2]
>   x_ful<- real[,7]
>   x_ful<- log(x_ful)
>   x_ful<- scale(x_ful)
>   u1<- real[,3]
>   u2<- real[,4]
>   theta<- 2/150000
>   n<- 56
>   p<- 0.1
>  dzexpm(y_ful, x_ful, n_ful, n, u1, u2, theta, p, 50, 20)
Error in chol.default(Cpred) : 
  the leading minor of order 19 is not positive definite
Calls: dzexpm -> t -> chol -> chol.default
Execution halted
Running examples in ‘earlywarnings-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PlotPotential
> ### Title: Description: Plot Potential
> ### Aliases: PlotPotential
> ### Keywords: early-warning
> 
> ### ** Examples
> 
> X = c(rnorm(1000, mean = 0), rnorm(1000, mean = -2), rnorm(1000, mean = 2)); 
> param = seq(0,5,length=3000); res <- movpotential_ews(X, param); 
> PlotPotential(res$res, title = '', xlab.text = '', ylab.text = '', 
+ cutoff = 0.5, plot.contours = TRUE, binwidth = 0.2)
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
Running examples in ‘easyalluvial-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: alluvial_long
> ### Title: alluvial plot of data in long format
> ### Aliases: alluvial_long
> 
> ### ** Examples
> 
> 
> 
>  data = quarterly_flights
> 
>  alluvial_long( data, key = qu, value = mean_arr_delay, id = tailnum, fill_by = 'last_variable' )
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 ‘ebayesthresh.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 49-60 (ebayesthresh.Rmd) 
Error: processing vignette 'ebayesthresh.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ebayesthresh.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ecb_sdw.Rmd’ using rmarkdown
Warning: Removed 28 rows containing non-finite values (stat_smooth).
Warning: Removed 28 rows containing missing values (geom_point).
Quitting from lines 163-178 (ecb_sdw.Rmd) 
Error: processing vignette 'ecb_sdw.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ecb_sdw.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘echo-vignette.Rmd’ using rmarkdown
Quitting from lines 49-98 (echo-vignette.Rmd) 
Error: processing vignette 'echo-vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘echo-vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘eclust.Rmd’ using rmarkdown
See example usage at http://sahirbhatnagar.com/eclust/
Quitting from lines 470-471 (eclust.Rmd) 
Error: processing vignette 'eclust.Rmd' failed with diagnostics:
`heatmap_width` and `width` should not all be the absolute units.
--- failed re-building ‘eclust.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coalesc
> ### Title: Coalescent-based simulation of ecological communities undergoing
> ###   both neutral and niche-base dynamics
> ### Aliases: coalesc
> ### Keywords: coalescent neutral dynamics niche-based dynamics
> 
> ### ** Examples
> 
> # Simulation of a neutral community including 100 individuals
> J <- 500; theta <- 50; m <- 0.1
> comm1 <- coalesc(J, m, theta) 
> # Regional and local trait distributions
> plot_comm(comm1)
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 ‘Barro_Colorado.Rmd’ using rmarkdown
--- finished re-building ‘Barro_Colorado.Rmd’

--- re-building ‘coalesc_vignette.Rmd’ using rmarkdown
Quitting from lines 112-121 (coalesc_vignette.Rmd) 
Error: processing vignette 'coalesc_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘coalesc_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 36-42 (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 ‘EDA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EDA
> ### Title: Energy consumption analysis for calculating carbon emission
> ###   changes
> ### Aliases: EDA print.EDA plot.EDA
> 
> ### ** Examples
> 
> library(EDA)
> data(carbon)
> data(factordata)
> ## set parameters
> cdata <- carbon[,-c(1,2)]
> Year <- 2001:2005
> Sector <- c("b1", "b2", "b3")
> Fuel <- colnames(cdata)
> Factor <- names(factordata)
> ## run EDA model
> eda1 <- EDA(cdata, factordata, Year = Year, Factor = Factor, 
+     Fuel = Fuel, Sector = Sector, method = "LMDI")
> eda1
Annual changes:
  Year    Change
1 2002  43054129
2 2003  99178362
3 2004 117880293
4 2005  94842144
Total change:  354954928> plot(eda1)
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 ‘EDA.Rmd’ using rmarkdown
Quitting from lines 116-129 (EDA.Rmd) 
Error: processing vignette 'EDA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘EDA.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_imp
> ### Title: Plot variable importance from random forests
> ### Aliases: plot_imp
> 
> ### ** Examples
> 
> library(randomForest)
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
> data(iris)
> fit = randomForest(Species ~ ., iris)
> imp = variable_importance(fit, nperm = 2, data = iris)
> plot_imp(imp)
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 ‘filters.Rmd’ using rmarkdown
--- finished re-building ‘filters.Rmd’

--- re-building ‘metrics.Rmd’ using rmarkdown
Quitting from lines 41-44 (metrics.Rmd) 
Error: processing vignette 'metrics.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘metrics.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘edfReaderVignette.Rmd’ using rmarkdown
Quitting from lines 434-470 (edfReaderVignette.Rmd) 
Error: processing vignette 'edfReaderVignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘edfReaderVignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘edgarWebR.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 109-112 (edgarWebR.Rmd) 
Error: processing vignette 'edgarWebR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘edgarWebR.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘eechidna-intro.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 86-105 (eechidna-intro.Rmd) 
Error: processing vignette 'eechidna-intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘eechidna-intro.Rmd’

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

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

--- re-building ‘vignette.Rmd’ using knitr
Quitting from lines 103-111 (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
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 81-114 (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 ‘eeptools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: autoplot.lm
> ### Title: A function to replicate the basic plot function for linear
> ###   models in ggplot2
> ### Aliases: autoplot.lm
> 
> ### ** Examples
> 
> # Univariate
> a <- runif(1000)
> b <- 7 * a + rnorm(1)
> mymod <- lm(b~a)
> autoplot(mymod)
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 ‘test-all.R’ [10s/11s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  ── 1. Error: Autoplot works as expected for linear models (@test-plots.R#12)  ──
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
  1: autoplot(mymod) at testthat/test-plots.R:12
  2: autoplot.lm(mymod)
  3: print(plots[[i]], vp = grid::viewport(layout.pos.row = mypos[j, ][1], layout.pos.col = mypos[j, 
         ][2]))
  4: print.ggplot(plots[[i]], vp = grid::viewport(layout.pos.row = mypos[j, ][1], layout.pos.col = mypos[j, 
         ][2]))
  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: 516 SKIPPED: 0 FAILED: 1
  1. Error: Autoplot works as expected for linear models (@test-plots.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 170-173 (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’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calendar_plot
> ### Title: Create calendar plot
> ### Aliases: calendar_plot
> 
> ### ** Examples
> 
> testdat <- sim_exposure(n = 1000, central = 0.1,
+            exposure_type = "binary")
> testdat$x[c(89,101,367,500,502,598,678,700,895)] <- 3
> calendar_plot(testdat, type = "discrete", labels = c("no", "yes", "maybe"))
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 ‘eesim.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

This is dlnm 2.3.9. For details: help(dlnm) and vignette('dlnmOverview').
Quitting from lines 35-50 (eesim.Rmd) 
Error: processing vignette 'eesim.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘eesim.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: conditionalEffectsPlot
> ### Title: Plot conditional effects
> ### Aliases: conditionalEffectsPlot
> 
> ### ** Examples
> 
> m1 <- effectLite(y="dv", x="x", k="k1", z="z1", control="control", data=example01)
> conditionalEffectsPlot(m1, zsel="z1", gxsel="g1", colour="k1")
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 ‘ega-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotClarkeGrid
> ### Title: Plot a Clarke Error Grid
> ### Aliases: plotClarkeGrid
> 
> ### ** Examples
> 
> library(ggplot2)
> 
> # default
> plotClarkeGrid(glucose_data$ref, glucose_data$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 ‘ega.Rmd’ using rmarkdown
Quitting from lines 26-30 (ega.Rmd) 
Error: processing vignette 'ega.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ega.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: expose_layout
> ### Title: expose_layout
> ### Aliases: expose_layout
> 
> ### ** Examples
> 
> p1 <- qplot(mpg, wt, data=mtcars, colour=cyl)
> p2 <- qplot(mpg, data = mtcars) + ggtitle('title')
> p3 <- qplot(mpg, data = mtcars, geom = 'dotplot')
> p4 <- p1 + facet_wrap(~carb, nrow=1) + theme(legend.position='none') +
+   ggtitle('facetted plot')
> pl <- lapply(list(p1,p2, p3, p4), expose_layout, FALSE, FALSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: lapply ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Ecosystem.Rmd’ using rmarkdown
Loading required package: ggplot2
Quitting from lines 38-54 (Ecosystem.Rmd) 
Error: processing vignette 'Ecosystem.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘Ecosystem.Rmd’

--- re-building ‘Overview.Rmd’ using rmarkdown
Loading required package: gridExtra
Loading required package: ggplot2
Quitting from lines 33-46 (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:
  ‘Ecosystem.Rmd’ ‘Overview.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_ego_tergm
> ### Title: Function to plot role assignments.
> ### Aliases: plot_ego_tergm
> ### Keywords: assignments interpretation plot summary
> 
> ### ** Examples
> 
> plots <- plot_ego_tergm(ego_tergm_fit = ego_tergm_fit)
> plots[[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 examples in ‘EleChemr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CV
> ### Title: Cyclic voltammetry digitial simulation
> ### Aliases: CV
> 
> ### ** Examples
> 
> CV(Co = 0.001, DerApprox = 2, errCheck = FALSE, Method = "Euler")
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 ‘emil-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: learning_curve
> ### Title: Learning curve analysis
> ### Aliases: learning_curve
> 
> ### ** Examples
> 
> options(emil_max_indent=3)
> lc <- learning_curve(c(Linear="lda", Quadratic="qda"),
+                      iris[-5], iris$Species, test_fraction=c(.7, .5, .3))
29 Mar 20:56  Learning curve analysis
29 Mar 20:56    Test set test_fraction 1 of 3 (0.7)
29 Mar 20:56      Evaluating modeling performance...
29 Mar 20:56    Test set test_fraction 2 of 3 (0.5)
29 Mar 20:56      Evaluating modeling performance...
29 Mar 20:56    Test set test_fraction 3 of 3 (0.3)
29 Mar 20:56      Evaluating modeling performance...
> plot(lc)
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 ‘testthat.R’ [14s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.9.1") {
  +   library(testthat)
  +   test_check("emil")
  + }
  Loading required package: emil
  
  Attaching package: 'emil'
  
  The following object is masked from 'package:base':
  
      mode
  
  ── 1. Failure: k-NN imputation (@test-preprocess.r#30)  ────────────────────────
  sets$test$x[na.ind] not equivalent to ifelse(na.ind[, 2] <= 3, 5, 4.5).
  3/10 mismatches (average diff: 0.5)
  [5]  5 - 4.5 == 0.5
  [7]  5 - 4.5 == 0.5
  [10] 5 - 4.5 == 0.5
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 183 SKIPPED: 1 FAILED: 1
  1. Failure: k-NN imputation (@test-preprocess.r#30) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘emmeans-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: auto.noise
> ### Title: Auto Pollution Filter Noise
> ### Aliases: auto.noise
> ### Keywords: datasets
> 
> ### ** Examples
> 
> noise.lm <- lm(noise ~ size * type * side, data = auto.noise)
> 
> # Interaction plot of predictions
> emmip(noise.lm, type ~ size | side)
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 ‘EMMIXmfa-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: factor_scores
> ### Title: Computes Factor Scores
> ### Aliases: factor_scores factor_scores.mcfa factor_scores.mctfa
> ###   plot.emmix
> ### Keywords: cluster multivariate models
> 
> ### ** Examples
> 
> # Fit a MCFA model to a subset
> set.seed(1)
> samp_size <- dim(iris)[1]
> sel_subset <- sample(1 : samp_size, 50)
> model <- mcfa(iris[sel_subset, -5], g = 3, q = 2, 
+                           nkmeans = 1, nrandom = 0, itmax = 100)

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |......................................................................| 100%
> 
> # plot the data points in the factor space
> plot(model)
> 
> # Allocating new samples to the clusters
> Y <- iris[-c(sel_subset), -5]
> Y <- as.matrix(Y)
> clust <- predict(model, Y)
> 
> fa_scores <- factor_scores(model, Y)
> # Visualizing new data in factor space
> plot_factors(fa_scores, type = "Umean", clust = clust)
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_factors ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘emojifont.Rmd’ using rmarkdown
Quitting from lines 102-109 (emojifont.Rmd) 
Error: processing vignette 'emojifont.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘emojifont.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCalibration
> ### Title: Create a calibration plot
> ### Aliases: plotCalibration
> 
> ### ** Examples
> 
> data(sccs)
> negatives <- sccs[sccs$groundTruth == 0, ]
> plotCalibration(negatives$logRr, negatives$seLogRr)
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 ‘EmpiricalCiCalibrationVignette.Rmd’ using rmarkdown
Quitting from lines 68-70 (EmpiricalCiCalibrationVignette.Rmd) 
Error: processing vignette 'EmpiricalCiCalibrationVignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘EmpiricalCiCalibrationVignette.Rmd’

--- re-building ‘EmpiricalPCalibrationVignette.Rmd’ using rmarkdown
Quitting from lines 52-53 (EmpiricalPCalibrationVignette.Rmd) 
Error: processing vignette 'EmpiricalPCalibrationVignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘EmpiricalPCalibrationVignette.Rmd’

SUMMARY: processing the following files failed:
  ‘EmpiricalCiCalibrationVignette.Rmd’
  ‘EmpiricalPCalibrationVignette.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_MST
> ### Title: Euclidean Minimum Spanning Tree Stat Function
> ### Aliases: stat_MST
> 
> ### ** Examples
> 
> 
> ## 2D artificial data:
> set.seed(1984)
> n <- 15
> c1 <- data.frame(x = rnorm(n, -0.2, sd = 0.2), y = rnorm(n, -2, sd = 0.2))
> c2 <- data.frame(x = rnorm(n, -1.1, sd = 0.15), y = rnorm(n, -2, sd = 0.3)) 
> d <- rbind(c1, c2)
> d <- as.data.frame(d)
> 
> ## MST:
> out <- ComputeMST(d)
18 edges found so far.
482 cumulative base cases.
4 cumulative node combinations scored.
25 edges found so far.
891 cumulative base cases.
8 cumulative node combinations scored.
29 edges found so far.
1224 cumulative base cases.
12 cumulative node combinations scored.
Total spanning tree length: 11.6963
> 
> #1) simple plot
> library(ggplot2)
> ggplot(data = out, 
+     aes(x = x, y = y, 
+     from = from, to = to))+ 
+     geom_point()+
+     stat_MST(colour = "red", linetype = 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 ‘EQL.Rmd’ using rmarkdown

Attaching package: 'emuR'

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

    norm

--- finished re-building ‘EQL.Rmd’

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

Attaching package: 'emuR'

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

    norm

Warning: call dbDisconnect() when finished working with a connection
--- finished re-building ‘emuDB.Rmd’

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

Attaching package: 'emuR'

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

    norm

Quitting from lines 262-275 (emuR_intro.Rmd) 
Error: processing vignette 'emuR_intro.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘emuR_intro.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cv.enpls
> ### Title: Cross Validation for Ensemble Partial Least Squares Regression
> ### Aliases: cv.enpls
> 
> ### ** Examples
> 
> data("alkanes")
> x = alkanes$x
> y = alkanes$y
> 
> set.seed(42)
> cvfit = cv.enpls(x, y, reptimes = 10)
Beginning fold 1 
Beginning fold 2 
Beginning fold 3 
Beginning fold 4 
Beginning fold 5 
> print(cvfit)
Cross Validation Result for Ensemble Partial Least Squares
---
RMSE = 3.6481
MAE = 2.515792
Rsquare = 0.999961
> plot(cvfit)
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 ‘enpls.Rmd’ using rmarkdown
Quitting from lines 62-73 (enpls.Rmd) 
Error: processing vignette 'enpls.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘enpls.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GLMs.Rmd’ using rmarkdown
Quitting from lines 50-69 (GLMs.Rmd) 
Error: processing vignette 'GLMs.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘GLMs.Rmd’

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

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

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lambda_alpha_grid
> ### Title: Lambda Alpha Grid
> ### Aliases: lambda_alpha_grid
> 
> ### ** Examples
> 
> 
> data(tbi)
> Xmat <- model.matrix( ~ . - injury1 - injury2 - injury3 - 1, data = tbi)
> Yvec <- matrix(tbi$injury1, ncol = 1)
> alphas <- seq(0, 1, length = 20)
> 
> lga <- lambda_alpha_grid(alphas = alphas, lambdas = lambda_max(Yvec, Xmat, alpha = alphas))
> 
> ggplot2::ggplot() +
+   ggplot2::theme_bw() +
+   ggplot2::aes_string(x = "a", y = "log10(l)") +
+   ggplot2::geom_path(data = lga$top) +
+   ggplot2::geom_point(data = lga$lgrid,
+                       mapping = ggplot2::aes(color = cos(a) + sin(log10(l)))) +
+   ggplot2::geom_contour(data = lga$lgrid,
+                         mapping = ggplot2::aes(z = cos(a) + sin(log10(l)))) +
+   ggplot2::scale_color_gradient2(low = "blue", high = "red", mid = "grey")
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 ‘envalysis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: theme_publish
> ### Title: ggplot2 theme for scientific publications
> ### Aliases: theme_publish
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
> p <- ggplot(mtcars) + geom_point(aes(x = wt, y = mpg,
+      colour=factor(gear))) + facet_wrap( ~ am)
> 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: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘texture.Rmd’ using rmarkdown
--- finished re-building ‘texture.Rmd’

--- re-building ‘theme_publish.Rmd’ using rmarkdown
Loading required package: envalysis
Loading required package: ggplot2
Quitting from lines 29-35 (theme_publish.Rmd) 
Error: processing vignette 'theme_publish.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘theme_publish.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  main.c:334:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:575:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:518:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:805:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:755:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1034:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:983:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1377:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1279:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1678:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1962:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1912:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2316:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2212:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/enviPat.Rcheck/00install.out’ for details.
Running examples in ‘EnvStats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_stripchart
> ### Title: 1-D Scatter Plots with Confidence Intervals Using ggplot2
> ### Aliases: geom_stripchart
> ### Keywords: hplot htest
> 
> ### ** Examples
> 
> 
>   # First, load and attach the ggplot2 package.
>   #--------------------------------------------
> 
>   library(ggplot2)
> 
>   #==========
> 
>   #---------------------
>   # 3 Independent Groups
>   #---------------------
> 
>   # Example 1:
> 
>   # Using the built-in data frame mtcars, 
>   # create a stipchart of miles per gallon vs. number of cylinders
>   # using different colors for each level of the number of cylinders.
>   #------------------------------------------------------------------
> 
>   p <- ggplot(mtcars, aes(x = factor(cyl), y = mpg, color = factor(cyl))) 
> 
>   p + geom_stripchart() + 
+     labs(x = "Number of Cylinders", y = "Miles per Gallon")
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:
  epanet.c:999:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1000:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1492:3: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2308:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2309:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:454:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:455:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input3.c:604:2: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/epanet2toolkit.Rcheck/00install.out’ for details.
Running examples in ‘EpiCurve-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EpiCurve
> ### Title: Plot an Epidemic Curve
> ### Aliases: EpiCurve
> 
> ### ** Examples
> 
> # library(Epicurve)
> date <- seq(as.timeDate("2017-05-10 21:35:22"), as.timeDate("2017-05-12 06:15:12"), by="12 min")
> val <- rep(1, length(date))
> tri <- rep(c("Alive", "Died","Unknown"), length.out=length(date))
> DF <- data.frame(date, val, tri)
> names(DF) <- c("date","value", "tri")
> 
> 
> EpiCurve(DF,
+          date = "date",
+          freq = "value",
+          period = "hour",
+          split = 4,
+          cutvar = "tri",
+          ylabel="Number of cases",
+          xlabel= "From 2017-05-10 21:35:22 To 2017-05-12 06:15:12",
+          title = "Epidemic Curve")
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 ‘EpiCurve.Rmd’ using rmarkdown
Loading required package: ggplot2
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: ISOweek
Loading required package: scales
Quitting from lines 132-137 (EpiCurve.Rmd) 
Error: processing vignette 'EpiCurve.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘EpiCurve.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MultiStrainPartialImmunity
> ### Title: Partial immunity model that cycles (P 4.2).
> ### Aliases: MultiStrainPartialImmunity
> 
> ### ** Examples
> 
> # Parameters and initial conditions.
> parameters <- c(beta = rep(40, 4), gamma = rep(9.98, 4),
+                        mu = 0.02, a = 0.4 )
> 
> initials <- c(S = c(0.08, 0.1, 0.1, 0.11),
+                        P = c(0.4, 0.3, 0.3, 0.29),
+                        L = c(0.15, 0.02, 0.1, 0.01))
> 
> # Solve and plot.
> mlti.strain.pi <- MultiStrainPartialImmunity(pars = parameters, 
+                                              init = initials, 
+                                              time = 0:200)
> PlotMods(mlti.strain.pi, variables = c('L1', 'L2', 'L3', 'L4'), grid = FALSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: PlotMods ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Running examples in ‘epiflows-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.epiflows
> ### Title: Various plots for epiflows objects
> ### Aliases: plot.epiflows
> 
> ### ** Examples
> 
> data("Brazil_epiflows")
> 
> # no coordinates, defaults to network
> plot(Brazil_epiflows) 
type 'map' requested but 'x' has no spatial coordinates
using 'network' instead
> 
> # grid bubbleplot
> plot(Brazil_epiflows, "grid")
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 ‘epiflows-class.Rmd’ using rmarkdown
Quitting from lines 108-117 (epiflows-class.Rmd) 
Error: processing vignette 'epiflows-class.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘epiflows-class.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Quitting from lines 50-70 (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 files failed:
  ‘epiflows-class.Rmd’ ‘introduction.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: geom_bands
> ### Title: ggplot2 geom for Quantile Bands
> ### Aliases: geom_bands
> ### Keywords: plot
> 
> ### ** Examples
> 
> param <- param.icm(inf.prob = 0.2, act.rate = 0.25)
> init <- init.icm(s.num = 500, i.num = 1)
> control <- control.icm(type = "SI", nsteps = 250, nsims = 5)
> mod1 <- icm(param, init, control)
> df <- as.data.frame(mod1)
> df.mean <- as.data.frame(mod1, out = "mean")
> 
> library(ggplot2)
> ggplot() +
+    geom_line(data = df, mapping = aes(time, i.num, group = sim), alpha = 0.25,
+              lwd = 0.25, color = "firebrick") +
+    geom_bands(data = df, mapping = aes(time, i.num),
+               lower = 0.1, upper = 0.9, fill = "firebrick") +
+    geom_line(data = df.mean, mapping = aes(time, i.num)) +
+    theme_minimal()
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 ‘epiphy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: clump
> ### Title: Regroup observational data into even clumps of individuals.
> ### Aliases: clump clump.intensity
> 
> ### ** Examples
> 
> my_incidence <- incidence(tomato_tswv$field_1929)
> plot(my_incidence, type = "all")
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 ‘defs-and-eqns.Rmd’ using rmarkdown
--- finished re-building ‘defs-and-eqns.Rmd’

--- re-building ‘epiphy.Rmd’ using rmarkdown
Quitting from lines 84-85 (epiphy.Rmd) 
Error: processing vignette 'epiphy.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘epiphy.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getAER
> ### Title: Get full disease-specific epidemiological report
> ### Aliases: getAER
> 
> ### ** Examples
> 
> # --- Generating the AER report using the default Salmonellosis dataset
> getAER()
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: getAER ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EpiReport_Vignette.Rmd’ using rmarkdown
Quitting from lines 273-291 (EpiReport_Vignette.Rmd) 
Error: processing vignette 'EpiReport_Vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘EpiReport_Vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘episensr.Rmd’ using rmarkdown
Warning: Removed 438 rows containing non-finite values (stat_bin).
Warning: Removed 438 rows containing non-finite values (stat_density).
Quitting from lines 296-297 (episensr.Rmd) 
Error: processing vignette 'episensr.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘episensr.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pvalueplot
> ### Title: Plot the p-value function
> ### Aliases: pvalueplot
> ### Keywords: R Rothman episheet pvalues
> 
> ### ** Examples
> 
> pvalueplot(
+   est1.ll = 0.9,
+   est1.ul = 12,
+   xlabel = "Relative Risk"
+ )
Confidence interval type is  95%CI
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 ‘pvalueplot.Rmd’ using rmarkdown
Confidence interval type is  95%CI
Quitting from lines 21-26 (pvalueplot.Rmd) 
Error: processing vignette 'pvalueplot.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘pvalueplot.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epitrix.Rmd’ using rmarkdown
Quitting from lines 122-133 (epitrix.Rmd) 
Error: processing vignette 'epitrix.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘epitrix.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pcpPlot
> ### Title: A PCP plot of the data, residuals or hat values from regression
> ###   fits
> ### Aliases: pcpPlot
> 
> ### ** Examples
> 
> f <- lm(mpg ~ wt+hp+disp, data=mtcars)
> pcpPlot(mtcars, f, type="Residuals")
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 ‘ERSA.Rmd’ using rmarkdown
Quitting from lines 101-104 (ERSA.Rmd) 
Error: processing vignette 'ERSA.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ERSA.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: esgplotts
> ### Title: Plot time series objects
> ### Aliases: esgplotts
> 
> ### ** Examples
> 
> kappa <- 1.5
> V0 <- theta <- 0.04
> sigma <- 0.2
> theta1 <- kappa*theta
> theta2 <- kappa
> theta3 <- sigma
> x <- simdiff(n = 10, horizon = 5, frequency = "quart",
+ model = "OU",
+ x0 = V0, theta1 = theta1, theta2 = theta2, theta3 = theta3)
> 
> esgplotts(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 ‘ESG2toolkit_Intro_062014.Rnw’ using knitr
Loading required package: CDVine
The CDVine package is no longer developed actively.
Please consider using the more general VineCopula package
(see https://CRAN.R-project.org/package=VineCopula),
which extends and improves the functionality of CDVine.

Loading required package: ggplot2
Loading required package: gridExtra
Loading required package: reshape2
Loading required package: ycinterextra
Loading required package: compiler

Attaching package: 'ycinterextra'

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

    deviance, fitted, residuals

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

    as.list

Quitting from lines 369-370 (ESG2toolkit_Intro_062014.Rnw) 
Error: processing vignette 'ESG2toolkit_Intro_062014.Rnw' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ESG2toolkit_Intro_062014.Rnw’

SUMMARY: processing the following file failed:
  ‘ESG2toolkit_Intro_062014.Rnw’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: theme_edi
> ### Title: Custom ggplot2 theme
> ### Aliases: theme_edi
> 
> ### ** Examples
> 
> library(ggplot2)
> p <- ggplot(mtcars) + 
+  geom_point(aes(x = wt, y = mpg, 
+ colour=factor(gear))) + facet_wrap(~am)
> 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: <Anonymous> ... render_strips -> build_strip -> ggstrip -> Summary.unit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ESTER.Rmd’ using rmarkdown
Quitting from lines 95-102 (ESTER.Rmd) 
Error: processing vignette 'ESTER.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ESTER.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Radial_plot
> ### Title: Radial bar plot of use reports (UR) per species
> ### Aliases: Radial_plot
> ### Keywords: cultural ethnobotany, report use value,
> 
> ### ** Examples
> 
> 
> #Use built-in ethnobotany data example and Frequency of Citation function FCs()
> Radial_plot(ethnobotanydata, analysis = FCs)
  sp_name FCs
1    sp_c  17
2    sp_a  15
3    sp_b  12
4    sp_d  12
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: Radial_plot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ethnobotanyr_vignette.Rmd’ using rmarkdown
Quitting from lines 47-48 (ethnobotanyr_vignette.Rmd) 
Error: processing vignette 'ethnobotanyr_vignette.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ethnobotanyr_vignette.Rmd’

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

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘evergreenreviewgraphs.Rmd’ using rmarkdown
Quitting from lines 59-68 (evergreenreviewgraphs.Rmd) 
Error: processing vignette 'evergreenreviewgraphs.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘evergreenreviewgraphs.Rmd’

--- re-building ‘introducing-europepmc.Rmd’ using rmarkdown
171349 records found, returning 100
168667 records found, returning 100
1456 records found, returning 100
1456 records found, returning 10
1 records found, returning 1
1 records found, returning 1
1 records found, returning 1
1 records found, returning 1
10 records found, returning 10
564 records found, returning 564
135 records found, returning 135
73452 records found, returning 100
3521 records found, returning 100
231 records found. Returning 231
169 records found. Returning 169
--- finished re-building ‘introducing-europepmc.Rmd’

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

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

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

--- re-building ‘eurostat_tutorial.Rmd’ using rmarkdown
Loading required package: xml2
trying URL ‘https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ft2020_rk310.tsv.gz’
Content type 'application/octet-stream;charset=UTF-8' length 4476 bytes
==================================================
downloaded 4476 bytes

Table t2020_rk310 cached at /tmp/Rtmp4Mw4B0/eurostat/t2020_rk310_num_code_TF.rds
Quitting from lines 219-223 (eurostat_tutorial.Rmd) 
Error: processing vignette 'eurostat_tutorial.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘eurostat_tutorial.Rmd’

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

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

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [3s/3s]
  Running ‘test-parse.R’ [0s/0s]
  Running ‘test-replay.R’ [0s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(evaluate)
  > 
  > if (require("testthat", quietly = TRUE)) test_check("evaluate")
  ── 1. Failure: ggplot is captured (@test-graphics.r#13)  ───────────────────────
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 4 - 3 == 1
  
  ── 2. Failure: ggplot is captured (@test-graphics.r#15)  ───────────────────────
  `x` not equal to `expected`.
  Lengths differ: 4 is not 3
  
  ── 3. Failure: ggplot2 plots in a single expression are captured (@test-graphics
  `x` not equal to `expected`.
  1/4 mismatches
  x[3]: "simpleError"
  y[3]: "recordedplot"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 50 SKIPPED: 1 FAILED: 3
  1. Failure: ggplot is captured (@test-graphics.r#13) 
  2. Failure: ggplot is captured (@test-graphics.r#15) 
  3. Failure: ggplot2 plots in a single expression are captured (@test-graphics.r#49) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘evaluator-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: generate_event_outcomes_plot
> ### Title: Display the distribution of threat events contained vs. realized
> ###   across all domains
> ### Aliases: generate_event_outcomes_plot
> 
> ### ** Examples
> 
> data(domain_summary)
> generate_event_outcomes_plot(domain_summary)
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 ‘EValue-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sens_plot
> ### Title: Plots for sensitivity analyses
> ### Aliases: sens_plot
> ### Keywords: confounding, meta-analysis, sensitivity
> 
> ### ** Examples
> 
> # with variable bias and with confidence band
> sens_plot( type="line", q=log(1.1), Bmin=log(1), Bmax=log(4), sigB=0.1,
+            yr=log(1.3), vyr=0.005, t2=0.4, vt2=0.03 )
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 ‘evolqg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CalcR2CvCorrected
> ### Title: Corrected integration value
> ### Aliases: CalcR2CvCorrected CalcR2CvCorrected.default
> ###   CalcR2CvCorrected.lm
> ### Keywords: correlation integration
> 
> ### ** Examples
> 
> integration.dist = CalcR2CvCorrected(iris[,1:4])
> 
> #adjusted values
> integration.dist[[1]]
       r2  eVals_cv 
0.3122038 1.6792943 
> 
> #ploting models
> library(ggplot2)
> ggplot(integration.dist$dist, aes(r2, mean_cv)) + geom_point() + 
+        geom_smooth(method = 'lm', color= 'black') + 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
Running examples in ‘EvolutionaryGames-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ILogit
> ### Title: ILogit dynamic
> ### Aliases: ILogit
> 
> ### ** Examples
> 
> dynamic <- ILogit
> A <- matrix(c(-1, 0, 0, 0, -1, 0, 0, 0, -1), 3, byrow=TRUE)
> state <- matrix(c(0.1, 0.2, 0.7, 0.2, 0.7, 0.1, 0.9, 0.05, 0.05), 3, 3, byrow=TRUE)
> eta <- 0.7
> phaseDiagram3S(A, dynamic, eta, state, TRUE, FALSE)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: phaseDiagram3S ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsingEvolutionaryGames.Rmd’ using rmarkdown
Quitting from lines 204-207 (UsingEvolutionaryGames.Rmd) 
Error: processing vignette 'UsingEvolutionaryGames.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘UsingEvolutionaryGames.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: DistancesPlot
> ### Title: Plot the Procrustes distances between a set of shapes and a
> ###   reference
> ### Aliases: DistancesPlot
> 
> ### ** Examples
> 
> 
> data("simulated_shape_distances")
> 
> #Plot distances between a set of simulated shapes a reference.
> 
> DistancesPlot(simulated_shape_distances)
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
Errors in running code in vignettes:
when running code in ‘evtree.Rnw’
  ...

> options(prompt = "R> ", continue = "+  ", width = 70, 
+     useFancyQuotes = FALSE)

> library("rpart")

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

> library("lattice")

> data("BBBClub", package = "evtree")

> cache <- FALSE

> X1 <- rep(seq(0.25, 1.75, 0.5), each = 4)

> X2 <- rep(seq(0.25, 1.75, 0.5), 4)

> Y <- rep(1, 16)

> Y[(X1 < 1 & X2 < 1) | (X1 > 1 & X2 > 1)] <- 2

> Y <- factor(Y, labels = c("O", "X"))

> chess22 <- data.frame(Y, X1, X2)

> set.seed(1090)

> print(evtree(Y ~ ., data = chess22, minbucket = 1, 
+     minsplit = 2))

Model formula:
Y ~ X1 + X2

Fitted party:
[1] root
|   [2] X1 < 1.25
|   |   [3] X2 < 1.25: X (n = 4, err = 0.0%)
|   |   [4] X2 >= 1.25: O (n = 4, err = 0.0%)
|   [5] X1 >= 1.25
|   |   [6] X2 < 1.25: O (n = 4, err = 0.0%)
|   |   [7] X2 >= 1.25: X (n = 4, err = 0.0%)

Number of inner nodes:    3
Number of terminal nodes: 4

> par(mar = c(4, 4, 1, 1))

> plot(X2 ~ X1, data = chess22, xlim = c(0, 2), ylim = c(0, 
+     2), pch = c(1, 4)[Y], col = c("black", "slategray")[Y])

> if (cache & file.exists("BBBClub-trees.rda")) {
+     load("BBBClub-trees.rda")
+ } else {
+     data("BBBClub", package = "evtree")
+     library(" ..." ... [TRUNCATED] 

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

Error: processing vignette 'evtree.Rnw' failed with diagnostics:
 chunk 6 (label = BBBClub-cache) 
Error in unit(1, "strwidth", split) : 
  no string supplied for 'strwidth/height' unit

--- failed re-building 'evtree.Rnw'

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ewoc_d1classic
> ### Title: Escalation With Overdose Control
> ### Aliases: ewoc_d1classic
> 
> ### ** Examples
> 
> DLT <- 0
> dose <- 20
> test <- ewoc_d1classic(DLT ~ dose, type = 'discrete',
+                       theta = 0.33, alpha = 0.25,
+                       min_dose = 0, max_dose = 100,
+                       dose_set = seq(0, 100, 20),
+                       rho_prior = matrix(1, ncol = 2, nrow = 1),
+                       mtd_prior = matrix(1, ncol = 2, nrow = 1),
+                       rounding = "nearest")
Warning in limits_d1nocov(first_dose = first_dose, last_dose = last_dose,  :
  'first_dose' and  'last_dose' were defined as the first and last elements of 'dose_set', respectively.
Compiling model graph
   Resolving undeclared variables
   Allocating nodes
Graph information:
   Observed stochastic nodes: 1
   Unobserved stochastic nodes: 2
   Total graph size: 27

Initializing model

> summary(test)
Conditions
  Minimum Dose Maximum Dose Theta Alpha Number of patients
1            0          100  0.33  0.25                  1

Next Dose
  Estimate      95% HPD
1       40 (12 ; 99.99)

P(DLT| next dose)
  Estimate       95% HPD
1      0.3 (0.04 ; 0.74)
> plot(test)
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 ‘ExPanDaR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: prepare_by_group_bar_graph
> ### Title: Prepares a by Group Bar Graph
> ### Aliases: prepare_by_group_bar_graph
> 
> ### ** Examples
> 
> data(russell_3000)
> graph <- prepare_by_group_bar_graph(russell_3000, "sector", "ni_sales", median)
> graph$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
Error(s) in re-building vignettes:
  ...
--- re-building ‘ExPanDaR-functions.Rmd’ using rmarkdown
Quitting from lines 77-78 (ExPanDaR-functions.Rmd) 
Error: processing vignette 'ExPanDaR-functions.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘ExPanDaR-functions.Rmd’

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

SUMMARY: processing the following file failed:
  ‘ExPanDaR-functions.Rmd’

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: massregplot
> ### Title: Mass Regression Plot
> ### Aliases: massregplot
> 
> ### ** Examples
> 
> exam.df <- iris
> massregplot(exam.df, "Sepal.Length", ignore = "Species")
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: massregplot ... lapply -> FUN -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘exploreR.Rmd’ using rmarkdown
Quitting from lines 69-71 (exploreR.Rmd) 
Error: processing vignette 'exploreR.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘exploreR.Rmd’

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

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

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: graph2bitmap
> ### Title: Save currently active R graph to bitmap format
> ### Aliases: graph2bitmap graph2png graph2tif graph2jpg graph2png graph2tif
> ###   graph2jpg
> 
> ### ** Examples
> 
> # Create a file name
> filen <- tempfile(pattern = "ggplot") # or 
> # filen <- paste("YOUR_DIR/ggplot")
> 
> # Generate graphical output
> library(ggplot2)
> library(datasets)
> x=qplot(Sepal.Length, Petal.Length, data = iris, 
+         color = Species, size = Petal.Width, alpha = I(0.7))
> plot.fun <- function(){
+   print(qplot(Sepal.Length, Petal.Length, data = iris, 
+               color = Species, size = Petal.Width, alpha = 0.7))
+ }
> 
> # There are 3 ways to use graph2bitmap():
> ### 1. Pass the plot as an object
> graph2png(x=x, file=filen, dpi=400, height = 5, aspectr=4)
Error in grid.Call.graphics(C_setviewport, vp, TRUE) : 
  VECTOR_ELT() can only be applied to a 'list', not a 'double'
Calls: graph2png ... push.vp.vpTree -> push.vp -> push.vp.viewport -> grid.Call.graphics
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘labels-support.Rmd’ using rmarkdown

Use 'expss_output_viewer()' to display tables in the RStudio Viewer.
 To return to the console output, use 'expss_output_default()'.

Quitting from lines 111-119 (labels-support.Rmd) 
Error: processing vignette 'labels-support.Rmd' failed with diagnostics:
VECTOR_ELT() can only be applied to a 'list', not a 'double'
--- failed re-building ‘labels-support.Rmd’

--- re-building ‘tables-with-labels.Rmd’ using rmarkdown

Use 'expss_output_rnotebook()' to display tables inside R Notebooks.
 To return to the console output, use 'expss_output_default()'.

Quitting from lines 79-138 (tables-with-labels.Rmd) 
Error: processing vignette 'tables-with-labels.Rmd' failed with diagnostics:
<text>:1:12: unexpected symbol
1: Miles/(US) gallon
               ^
--- failed re-building ‘tables-with-labels.Rmd’

--- re-building ‘xlsx-export.Rmd’ using rmarkdown
--- finished re-building ‘xlsx-export.Rmd’

SUMMARY: processing the following files failed:
  ‘labels-support.Rmd’ ‘tables-with-labels.Rmd’

Error: Vignette re-building failed.
Execution halted