Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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.
Package in Depends field not imported from: ‘lpSolveAPI’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glm: no visible binding for global variable ‘gaussian’
glm: no visible global function definition for ‘glm.control’
glm: no visible global function definition for ‘model.response’
glm: no visible global function definition for ‘is.empty.model’
glm: no visible global function definition for ‘model.matrix’
glm: no visible global function definition for ‘model.weights’
glm: no visible global function definition for ‘model.offset’
glm: no visible global function definition for ‘model.extract’
glm: no visible global function definition for ‘glm.fit’
glm: no visible global function definition for ‘.getXlevels’
separator: no visible global function definition for ‘make.lp’
separator: no visible global function definition for ‘set.column’
separator: no visible global function definition for ‘set.rhs’
separator: no visible global function definition for ‘set.constr.type’
separator: no visible global function definition for ‘set.objfn’
separator: no visible global function definition for ‘set.bounds’
separator: no visible global function definition for ‘lp.control’
separator: no visible global function definition for ‘get.variables’
separator: no visible global function definition for ‘set.basis’
separator: no visible global function definition for
  ‘get.dual.solution’
Undefined global functions or variables:
  .getXlevels gaussian get.dual.solution get.variables glm.control
  glm.fit is.empty.model lp.control make.lp model.extract model.matrix
  model.offset model.response model.weights set.basis set.bounds
  set.column set.constr.type set.objfn set.rhs
Consider adding
  importFrom("stats", ".getXlevels", "gaussian", "glm.control",
             "glm.fit", "is.empty.model", "model.extract",
             "model.matrix", "model.offset", "model.response",
             "model.weights")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.safidesign plot.safimodel
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.safidesign: no visible global function definition for ‘par’
plot.safidesign: no visible global function definition for ‘matplot’
plot.safidesign: no visible global function definition for ‘axis’
plot.safimodel : plot.coef: no visible global function definition for
  ‘colorRampPalette’
plot.safimodel : plot.coef: no visible global function definition for
  ‘barplot’
plot.safimodel : plot.coef: no visible global function definition for
  ‘axis’
plot.safimodel : plot.coef: no visible global function definition for
  ‘abline’
plot.safimodel : plot.coef: no visible global function definition for
  ‘box’
plot.safimodel: no visible global function definition for ‘par’
safiModel: no visible global function definition for ‘lm’
Undefined global functions or variables:
  abline axis barplot box colorRampPalette lm matplot par
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "axis", "barplot", "box", "matplot",
             "par")
  importFrom("stats", "lm")
to your NAMESPACE file.
Running examples in ‘safi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.safidesign
> ### Title: Plotting SAFI designs
> ### Aliases: plot.safidesign
> 
> ### ** Examples
> 
> # 1 functional input
> s.d <- createSafiDesign(d.f = 1)
> plot(s.d)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
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.
File ‘SAMM/libs/SAMM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Rd file 'mudiff.acc.Rd':
  \usage lines wider than 90 characters:
     mudiff.acc(len, alpha1, beta1, alpha2, beta2, n01, n02, level = 0.95, equal = TRUE, m = 10000, mcs = 3)

Rd file 'mudiff.alc.Rd':
  \usage lines wider than 90 characters:
     mudiff.alc(len, alpha1, beta1, alpha2, beta2, n01, n02, level = 0.95, equal = TRUE, m = 10000, mcs = 3)

Rd file 'mudiff.mblmodwoc.Rd':
  \usage lines wider than 90 characters:
     mudiff.mblmodwoc(len, alpha1, beta1, alpha2, beta2, level = 0.95, worst.level = 0.95, m = 50000, mcs = 3)

Rd file 'mudiff.mblmodwoc.equalvar.Rd':
  \usage lines wider than 90 characters:
     mudiff.mblmodwoc.equalvar(len, alpha, beta, level = 0.95, worst.level = 0.95, m = 50000, mcs = 3)

Rd file 'mudiff.modwoc.Rd':
  \usage lines wider than 90 characters:
     mudiff.modwoc(len, alpha1, beta1, alpha2, beta2, n01, n02, level = 0.95, worst.level = 0.95, equal = TRUE, m = 50000, mcs = 3)

Rd file 'mudiff.modwoc.equalvar.Rd':
  \usage lines wider than 90 characters:
     mudiff.modwoc.equalvar(len, alpha, beta, n01, n02, level = 0.95, worst.level = 0.95, equal = TRUE)

These lines will be truncated in the PDF manual.
propdiff.acc: no visible global function definition for ‘rbeta’
propdiff.acc: no visible global function definition for ‘rbinom’
propdiff.acc: no visible global function definition for ‘pbeta’
propdiff.alc: no visible global function definition for ‘rbeta’
propdiff.alc: no visible global function definition for ‘rbinom’
propdiff.alc: no visible global function definition for ‘qbeta’
propdiff.freq: no visible global function definition for ‘qnorm’
propdiff.mblacc: no visible global function definition for ‘rbeta’
propdiff.mblacc: no visible global function definition for ‘rbinom’
propdiff.mblacc: no visible global function definition for ‘pbeta’
propdiff.mblalc: no visible global function definition for ‘rbeta’
propdiff.mblalc: no visible global function definition for ‘rbinom’
propdiff.mblalc: no visible global function definition for ‘qbeta’
propdiff.mblmodwoc: no visible global function definition for ‘qchisq’
propdiff.mblmodwoc: no visible global function definition for ‘pbeta’
propdiff.mblwoc: no visible global function definition for ‘pbeta’
propdiff.modwoc: no visible global function definition for ‘qchisq’
propdiff.modwoc: no visible global function definition for ‘pbeta’
propdiff.woc: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  pbeta qbeta qchisq qnorm rbeta rbinom
Consider adding
  importFrom("stats", "pbeta", "qbeta", "qchisq", "qnorm", "rbeta",
             "rbinom")
to your NAMESPACE file.
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.
plot.samEL: no visible global function definition for ‘matplot’
plot.samHL: no visible global function definition for ‘matplot’
plot.samLL: no visible global function definition for ‘matplot’
plot.samQL: no visible global function definition for ‘matplot’
predict.samEL: no visible global function definition for ‘ns’
predict.samHL: no visible global function definition for ‘ns’
predict.samLL: no visible global function definition for ‘ns’
predict.samQL: no visible global function definition for ‘ns’
samEL: no visible global function definition for ‘ns’
samHL: no visible global function definition for ‘ns’
samHL: no visible binding for global variable ‘median’
samLL: no visible global function definition for ‘ns’
samQL: no visible global function definition for ‘ns’
Undefined global functions or variables:
  matplot median ns
Consider adding
  importFrom("graphics", "matplot")
  importFrom("stats", "median")
to your NAMESPACE file.
File ‘SAM/libs/SAM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘impute’ ‘matrixStats’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘impute’ ‘matrixStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.SAMoutput print.SAMoutput
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'samr-internal':
  ‘plot.SAMoutput’ ‘print.SAMoutput’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘samr/libs/samr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GraphBinaryForestPlot: no visible global function definition for
  ‘abline’
GraphBinaryForestPlot: no visible global function definition for ‘text’
GraphContinuousForestPlot: no visible global function definition for
  ‘abline’
GraphContinuousForestPlot: no visible global function definition for
  ‘text’
ImputeBinaryEvents: no visible global function definition for ‘rbinom’
ImputeSMD: no visible global function definition for ‘rnorm’
funnelplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline rbinom rnorm text
Consider adding
  importFrom("graphics", "abline", "text")
  importFrom("stats", "rbinom", "rnorm")
to your NAMESPACE file.
generate.sample.core: no visible global function definition for
  ‘predict’
mdh: no visible global function definition for ‘model.frame’
mdh: no visible binding for global variable ‘na.fail’
mdh: no visible global function definition for ‘.getXlevels’
mdh: no visible global function definition for ‘quantile’
mdh: no visible global function definition for ‘hist’
predict.mdh: no visible global function definition for ‘model.frame’
samur: no visible global function definition for ‘predict’
Undefined global functions or variables:
  .getXlevels hist model.frame na.fail predict quantile
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", ".getXlevels", "model.frame", "na.fail", "predict",
             "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: ‘mixer’
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.
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.
download.sas7bdat.sources : <anonymous>: no visible global function
  definition for ‘download.file’
generate.sas7bdat.source: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
parse.SAScii: no visible binding for global variable ‘end’
parse.SAScii: no visible binding for global variable ‘start’
read.SAScii: no visible global function definition for ‘download.file’
read.SAScii: no visible global function definition for ‘unzip’
read.SAScii: no visible global function definition for ‘read.fwf’
read.SAScii: no visible global function definition for ‘capture.output’
Undefined global functions or variables:
  capture.output download.file end read.fwf start unzip
Consider adding
  importFrom("stats", "end", "start")
  importFrom("utils", "capture.output", "download.file", "read.fwf",
             "unzip")
to your NAMESPACE file.
Rd file 'read.SAScii.Rd':
  \usage lines wider than 90 characters:
     read.SAScii( fn, sas_ri, beginline = 1, buffersize = 50, zipped = F , n = -1 , intervals.to.print = 1000 , lrecl = NULL , skip.decimal. ... [TRUNCATED]
  \examples lines wider than 100 characters:
                     paste( "http://smpbff2.dsd.census.gov/pub/sipp/2004/l04puw" , i , ".zip" , sep = "" )

These lines will be truncated in the PDF manual.
SASPECT: no visible global function definition for ‘dbinom’
my.SOnePro: missing arguments not allowed in calls to ‘c’
my.ttest: no visible global function definition for ‘var’
Undefined global functions or variables:
  dbinom var
Consider adding
  importFrom("stats", "dbinom", "var")
to your NAMESPACE file.
Running examples in ‘satscanMapper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: satscanMapper
> ### Title: Function to map Results data produced by a SaTScan (TM) cluster
> ###   analysis
> ### Aliases: satscanMapper
> 
> ### ** Examples
> 
> ######
> #
> #  These examples focus on mapping the SaTScan (TM) data after the analysis
> #  has been completed.
> #  See the section on the CreateGeo4SS function for an example of how 
> #  to build a coordinates file (.geo) that matches the satscanMapper 
> #  boundary data.
> #
> ######
> 
> ######
> #
> #  Example # 1 - Mapping existing SaTScan (TM) results - "USStateLung" result files
> #     Make sure SaTScan (TM) results files are still located in the directories
> #     documented in the session saved (.prm) file.
> #
> #     This example maps data for the US States containing circular clusters.
> #
> #   Get location of .prm file and location to write mapping output files
> #
> 
> SSMInstDir <- system.file(package="satscanMapper", "extdata")
> 
> TT =c("Contiguous US States All Lung Cancer Mortality, 2004")
> 
> satscanMapper(resDir=SSMInstDir,                # path to .prm file location for output files. 
+                      prmFile  = "stateLung.prm", 
+                      title    = TT          )
Error in pdf(file = OutputFNpdf, width = vW, height = vH) : 
  cannot open file '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/satscanMapper/extdata/stateLung-R01.pdf'
Calls: satscanMapper -> pdf
Execution halted
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.
loads: no visible global function definition for ‘untar’
saves: no visible global function definition for ‘tar’
Undefined global functions or variables:
  tar untar
Consider adding
  importFrom("utils", "tar", "untar")
to your NAMESPACE file.
clogistCalc: no visible global function definition for ‘model.matrix’
clogistCalc: no visible global function definition for ‘glm.fit’
clogistCalc: no visible global function definition for ‘binomial’
clogistInfo : all.not.equal: no visible global function definition for
  ‘var’
geeUOmega: no visible global function definition for ‘model.extract’
geeUOmega: no visible global function definition for ‘model.matrix’
geeUOmega: no visible binding for global variable ‘contrasts’
mgee: no visible binding for global variable ‘gaussian’
sawsCalc: no visible global function definition for ‘pf’
sawsCalc: no visible global function definition for ‘qt’
Undefined global functions or variables:
  binomial contrasts gaussian glm.fit model.extract model.matrix pf qt
  var
Consider adding
  importFrom("stats", "binomial", "contrasts", "gaussian", "glm.fit",
             "model.extract", "model.matrix", "pf", "qt", "var")
to your NAMESPACE file.
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.
K: no visible global function definition for ‘dnorm’
sBF: no visible global function definition for ‘density’
sBF: no visible global function definition for ‘txtProgressBar’
sBF: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  density dnorm setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "density", "dnorm")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.psgc print.sum.psgc summary.psgc
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.psgc: no visible global function definition for ‘par’
plot.psgc: no visible global function definition for ‘barplot’
plot.psgc: no visible global function definition for ‘hist’
plotci.sA: no visible global function definition for ‘par’
plotci.sA: no visible global function definition for ‘plot’
plotci.sA: no visible global function definition for ‘points’
plotci.sA: no visible global function definition for ‘segments’
plotci.sA: no visible global function definition for ‘abline’
plotci.sA: no visible global function definition for ‘axis’
qM.sM: no visible binding for global variable ‘quantile’
rwish: no visible global function definition for ‘rnorm’
sbgcop.mcmc: no visible global function definition for ‘qnorm’
sbgcop.mcmc: no visible global function definition for ‘rnorm’
sbgcop.mcmc: no visible global function definition for ‘cov’
sbgcop.mcmc: no visible global function definition for ‘runif’
sbgcop.mcmc: no visible global function definition for ‘pnorm’
sbgcop.mcmc: no visible global function definition for ‘quantile’
summary.psgc: no visible global function definition for ‘acf’
Undefined global functions or variables:
  abline acf axis barplot cov hist par plot pnorm points qnorm quantile
  rnorm runif segments
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "hist", "par",
             "plot", "points", "segments")
  importFrom("stats", "acf", "cov", "pnorm", "qnorm", "quantile",
             "rnorm", "runif")
to your NAMESPACE file.
Running examples in ‘sbgcop-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sbgcop.mcmc
> ### Title: Semiparametric Bayesian Gaussian copula estimation and
> ###   imputation
> ### Aliases: sbgcop.mcmc plot.psgc summary.psgc print.sum.psgc
> ### Keywords: multivariate models
> 
> ### ** Examples
> 
> fit<-sbgcop.mcmc(swiss)
10 percent done  Fri May  4 10:39:39 2018 
20 percent done  Fri May  4 10:39:39 2018 
30 percent done  Fri May  4 10:39:40 2018 
40 percent done  Fri May  4 10:39:40 2018 
50 percent done  Fri May  4 10:39:40 2018 
60 percent done  Fri May  4 10:39:41 2018 
70 percent done  Fri May  4 10:39:41 2018 
80 percent done  Fri May  4 10:39:41 2018 
90 percent done  Fri May  4 10:39:41 2018 
100 percent done  Fri May  4 10:39:42 2018 
> summary(fit)
         Length Class  Mode   
C.psamp  3600   -none- numeric
Y.pmean   282   -none- numeric
Y.impute    0   -none- NULL   
LPC       100   -none- numeric
> plot(fit)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
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.
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
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.
fitSBSA: no visible binding for global variable ‘var’
fitSBSA: no visible global function definition for ‘var’
fitSBSA: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  qnorm var
Consider adding
  importFrom("stats", "qnorm", "var")
to your NAMESPACE file.
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.
Non-standard file/directory found at top level:
  ‘src-java’
ChooseBest: no visible global function definition for ‘head’
GetScores: no visible global function definition for ‘write.table’
ReportTable: no visible binding for global variable ‘sd’
ReportTable: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  head sd write.table
Consider adding
  importFrom("stats", "sd")
  importFrom("utils", "head", "write.table")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘MASS’ ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  predict.scalreg print.scalreg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
lse: no visible global function definition for ‘lm’
predict.scalreg: no visible global function definition for ‘fitted’
slassoEst: no visible global function definition for ‘qnorm’
slassoEst: no visible global function definition for ‘lars’
slassoEst: no visible global function definition for ‘predict.lars’
Undefined global functions or variables:
  fitted lars lm predict.lars qnorm
Consider adding
  importFrom("stats", "fitted", "lm", "qnorm")
to your NAMESPACE file.
plot.scair: no visible global function definition for ‘par’
plot.scair: no visible global function definition for ‘plot’
plot.scair: no visible global function definition for ‘points’
plot.scar: no visible global function definition for ‘par’
plot.scar: no visible global function definition for ‘plot’
plot.scar: no visible global function definition for ‘points’
predict.scair: no visible global function definition for ‘approx’
predict.scar: no visible global function definition for ‘approx’
scair: no visible global function definition for ‘gaussian’
scair: no visible global function definition for ‘runif’
scair: no visible global function definition for ‘rnorm’
scar: no visible global function definition for ‘gaussian’
scar: no visible global function definition for ‘glm.fit’
scar: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx gaussian glm.fit par plot points rnorm runif
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "approx", "gaussian", "glm.fit", "rnorm", "runif")
to your NAMESPACE file.
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.
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.
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.
prime.factor: no visible global function definition for ‘data’
prime.factor: no visible binding for global variable ‘primlist’
Undefined global functions or variables:
  data primlist
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘schoolmath/R/prime.factor.R’:
  data(primlist)
See section ‘Good practice’ in ‘?data’.
'library' or 'require' call to ‘QUIC’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
scio.cv: no visible global function definition for ‘cov’
scio.refit: no visible global function definition for ‘QUIC’
Undefined global functions or variables:
  QUIC cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
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.
Running examples in ‘scorecard-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: iv
> ### Title: Information Value
> ### Aliases: iv
> 
> ### ** Examples
> 
> # Load German credit data
> data(germancredit)
> 
> # information values
> dt_info_value = iv(germancredit, y = "creditability")
Warning in check_y(dt, y, positive) :
  The positive value in "creditability" was replaced by 1 and negative value by 0.
Error in `[.data.table`(data.table(x = x, y = y), , .(good = sum(y ==  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: iv ... eval -> sapply -> lapply -> FUN -> [ -> [.data.table
Execution halted
score.GGUM: no visible global function definition for ‘dnorm’
score.GGUM: no visible global function definition for ‘hist’
score.GGUM: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dnorm hist write.table
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "dnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
CreatePssm: no visible binding for global variable ‘training’
Undefined global functions or variables:
  training
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.
Running examples in ‘ScottKnottESD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ScottKnottESD-package
> ### Title: The Scott-Knott Effect Size Difference (ESD) Test
> ### Aliases: ScottKnottESD-package ScottKnottESD
> ### Keywords: ScottKnottESD
> 
> ### ** Examples
> 
> library(ScottKnottESD)
> 
> sk <- sk_esd(example)
Error in if (a != b) { : the condition has length > 1
Calls: sk_esd -> scottknott -> Partition -> diff
Execution halted
Found the following apparent S3 methods exported but not registered:
  SK.aov SK.aovlist SK.default SK.nest SK.nest.aov SK.nest.aov
  SK.nest.aovlist SK.nest.aovlist SK.nest.default SK.nest.default
  plot.SK summary.SK summary.SK.nest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.SK: no visible global function definition for ‘plot’
plot.SK: no visible global function definition for ‘segments’
plot.SK: no visible global function definition for ‘axis’
plot.SK: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis mtext plot segments
Consider adding
  importFrom("graphics", "axis", "mtext", "plot", "segments")
to your NAMESPACE file.
Running examples in ‘ScottKnott-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SK
> ### Title: The ScottKnott Clustering Algoritm for Single Experiments
> ### Aliases: SK SK.default SK.aov SK.aovlist
> ### Keywords: package htest univar tree design
> 
> ### ** Examples
> 
>   ##
>   ## Examples: Completely Randomized Design (CRD)
>   ## More details: demo(package='ScottKnott')
>   ##
>   
>   ## The parameters can be: vectors, design matrix and the response variable,
>   ## data.frame or aov
>   data(CRD2)
>   
>   ## From: design matrix (dm) and response variable (y)
>   sk1 <- with(CRD2,
+               SK(x=dm,
+                  y=y,
+                  model='y ~ x',
+                  which='x'))
Error in UseMethod("SK") : 
  no applicable method for 'SK' applied to an object of class "data.frame"
Calls: with -> with.default -> eval -> eval -> SK
Execution halted
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.
License components which are templates and need '+ file LICENSE':
  MIT License
'library' or 'require' calls to packages already attached by Depends:
  ‘RCurl’ ‘XML’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
scrape: no visible global function definition for ‘getURLAsynchronous’
scrape: no visible global function definition for ‘runif’
scrape: no visible global function definition for ‘capture.output’
scrape: no visible binding for global variable ‘xmlParse’
scrape: no visible binding for global variable ‘htmlParse’
Undefined global functions or variables:
  capture.output getURLAsynchronous htmlParse runif xmlParse
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘MASS’ ‘oligoClasses’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following calls to attach():
File ‘scriptests/R/source.pkg.R’:
  attach(NULL, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
  attach(envir, pos = pos, name = paste("pkgcode", pkg.name, sep = ":"))
See section ‘Good practice’ in ‘?attach’.
Files which contain pragma(s) suppressing diagnostics:
  ‘src/scrm/macros.h’ ‘src/scrm/model.h’
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.
lahiri.design: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘sdcMicro-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: freqCalc
> ### Title: Frequencies calculation for risk estimation
> ### Aliases: freqCalc
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
> data(francdat)
> f <- freqCalc(francdat, keyVars=c(2,4,5,6),w=8)
> f

 --------------------------
4 obs. violate 2-anonymity 
8 obs. violate 3-anonymity 
 --------------------------
> f$freqCalc
  Num1 Key1 Num2 Key2 Key3 Key4 Num3     w
1 0.30    1 0.40    2    5    1    4  18.0
2 0.12    1 0.22    2    1    1   22  45.5
3 0.18    1 0.80    2    1    1    8  39.0
4 1.90    3 9.00    3    1    5   91  17.0
5 1.00    4 1.30    3    1    4   13 541.0
6 1.00    4 1.40    3    1    1   14   8.0
7 0.10    6 0.01    2    1    5    1   5.0
8 0.15    1 0.50    2    5    1    5  92.0
> f$fk
[1] 2 2 2 1 1 1 1 2
> f$Fk
[1] 110.0  84.5  84.5  17.0 541.0   8.0   5.0 110.0
> ## with missings:
> x <- francdat
> x[3,5] <- NA
> x[4,2] <- x[4,4] <- NA
> x[5,6]  <- NA
> x[6,2]  <- NA
> f2 <- freqCalc(x, keyVars=c(2,4,5,6),w=8)
Error in `[.data.table`(dat_with_na, , `:=`(tmpid, .I)) : 
  Cannot use := to add columns to a null data.table (no columns), currently. You can use := to add (empty) columns to a 0-row data.table (1 or more empty columns), though.
Calls: freqCalc -> [ -> [.data.table
Execution halted
Running ‘globalRecoding_test.R’ [5s/7s]
  Running ‘microaggregation_test.R’ [2s/3s]
Running the tests in ‘tests/microaggregation_test.R’ failed.
Complete output:
  > require(sdcMicro)
  Loading required package: sdcMicro
  --------
  This is sdcMicro v5.2.0.
  For references, please have a look at citation('sdcMicro')
  Note: since version 5.0.0, the graphical user-interface is a shiny-app that can be started with sdcApp().
  Please submit suggestions and bugs at: https://github.com/sdcTools/sdcMicro/issues
  --------
  > ### for a data.frame
  > dat <- data.frame(x = rnorm(100))
  > microaggregation(obj = dat, variables = "x", method = "mdav", aggr = 3, measure = "mean")
  Error in `[.data.table`(xdat, , j = list(idvariableforresorting = idf(idvariableforresorting),  : 
    SETLENGTH() cannot be applied to an ALTVEC object.
  Calls: microaggregation ... mafastX -> mafastWORK -> eval -> eval -> [ -> [.data.table
  Execution halted
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘flush.console’
estimateTimeToComputeTargetDefinition: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘flush.console’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘combn’
initialize,sdcTargetDefinitionClass: no visible global function
  definition for ‘quantile’
initialize,sdcTargetMatrixClass: no visible global function definition
  for ‘flush.console’
Undefined global functions or variables:
  combn flush.console quantile
Consider adding
  importFrom("stats", "quantile")
  importFrom("utils", "combn", "flush.console")
to your NAMESPACE file.
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.
prepare_Rd: sdd.Rd:46-47: Dropping empty section \seealso
prepare_Rd: sddpack-package.Rd:31-32: Dropping empty section \seealso
prepare_Rd: sddsolve.Rd:29-30: Dropping empty section \references
prepare_Rd: sddsolve.Rd:38-39: Dropping empty section \seealso
prepare_Rd: sddsolve.Rd:40-41: Dropping empty section \examples
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.
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 ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SDMTools.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘raster’ ‘sp’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
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.
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.
Package in Depends field not imported from: ‘lars’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
sealasso: no visible global function definition for ‘lars’
weight.calc: no visible global function definition for ‘lars’
Undefined global functions or variables:
  lars
Rd file 'createTree.Rd':
  \usage lines wider than 90 characters:
     createTree(data, treeType = "quad", dataType = "point", columns = if (dataType=="point") 1:2 else 1:4, ...)

These lines will be truncated in the PDF manual.
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.
adx: no visible global function definition for ‘abline’
adx: no visible global function definition for ‘legend’
dx: no visible global function definition for ‘abline’
dx: no visible global function definition for ‘legend’
maxd: no visible global function definition for ‘abline’
maxd: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘rainbow’
pc: no visible global function definition for ‘plot’
pc: no visible global function definition for ‘abline’
pc: no visible global function definition for ‘legend’
pc: no visible global function definition for ‘points’
pcu: no visible global function definition for ‘rainbow’
pcu: no visible global function definition for ‘plot’
pcu: no visible global function definition for ‘abline’
pcu: no visible global function definition for ‘legend’
pcu: no visible global function definition for ‘points’
rmsd: no visible global function definition for ‘abline’
rmsd: no visible global function definition for ‘legend’
rsd: no visible global function definition for ‘abline’
rsd: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend plot points rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "plot", "points")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  image.seas.sum plot.interarrival plot.seas.norm plot.seas.sum
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘seas/libs/seas.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘seas-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: image.seas.sum
> ### Title: Show a seasonal sum data object
> ### Aliases: image.seas.sum
> ### Keywords: hplot
> 
> ### ** Examples
> 
> data(mscdata)
> dat <- mksub(mscdata, id=1108447)
> 
> dat.ss <- seas.sum(dat, width="mon")
> image(dat.ss)
Error in image.default(dat.ss) : 'z' must be a matrix
Calls: image -> image.default
Execution halted
Packages in Depends field not imported from:
  ‘NADA’ ‘lubridate’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package in Depends field not imported from: ‘JM’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SEchart: no visible global function definition for ‘plot’
SEchart: no visible global function definition for ‘rect’
SEchart: no visible global function definition for ‘par’
SEchart: no visible global function definition for ‘grid’
SEchart: no visible global function definition for ‘axis’
SEchart: no visible global function definition for ‘text’
SEchart: no visible global function definition for ‘lines’
SEchart: no visible global function definition for ‘heat.colors’
SEchart: no visible global function definition for ‘topo.colors’
SEchart: no visible global function definition for ‘cm.colors’
SEchart: no visible global function definition for ‘terrain.colors’
SEchart: no visible global function definition for ‘gray.colors’
SEchart: no visible global function definition for ‘rainbow’
SEchart: no visible global function definition for ‘points’
SEchart: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis cm.colors gray.colors grid heat.colors legend lines par plot
  points rainbow rect terrain.colors text topo.colors
Consider adding
  importFrom("grDevices", "cm.colors", "gray.colors", "heat.colors",
             "rainbow", "terrain.colors", "topo.colors")
  importFrom("graphics", "axis", "grid", "legend", "lines", "par",
             "plot", "points", "rect", "text")
to your NAMESPACE file.
fdc2s: no visible global function definition for ‘lm’
fdc3s: no visible global function definition for ‘lm’
fds2s: no visible global function definition for ‘lm’
fds3s: no visible global function definition for ‘lm’
Undefined global functions or variables:
  lm
Consider adding
  importFrom("stats", "lm")
to your NAMESPACE file.
.read.SeerStatTXT: no visible global function definition for
  ‘read.table’
.write.SeerStatTXT: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
prepare_Rd: SEER2RTestdata.Rd:77-78: Dropping empty section \source
Rd file 'SEER2R-package.Rd':
  \examples lines wider than 100 characters:
     #load testing data: there are three data objects, i.e. SEER2RTestData1,SEER2RTestData2,SEER2RTestData3 
     dicinfoused = write.SeerStat(SEER2RTestData2, DICfileName = "testrun1.dic",UseVarLabelsInTxtFile=FALSE);

Rd file 'read.SeerStat.Rd':
  \usage lines wider than 90 characters:
     read.SeerStat(DICfileName, TXTfileName = NULL, UseVarLabelsInData = FALSE,ReadHeaderOnly=FALSE,...)
  \examples lines wider than 100 characters:
     #load testing data: there are three data objects, i.e. SEER2RTestData1,SEER2RTestData2,SEER2RTestData3 
     dicinfoused = write.SeerStat(SEER2RTestData2, DICfileName = "testrun1.dic",UseVarLabelsInTxtFile=FALSE);

Rd file 'write.SeerStat.Rd':
  \usage lines wider than 90 characters:
     write.SeerStat(myData, DICfileName, TXTfileName = NULL, UseVarLabelsInTxtFile = TRUE, LabVarsNames = NULL,...)
  \examples lines wider than 100 characters:
     #load testing data: there are three data objects, i.e. SEER2RTestData1,SEER2RTestData2,SEER2RTestData3 
     dicinfoused = write.SeerStat(SEER2RTestData2, DICfileName = "testrun1.dic",UseVarLabelsInTxtFile=FALSE);

These lines will be truncated in the PDF manual.
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.
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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.
'library' or 'require' calls in package code:
  ‘rgdal’ ‘spdep’ ‘spgrass6’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.use.spgrass6: no visible global function definition for ‘listw2mat’
.use.spgrass6: no visible global function definition for ‘sn2listw’
conprof: no visible global function definition for ‘axis’
conprof: no visible global function definition for ‘lines’
isp: no visible global function definition for ‘combn’
points.SegLocal: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis combn lines listw2mat points sn2listw
Consider adding
  importFrom("graphics", "axis", "lines", "points")
  importFrom("utils", "combn")
to your NAMESPACE file.
File ‘seg/libs/seg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘segregation-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mutual_difference
> ### Title: Decomposes the difference between two M indices
> ### Aliases: mutual_difference
> 
> ### ** Examples
> 
> mutual_difference(schools00, schools05, unit="race", group="school",
+     weight="n", method="mrc")
Error in `[.data.table`(d1, , list(p_unit = sum(freq)/n_total1), by = unit) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: mutual_difference -> method -> [ -> [.data.table
Execution halted
get.infectiousness: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  qchisq
Consider adding
  importFrom("stats", "qchisq")
to your NAMESPACE file.
File ‘seismicRoll/libs/seismicRoll.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
get_statistics_from_file: no visible global function definition for
  ‘read.csv’
glm_anova: no visible global function definition for ‘aov’
glm_anova: no visible global function definition for ‘glm’
glm_anova: no visible global function definition for ‘gaussian’
glm_anova: no visible global function definition for ‘anova’
glm_anova: no visible global function definition for ‘quasipoisson’
glm_anova: no visible global function definition for ‘sd’
glm_anova: no visible global function definition for ‘p.adjust’
ttest_cohens_d: no visible global function definition for ‘t.test’
ttest_cohens_d: no visible global function definition for ‘sd’
Undefined global functions or variables:
  anova aov gaussian glm p.adjust quasipoisson read.csv sd t.test
Consider adding
  importFrom("stats", "anova", "aov", "gaussian", "glm", "p.adjust",
             "quasipoisson", "sd", "t.test")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
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.
Package in Depends field not imported from: ‘sem’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'semdiag.Rd':
  \usage lines wider than 90 characters:
     semdiag(x,  EQSmodel, varphi=0.1, EQSdata='data.txt', D='E', delete=integer(0), max_it=1000, EQSprog='C:/Progra~1/EQS61/WINEQS',serial= ... [TRUNCATED]

Rd file 'semdiag.robfit.Rd':
  \usage lines wider than 90 characters:
     semdiag.robfit(lisrel0, x, q, varphi, EQSmodel, EQSdata, max_it=1000, EQSprog='C:/Progra~1/EQS61/WINEQS',serial=1234)
     semdiag.robfit1(lisrel0, x, q, varphi, EQSmodel, EQSdata, max_it=1000, EQSprog='C:/Progra~1/EQS61/WINEQS',serial=1234)

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  chisqNull.objectiveML print.summaryGOF
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Packages in Depends field not imported from:
  ‘datautils’ ‘irlba’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  add.linkinfo check.linkinfo del.linkinfo length.linkinfo
  transform.linkinfo
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
computeKernel: no visible binding for global variable ‘sd’
computeKernel: no visible global function definition for ‘dist’
computeKernel: no visible global function definition for ‘quantile’
computeProjectionFromKernel : <anonymous>: no visible global function
  definition for ‘irlba’
distortions: no visible binding for global variable ‘sd’
distortions: no visible global function definition for ‘dist’
Undefined global functions or variables:
  dist irlba quantile sd
Consider adding
  importFrom("stats", "dist", "quantile", "sd")
to your NAMESPACE file.
Running examples in ‘semisupKernelPCA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add
> ### Title: Generic add method
> ### Aliases: add
> 
> ### ** Examples
> 
> data(iris)
> 
> krn <- computeKernel(iris[,1:4])
> lk <- linkinfo(krn)
> lk <- add(lk, 1, 5, "link")
Error in UseMethod("add") : 
  no applicable method for 'add' applied to an object of class "linkinfo"
Calls: add
Execution halted
ChiSquaredLRTest: no visible global function definition for ‘na.omit’
ChiSquaredLRTest: no visible global function definition for ‘cov’
ChiSquaredLRTest: no visible global function definition for ‘dmvnorm’
ChiSquaredLRTest: no visible global function definition for ‘pchisq’
NormalTheoryLRTest: no visible global function definition for ‘na.omit’
NormalTheoryLRTest: no visible global function definition for ‘cov’
NormalTheoryLRTest: no visible global function definition for ‘dmvnorm’
NormalTheoryLRTest: no visible global function definition for ‘sd’
NormalTheoryLRTest: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cov dmvnorm na.omit pchisq pnorm sd
Consider adding
  importFrom("stats", "cov", "na.omit", "pchisq", "pnorm", "sd")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘XML’ ‘boot’ ‘sem’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
  ‘boot:::const’ ‘stats:::AIC.logLik’ ‘stats:::BIC.logLik’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘addPath.plsm’ ‘endogenous’ ‘predecessors’ ‘qSquared’ ‘reorder’
  ‘resempls’ ‘residuals.sempls’
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.
.plot_attachment: no visible global function definition for ‘dev.off’
.update_list: no visible global function definition for ‘modifyList’
mime_part.data.frame: no visible global function definition for
  ‘write.table’
mime_part.ggplot: no visible binding for global variable ‘pdf’
mime_part.matrix: no visible global function definition for
  ‘write.table’
mime_part.trellis: no visible binding for global variable ‘pdf’
Undefined global functions or variables:
  dev.off modifyList pdf write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("utils", "modifyList", "write.table")
to your NAMESPACE file.
'library' or 'require' call to ‘rtiff’ which was already attached by Depends.
  Please remove these calls from your code.
Rd file 'addDefault.Rd':
  \examples lines wider than 100 characters:
     plot.calls = c("boxplot(count ~ spray, data = InsectSprays, col = 'lightgray')", "plot(1:3,1:3, col='blue', xlab='', ylab=''); points(1 ... [TRUNCATED]
     plt.extras=list(figure1= "rect(xleft=c(3,1), ytop=c(25,5),xright=c(4,2),  ybottom=c(20,0));title(main='A', cex=3)", figure2="polygon(x= ... [TRUNCATED]
     Splot = addDefault(Splot, data=c("This is default", "data2"), data.labels=c("label", "d2"), links=c("http://www.buffalo.edu, http://www ... [TRUNCATED]

Rd file 'sendplot.Rd':
  \examples lines wider than 100 characters:
     plot.calls = c("plot(x,y,col='green', pch=3)","plot(0,0, col='purple',pch=22,bg='purple')","plot(1:3,1:3, type='b',pch=21,bg='red',col= ... [TRUNCATED]
         "plot(0,0, col='purple',pch=22,bg='purple')","plot(1:3,1:3, type='b',pch=21,bg='red',col='red')","curve(x^3-3*x,-2,2, col='blue')")

These lines will be truncated in the PDF manual.
Running examples in ‘sensiPhy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tree_intra_phylm
> ### Title: Interaction between phylogenetic uncertainty and intraspecific
> ###   variability - Phylogenetic Linear Regression
> ### Aliases: tree_intra_phylm
> 
> ### ** Examples
> 
> # Load data:
> data(alien)
> # run PGLS accounting for intraspecific and phylogenetic variation:
> intra.tree <- tree_intra_phylm(gestaLen ~ adultMass, data = alien$data, phy = alien$phy,
+ Vy = "SD_gesta", n.intra = 3, n.tree = 3, y.transf = log, x.transf = log)
Warning in tree_intra_phylm(gestaLen ~ adultMass, data = alien$data, phy = alien$phy,  :
  distrib = normal: make sure that standard deviation is provided for Vx and/or Vy
Error in if ((model == "trend") & (ape::is.ultrametric(phy))) stop("Trend is unidentifiable for ultrametric trees., see ?phylolm for details") else datphy <- match_dataphy(formula,  : 
  the condition has length > 1
Calls: tree_intra_phylm
Execution halted
gconv: no visible global function definition for ‘convolve’
sens.analysis.aberrant.rank: no visible global function definition for
  ‘pnorm’
sens.analysis.mh: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  convolve pnorm
Consider adding
  importFrom("stats", "convolve", "pnorm")
to your NAMESPACE file.
mscorev: no visible global function definition for ‘quantile’
senmwCI : funcCI: no visible global function definition for ‘qnorm’
senmwCI : funcCI2: no visible global function definition for ‘qnorm’
separable1k: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm quantile
Consider adding
  importFrom("stats", "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
plot.sensitivity.2.0d: no visible global function definition for ‘gray’
sensitivitySGD: no visible global function definition for ‘tail’
sensitivitySGL: no visible global function definition for ‘tail’
Undefined global functions or variables:
  gray tail
Consider adding
  importFrom("grDevices", "gray")
  importFrom("utils", "tail")
to your NAMESPACE file.
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.
Running examples in ‘sentimentr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: extract_sentiment_terms
> ### Title: Extract Sentiment Words
> ### Aliases: extract_sentiment_terms
> 
> ### ** Examples
> 
> library(data.table)
> set.seed(10)
> x <- get_sentences(sample(cannon_reviews[[2]], 1000, TRUE))
> sentiment(x)
Error in `[.data.table`(sent_dat, , `:=`(id2, seq_len(.N)), by = "id") : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: sentiment ... sentiment.get_sentences_character -> [ -> [.data.table
Execution halted
Running examples in ‘sentometrics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ctr_merge
> ### Title: Set up control for merging sentiment measures
> ### Aliases: ctr_merge
> 
> ### ** Examples
> 
> data("usnews", package = "sentometrics")
> data("lexicons", package = "sentometrics")
> data("valence", package = "sentometrics")
> 
> # construct a sentomeasures object to start with
> corpus <- sento_corpus(corpusdf = usnews)
> corpusSample <- quanteda::corpus_sample(corpus, size = 500)
> l <- setup_lexicons(lexicons[c("LM_eng", "HENRY_eng")], valence[["valence_eng"]])
> ctr <- ctr_agg(howTime = c("equal_weight", "linear"), by = "year", lag = 3)
> sentomeasures <- sento_measures(corpusSample, l, ctr)
Modify corpus to account for valence words... Done. 
Compute sentiment... Done. 
Error in `[.data.table`(s, , lapply(.SD, function(x) (x * 1)/x), by = date) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: sento_measures -> perform_agg -> agg_documents -> [ -> [.data.table
Execution halted
Running ‘testthat.R’ [7s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  > library(sentometrics)
  Loading required package: data.table
  Loading required package: ggplot2
  Loading required package: foreach
  > 
  > test_check("sentometrics")
  Compute sentiment... Done. 
  ── 1. Error: (unknown) (@test_aggregation.R#15)  ───────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: sento_measures(corpus, lex, ctr) at testthat/test_aggregation.R:15
  2: perform_agg(toAgg, ctr)
  3: agg_documents(toAgg, by = by, how = howDocs, do.ignoreZeros = do.ignoreZeros)
  4: s[, lapply(.SD, function(x) (x * word_count)/x), by = date]
  5: `[.data.table`(s, , lapply(.SD, function(x) (x * word_count)/x), by = date)
  
  Compute sentiment... Done. 
  ── 2. Error: (unknown) (@test_attribution.R#15)  ───────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: sento_measures(corpus, lex, ctr) at testthat/test_attribution.R:15
  2: perform_agg(toAgg, ctr)
  3: agg_documents(toAgg, by = by, how = howDocs, do.ignoreZeros = do.ignoreZeros)
  4: s[, list(w = word_count/sum(word_count, na.rm = TRUE)), by = date]
  5: `[.data.table`(s, , list(w = word_count/sum(word_count, na.rm = TRUE)), by = date)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test_aggregation.R#15) 
  2. Error: (unknown) (@test_attribution.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘seoR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lastCached
> ### Title: Function to get the last Google Cache Date for a URL
> ### Aliases: lastCached
> 
> ### ** Examples
> 
> lastCached("https://www.r-project.org/")
Error in if (is.na(res)) { : argument is of length zero
Calls: lastCached
Execution halted
separationplot: no visible global function definition for ‘dev.new’
separationplot: no visible global function definition for ‘pdf’
separationplot: no visible global function definition for ‘par’
separationplot: no visible global function definition for ‘plot’
separationplot: no visible global function definition for ‘title’
separationplot: no visible global function definition for ‘segments’
separationplot: no visible global function definition for ‘rect’
separationplot: no visible global function definition for ‘points’
separationplot: no visible global function definition for ‘lines’
separationplot: no visible global function definition for
  ‘colorRampPalette’
separationplot: no visible global function definition for ‘layout’
separationplot: no visible global function definition for ‘plot.new’
separationplot: no visible global function definition for ‘legend’
separationplot: no visible global function definition for ‘dev.off’
separationplot: no visible global function definition for ‘locator’
sp.categorical: no visible global function definition for ‘dev.new’
sp.categorical: no visible global function definition for ‘pdf’
sp.categorical: no visible global function definition for ‘par’
sp.categorical: no visible global function definition for ‘layout’
sp.categorical: no visible global function definition for ‘plot’
sp.categorical: no visible global function definition for ‘text’
sp.categorical: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  colorRampPalette dev.new dev.off layout legend lines locator par pdf
  plot plot.new points rect segments text title
Consider adding
  importFrom("grDevices", "colorRampPalette", "dev.new", "dev.off",
             "pdf")
  importFrom("graphics", "layout", "legend", "lines", "locator", "par",
             "plot", "plot.new", "points", "rect", "segments", "text",
             "title")
to your NAMESPACE file.
Rd file 'sp.categorical.Rd':
  \examples lines wider than 100 characters:
       read.dta("http://www2.lse.ac.uk/dataFiles/geographyAndEnvironment/Replication/Article%20for%20JCR%20(Human%20Rights).dta")

These lines will be truncated in the PDF manual.
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.
GammaDist: no visible binding for global variable ‘rgamma’
VEpowerPP: no visible global function definition for ‘qnorm’
applyStopRules: no visible global function definition for ‘qnorm’
finalLogRankTest: no visible global function definition for ‘qnorm’
finalLogRankTest: no visible global function definition for ‘pchisq’
generateDropout: no visible global function definition for ‘rexp’
generateEnrollment: no visible global function definition for ‘rpois’
generateEnrollment: no visible global function definition for ‘runif’
generateInfection: no visible global function definition for ‘rexp’
generateInfection : <anonymous>: no visible global function definition
  for ‘rexp’
getAlphaPerTest: no visible global function definition for ‘uniroot’
getHarmBound: no visible global function definition for ‘dbinom’
getHarmBound: no visible global function definition for ‘write.csv’
getTreatmentAssignment : <anonymous>: no visible global function
  definition for ‘runif’
getTreatmentAssignment: no visible global function definition for
  ‘runif’
simTrial: no visible global function definition for ‘runif’
sumTrialOneTrtArm: no visible global function definition for ‘quantile’
testVE: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  dbinom pchisq qnorm quantile rexp rgamma rpois runif uniroot
  write.csv
Consider adding
  importFrom("stats", "dbinom", "pchisq", "qnorm", "quantile", "rexp",
             "rgamma", "rpois", "runif", "uniroot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
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.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
                user system elapsed
prepScores     8.029  0.044   9.793
prepScores2    7.837  0.079   9.783
skatMeta       5.334  0.020   7.086
burdenMeta     4.183  0.035   5.174
prepCondScores 4.125  0.055   5.585
Found the following significant warnings:
  vcf.c:253:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/seqminer.Rcheck/00install.out’ for details.
plotenz : addmark: no visible global function definition for ‘par’
plotenz : addmark: no visible global function definition for ‘plot’
plotenz : addmark: no visible global function definition for ‘text’
plotenz : addmark: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘segments’
plotenz : addband: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘layout’
plotenz: no visible global function definition for ‘text’
plotenz: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  dev.new layout par plot segments text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "layout", "par", "plot", "segments", "text")
to your NAMESPACE file.
Rd file 'plotenz.Rd':
  \usage lines wider than 90 characters:
     plotenz(sequences, enznames, enzdata, side = TRUE, type = c("RFLP", "TRFLP"), Terminal = c("T5", "T3"))

These lines will be truncated in the PDF manual.
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.
File ‘sequoia/libs/sequoia.so’:
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘sequoia.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.
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.

Found the following calls to attach():
File ‘session/R/session.R’:
  attach(sub("file:", "", i))
See section ‘Good practice’ in ‘?attach’.
setpath: no visible global function definition for ‘cov’
setpath: no visible global function definition for ‘median’
setpath: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  cov median pchisq
Consider adding
  importFrom("stats", "cov", "median", "pchisq")
to your NAMESPACE file.
random.number.test: no visible global function definition for ‘runif’
random.number.test: no visible global function definition for ‘rnorm’
setRNG: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
'library' or 'require' call to ‘graphics’ which was already attached by Depends.
  Please remove these calls from your code.
severity: no visible global function definition for ‘qnorm’
severity: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm qnorm
Consider adding
  importFrom("stats", "pnorm", "qnorm")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.extmod print.simpextmod
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
L_exp: no visible global function definition for ‘pnorm’
L_hNV: no visible global function definition for ‘pnorm’
L_trunc: no visible global function definition for ‘pnorm’
L_trunc_mufest: no visible global function definition for ‘pnorm’
dgp: no visible global function definition for ‘runif’
dgp: no visible global function definition for ‘rnorm’
eff.sfa: no visible global function definition for ‘predict’
fitted.sfa: no visible global function definition for ‘predict’
predict.sfa: no visible global function definition for ‘coef’
print.sfa: no visible global function definition for ‘coef’
residuals.sfa: no visible global function definition for ‘fitted’
sfa: no visible global function definition for ‘model.frame’
sfa: no visible global function definition for ‘model.response’
sfa.fit: no visible global function definition for ‘lm’
sfa.fit: no visible global function definition for ‘resid’
sfa.fit: no visible global function definition for ‘var’
sfa.fit: no visible global function definition for ‘optim’
summary.sfa: no visible global function definition for ‘logLik’
summary.sfa: no visible global function definition for ‘pchisq’
te.eff.sfa: no visible global function definition for ‘residuals’
te.eff.sfa: no visible global function definition for ‘pnorm’
u.sfa: no visible global function definition for ‘residuals’
u.sfa: no visible global function definition for ‘dnorm’
u.sfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coef dnorm fitted lm logLik model.frame model.response optim pchisq
  pnorm predict resid residuals rnorm runif var
Consider adding
  importFrom("stats", "coef", "dnorm", "fitted", "lm", "logLik",
             "model.frame", "model.response", "optim", "pchisq", "pnorm",
             "predict", "resid", "residuals", "rnorm", "runif", "var")
to your NAMESPACE file.
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.
File ‘sglasso/libs/sglasso.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
coxCrossVal: no visible binding for global variable ‘sd’
error.bars: no visible global function definition for ‘segments’
linCrossVal: no visible binding for global variable ‘sd’
logitCrossVal: no visible binding for global variable ‘sd’
plot.cv.SGL: no visible global function definition for ‘points’
Undefined global functions or variables:
  points sd segments
Consider adding
  importFrom("graphics", "points", "segments")
  importFrom("stats", "sd")
to your NAMESPACE file.
Rd file 'SGL.Rd':
  \usage lines wider than 90 characters:
     SGL(data, index, type = "linear", maxit = 1000, thresh = 0.001, min.frac = 0.1, nlam = 20, gamma = 0.8, standardize = TRUE, verbose = F ... [TRUNCATED]

Rd file 'cvSGL.Rd':
  \usage lines wider than 90 characters:
     cvSGL(data, index, type = "linear", maxit = 1000, thresh = 0.001, min.frac = 0.05, nlam = 20, gamma = 0.8, nfold = 10, standardize = TR ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘SGL/libs/SGL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.computePStar: no visible global function definition for ‘uniroot’
plotBoundary: no visible global function definition for
  ‘scale_y_continuous’
Undefined global functions or variables:
  scale_y_continuous uniroot
Consider adding
  importFrom("stats", "uniroot")
to your NAMESPACE file.
amse: no visible global function definition for ‘na.omit’
arb: no visible global function definition for ‘na.omit’
rdatagen: no visible global function definition for ‘qnorm’
rdatagen: no visible global function definition for ‘pbinom’
rdatagen: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  na.omit pbinom pnorm qnorm
Consider adding
  importFrom("stats", "na.omit", "pbinom", "pnorm", "qnorm")
to your NAMESPACE file.
UQnormalize.count: no visible binding for global variable ‘quantile’
plotNScores: no visible global function definition for ‘par’
plotNScores: no visible global function definition for ‘hist’
plotNScores: no visible global function definition for ‘title’
plotScores: no visible global function definition for ‘par’
plotScores: no visible global function definition for ‘hist’
plotScores: no visible global function definition for ‘title’
sgRSEA: no visible binding for global variable ‘sd’
sgRSEA: no visible global function definition for ‘p.adjust’
sgRSEA.mean: no visible binding for global variable ‘sd’
sgRSEA.mean: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  hist p.adjust par quantile sd title
Consider adding
  importFrom("graphics", "hist", "par", "title")
  importFrom("stats", "p.adjust", "quantile", "sd")
to your NAMESPACE file.
'library' or 'require' call to ‘foreign’ which was already attached by Depends.
  Please remove these calls from your code.
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.
popify: no visible global function definition for ‘runif’
tipify: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
get_selected_names: no visible global function definition for ‘tail’
get_selected_names: no visible global function definition for ‘head’
Undefined global functions or variables:
  head tail
Consider adding
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
shrink.estim: no visible global function definition for ‘cov’
shrink.estim: no visible global function definition for ‘cor’
shrink.estim: no visible global function definition for ‘cov2cor’
targetCor: no visible global function definition for ‘cor.test’
targetCor: no visible global function definition for ‘cor’
targetCor: no visible global function definition for ‘sd’
targetCor: no visible global function definition for ‘cov’
targetD: no visible binding for global variable ‘var’
targetF: no visible global function definition for ‘cov’
targetF: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘cor’
targetG: no visible global function definition for ‘sd’
targetG: no visible global function definition for ‘cov’
targetGpos: no visible global function definition for ‘cor’
targetGpos: no visible global function definition for ‘sd’
targetGpos: no visible global function definition for ‘cov’
targetGstar: no visible global function definition for ‘cor’
targetGstar: no visible global function definition for ‘sd’
targetGstar: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cor cor.test cov cov2cor sd var
Consider adding
  importFrom("stats", "cor", "cor.test", "cov", "cov2cor", "sd", "var")
to your NAMESPACE file.
.params: no visible binding for global variable ‘URLencode’
.params: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Depends: includes the non-default packages:
  ‘hdrcde’ ‘coda’ ‘MASS’ ‘bayesm’ ‘mnormt’ ‘spatstat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘MASS’ ‘bayesm’ ‘coda’ ‘hdrcde’ ‘mnormt’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'siarmcmcdirichletv4.Rd':
  \usage lines wider than 90 characters:
     siarmcmcdirichletv4(data, sources, corrections = 0, concdep = 0, iterations=200000, burnin=50000, howmany=10000, thinby=15, prior = rep ... [TRUNCATED]

Rd file 'siarplotdata.Rd':
  \usage lines wider than 90 characters:
     siarplotdata(siardata, siarversion = 0, grp=1:siardata$numgroups,panel=NULL,isos=c(0,0),leg=1)

Rd file 'siarproportionbygroupplot.Rd':
  \usage lines wider than 90 characters:
     siarproportionbygroupplot(siardata, siarversion=0,probs=c(95,75,50),xlabels=NULL, grp=NULL, type="boxes",clr=gray((9:1)/10),scl=1,xspc= ... [TRUNCATED]

Rd file 'siarproportionbysourceplot.Rd':
  \usage lines wider than 90 characters:
     siarproportionbysourceplot(siardata, siarversion=0,probs=c(95,75,50),xlabels=NULL, grp=NULL, type="boxes",clr=gray((9:1)/10),scl=1,xspc ... [TRUNCATED]

Rd file 'siarsolomcmcv4.Rd':
  \usage lines wider than 90 characters:
     siarsolomcmcv4(data, sources, corrections = 0, concdep = 0, iterations=200000, burnin=50000, howmany=10000, thinby=15, prior = rep(1, n ... [TRUNCATED]

These lines will be truncated in the PDF manual.
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.
Packages in Depends field not imported from:
  ‘ade4’ ‘corpcor’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
filter.PCA.default: no visible global function definition for
  ‘princomp’
filter.mRMR.default: no visible global function definition for
  ‘discretize’
gaussian.default: no visible global function definition for ‘cov’
gaussian.default: no visible global function definition for
  ‘cov.shrink’
plot.verify.cv: no visible global function definition for ‘plot’
plot.verify.cv: no visible global function definition for ‘points’
plot.verify.ho: no visible global function definition for ‘plot’
plot.verify.ho: no visible global function definition for ‘points’
plot.verify.loo: no visible global function definition for ‘plot’
plot.verify.loo: no visible global function definition for ‘points’
predict.dpa1: no visible global function definition for ‘cor’
predict.filter.PCA: no visible global function definition for ‘predict’
predict.filter.RegressionTreeFilter: no visible global function
  definition for ‘is.struct’
predict.filter.RegressionTreeFilter: no visible global function
  definition for ‘var’
simulator.Simple1: no visible global function definition for ‘rnorm’
verify.ho.default: no visible global function definition for ‘predict’
verify.loo.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  cor cov cov.shrink discretize is.struct plot points predict princomp
  rnorm var
Consider adding
  importFrom("graphics", "plot", "points")
  importFrom("stats", "cor", "cov", "predict", "princomp", "rnorm",
             "var")
to your NAMESPACE file.
Rd file 'plot.verify.ho.Rd':
  \examples lines wider than 100 characters:
     attack=verify.ho(model=gaussian,filter=filter.PCA,Xlearn=traces[1:128,],Ylearn=key[1:128],Xval=traces[129:256,],Yval=key[129:256],nbreV ... [TRUNCATED]

Rd file 'sideChannelAttack-package.Rd':
  \examples lines wider than 100 characters:
     attack=verify.ho(model=gaussian,filter=filter.PCA,Xlearn=traces[1:128,],Ylearn=key[1:128],Xval=traces[129:256,],Yval=key[129:256],nbreV ... [TRUNCATED]

Rd file 'verify.ho.Rd':
  \usage lines wider than 90 characters:
     verify.ho(model, filter, Xlearn, Ylearn, Xval, Yval, nbreVarX, param.model=list(), param.fs=list(), ...)
  \examples lines wider than 100 characters:
     attack=verify.ho(model=gaussian,filter=filter.PCA,Xlearn=traces[1:128,],Ylearn=key[1:128],Xval=traces[128:256,],Yval=key[128:256],nbreV ... [TRUNCATED]

These lines will be truncated in the PDF manual.
dSepAdji: no visible global function definition for ‘as’
dag2cpdagAdj: no visible global function definition for ‘as’
randomDAG: no visible global function definition for ‘rbinom’
structIntervDist: no visible global function definition for ‘as’
Undefined global functions or variables:
  as rbinom
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rbinom")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following apparent S3 methods exported but not registered:
  [.std c.std plot.std summary.std
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.std: no visible global function definition for ‘rainbow’
plot.std: no visible global function definition for ‘legend’
read.std: no visible global function definition for ‘read.table’
std: no visible global function definition for ‘na.exclude’
Undefined global functions or variables:
  legend na.exclude rainbow read.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend")
  importFrom("stats", "na.exclude")
  importFrom("utils", "read.table")
to your NAMESPACE file.
.cluster: no visible global function definition for ‘kmeans’
.plot.sigclust: no visible global function definition for ‘par’
.plot.sigclust: no visible global function definition for ‘density’
.plot.sigclust: no visible global function definition for ‘runif’
.plot.sigclust: no visible global function definition for ‘dnorm’
.plot.sigclust: no visible global function definition for ‘lines’
.plot.sigclust: no visible global function definition for ‘points’
.plot.sigclust: no visible global function definition for ‘title’
.plot.sigclust: no visible global function definition for ‘text’
.plot.sigclust: no visible global function definition for ‘qnorm’
.plot.sigclust: no visible global function definition for ‘abline’
.plot.sigclust: no visible global function definition for ‘quantile’
.plot.sigclust: no visible global function definition for ‘legend’
.simnull: no visible global function definition for ‘rnorm’
.vareigen: no visible global function definition for ‘mad’
.vareigen: no visible global function definition for ‘cov’
sigclust: no visible global function definition for ‘sd’
sigclust: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  abline cov density dnorm kmeans legend lines mad par pnorm points
  qnorm quantile rnorm runif sd text title
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "points",
             "text", "title")
  importFrom("stats", "cov", "density", "dnorm", "kmeans", "mad",
             "pnorm", "qnorm", "quantile", "rnorm", "runif", "sd")
to your NAMESPACE file.
Sight.Est: no visible global function definition for ‘glm’
Sight.Est: no visible global function definition for ‘binomial’
Sight.Est: no visible global function definition for ‘coef’
Sight.Est: no visible global function definition for ‘terms’
Sight.Est: no visible binding for global variable ‘binomial’
covtheta: no visible global function definition for ‘cov’
print.sightest: no visible global function definition for ‘qnorm’
summary.sightest: no visible global function definition for ‘qnorm’
vardiff: no visible global function definition for ‘vcov’
vardiff: no visible global function definition for ‘coef’
vardiff: no visible global function definition for ‘terms’
varlog.lam: no visible global function definition for ‘vcov’
varlog.lam: no visible global function definition for ‘coef’
varlog.lam: no visible global function definition for ‘terms’
Undefined global functions or variables:
  binomial coef cov glm qnorm terms vcov
Consider adding
  importFrom("stats", "binomial", "coef", "cov", "glm", "qnorm", "terms",
             "vcov")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  as.data.frame.intersect as.data.frame.receiver
  as.data.frame.transmitter plot.intersect plot.receiver
  plot.transmitter print.intersect print.receiver print.transmitter
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.intersect: no visible global function definition for ‘points’
plot.intersect: no visible global function definition for ‘plot’
plot.receiver: no visible global function definition for ‘points’
plot.receiver: no visible global function definition for ‘plot’
plot.receiver: no visible global function definition for ‘segments’
plot.transmitter: no visible global function definition for ‘points’
plot.transmitter: no visible global function definition for ‘plot’
plot.transmitter: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot points segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
to your NAMESPACE file.
Running examples in ‘sigloc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.receiver
> ### Title: Coerce to Class 'receiver'
> ### Aliases: as.receiver plot.receiver print.receiver
> ###   as.data.frame.receiver
> 
> ### ** Examples
> 
> ## Load the data
> data(bear)
> 
> ## Convert data to class 'receiver
> bear<-as.receiver(bear)
> 
> ## Display resulting object with bearings
> plot(bear,bearings=TRUE,xlab="Easting",ylab="Northing")
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
File ‘signalHsmm/libs/signalHsmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
signmedian.test: no visible global function definition for ‘median’
signmedian.test: no visible global function definition for ‘binom.test’
signmedian.test: no visible global function definition for ‘pbinom’
signmedian.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  binom.test median pbinom pnorm
Consider adding
  importFrom("stats", "binom.test", "median", "pbinom", "pnorm")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘gdata’ ‘splines’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.SII: no visible global function definition for ‘plot’
plot.SII: no visible global function definition for ‘lines’
plot.SII: no visible global function definition for ‘abline’
plot.SII: no visible global function definition for ‘legend’
sii : approx.l: no visible global function definition for ‘approx’
sii.excel: no visible global function definition for ‘predict’
sii.excel : approx.l: no visible global function definition for
  ‘approx’
Undefined global functions or variables:
  abline approx legend lines plot predict
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.simexaft summary.simexaft
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
linearextrapolation: no visible global function definition for ‘coef’
linearextrapolation: no visible global function definition for ‘lm’
plotsimexaft: no visible global function definition for ‘plot’
plotsimexaft: no visible global function definition for ‘lm’
plotsimexaft: no visible global function definition for ‘predict’
plotsimexaft: no visible global function definition for ‘lines’
plotsimexaft: no visible global function definition for ‘points’
plotsimexaft: no visible global function definition for ‘legend’
print.simexaft: no visible global function definition for ‘coef’
quadraticextrapolation: no visible global function definition for
  ‘coef’
quadraticextrapolation: no visible global function definition for ‘lm’
simexaft: no visible global function definition for ‘terms’
simexaft: no visible global function definition for ‘rnorm’
simexaft: no visible binding for global variable ‘var’
simexaft: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coef legend lines lm plot pnorm points predict rnorm terms var
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "coef", "lm", "pnorm", "predict", "rnorm", "terms",
             "var")
to your NAMESPACE file.
getFormula: no visible global function definition for ‘as.formula’
internalSimXyplot : f: no visible global function definition for
  ‘median’
runSimulation: no visible global function definition for ‘runif’
setup: no visible global function definition for ‘runif’
clusterSetup,ANY-data.frame-SampleControl: no visible binding for
  global variable ‘cnam’
clusterSetup,ANY-data.frame-TwoStageControl: no visible binding for
  global variable ‘cnam’
initialize,DCARContControl: no visible binding for global variable
  ‘rnorm’
initialize,DataControl: no visible binding for global variable ‘rnorm’
Undefined global functions or variables:
  as.formula cnam median rnorm runif
Consider adding
  importFrom("stats", "as.formula", "median", "rnorm", "runif")
to your NAMESPACE file.
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.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
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 189-213 (unbalanced.Rmd) 
Error: processing vignette ‘unbalanced.Rmd’ failed with diagnostics:
the condition has length > 1
Execution halted
File ‘simLife/libs/simLife.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.
cumallcausehr: no visible global function definition for ‘integrate’
plotbe: no visible global function definition for ‘plot’
plotbe: no visible global function definition for ‘lines’
plotbe: no visible global function definition for ‘legend’
plotcph: no visible global function definition for ‘confint’
plotcph: no visible global function definition for ‘plot’
plotcph: no visible global function definition for ‘abline’
plotcph: no visible global function definition for ‘axis’
plotcph: no visible global function definition for ‘polygon’
plotcph: no visible global function definition for ‘lines’
plotnae: no visible global function definition for ‘plot’
simCR: no visible global function definition for ‘rnorm’
simEBMT: no visible global function definition for ‘model.matrix’
simexit: no visible global function definition for ‘runif’
simexitinner: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  abline axis confint integrate legend lines model.matrix plot polygon
  rnorm runif uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "plot",
             "polygon")
  importFrom("stats", "confint", "integrate", "model.matrix", "rnorm",
             "runif", "uniroot")
to your NAMESPACE file.
'library' or 'require' call to ‘boot’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘boot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  pairs.boot
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘simpleboot/R/zzz.R’:
  .onLoad calls:
    require(boot)

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

lo.boot.resample: warning in sample(1:nrow(orig.data), rep = TRUE, prob
  = weights): partial argument match of ‘rep’ to ‘replace’
lo.boot.resample: warning in sample(res, rep = TRUE, prob = weights):
  partial argument match of ‘rep’ to ‘replace’
S3 methods shown with full name in documentation object 'pairs.boot':
  ‘pairs.boot’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
randInitializeWeights: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File
  LICENSE
is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘HISTORY’
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.
Running examples in ‘simPop-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ipu2
> ### Title: Iterative Proportional Updating
> ### Aliases: ipu2
> 
> ### ** Examples
> 
> data(eusilcS)
> setDT(eusilcS)
> eusilcS <- eusilcS[, list(db030,hsize,db040,age,rb090,netIncome,db090,rb050)]
> 
> ## rename columns
> setnames(eusilcS, "rb090", "gender")
> setnames(eusilcS, "db040", "state")
> setnames(eusilcS, "db030", "household")
> setnames(eusilcS, "rb050", "weight")
> 
> ## some recoding
> # generate age groups
> eusilcS[, agegroup := cut(age, c(-Inf, 10*1:9, Inf), right = FALSE)]
> # some recoding of netIncome for reasons of simplicity
> eusilcS[is.na(netIncome), netIncome := 0] 
> eusilcS[netIncome < 0, netIncome := 0] 
> # set hsize to 1,...,5+
> eusilcS[, hsize := cut(hsize, c(0:4, Inf), labels = c(1:4, "5+"))]
> # treat households as a factor variable
> eusilcS[, household := as.factor(household)]
> 
> ## example for base weights assuming a simple random sample of households stratified per region
> eusilcS[, regSamp := .N, by = state]
Error in `[.data.table`(eusilcS, , `:=`(regSamp, .N), by = state) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: [ -> [.data.table
Execution halted
Package in Depends field not imported from: ‘mclust’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Simpsons: no visible global function definition for ‘Mclust’
Simpsons: no visible global function definition for ‘lm’
Simpsons: no visible global function definition for ‘plot’
Simpsons: no visible global function definition for ‘abline’
Simpsons: no visible global function definition for ‘par’
Simpsons: no visible global function definition for ‘legend’
Simpsons: no visible global function definition for ‘txtProgressBar’
Simpsons: no visible global function definition for ‘setTxtProgressBar’
Simpsons: no visible global function definition for ‘quantile’
plot.Simpson: no visible global function definition for ‘plot’
plot.Simpson: no visible global function definition for ‘lm’
plot.Simpson: no visible global function definition for ‘abline’
plot.Simpson: no visible global function definition for ‘par’
plot.Simpson: no visible global function definition for ‘legend’
Undefined global functions or variables:
  Mclust abline legend lm par plot quantile setTxtProgressBar
  txtProgressBar
Consider adding
  importFrom("graphics", "abline", "legend", "par", "plot")
  importFrom("stats", "lm", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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.
simrel: no visible global function definition for ‘runif’
simrel: no visible global function definition for ‘rnorm’
simrelplot: no visible global function definition for ‘par’
simrelplot: no visible global function definition for ‘layout’
simrelplot: no visible global function definition for ‘devAskNewPage’
simrelplot: no visible global function definition for ‘dev.hold’
simrelplot: no visible global function definition for ‘plot’
simrelplot: no visible global function definition for ‘abline’
simrelplot: no visible global function definition for ‘dev.flush’
simrelplot: no visible global function definition for ‘points’
simrelplot: no visible global function definition for ‘axis’
simrelplot: no visible global function definition for ‘mtext’
simrelplot: no visible global function definition for ‘box’
simrelplot: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cov dev.flush dev.hold devAskNewPage layout mtext par
  plot points rnorm runif
Consider adding
  importFrom("grDevices", "dev.flush", "dev.hold", "devAskNewPage")
  importFrom("graphics", "abline", "axis", "box", "layout", "mtext",
             "par", "plot", "points")
  importFrom("stats", "cov", "rnorm", "runif")
to your NAMESPACE file.
Running examples in ‘simstudy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addPeriods
> ### Title: Create longitudinal/panel data
> ### Aliases: addPeriods
> 
> ### ** Examples
> 
> tdef <- defData(varname = "T", dist="binary", formula = 0.5)
> tdef <- defData(tdef, varname = "Y0", dist = "normal", formula = 10, variance = 1)
> tdef <- defData(tdef, varname = "Y1", dist = "normal", formula = "Y0 + 5 + 5 * T", variance = 1)
> tdef <- defData(tdef, varname = "Y2", dist = "normal", formula = "Y0 + 10 + 5 * T", variance = 1)
> 
> dtTrial <- genData( 5, tdef)
> dtTrial
   id T        Y0       Y1       Y2
1:  1 0 11.272429 16.26666 20.98297
2:  2 0 10.414641 17.81929 20.11543
3:  3 1  8.460050 19.22364 23.04854
4:  4 1  9.071433 18.27242 24.32366
5:  5 0  9.705280 13.55762 18.81336
> 
> dtTime <- addPeriods(dtTrial, nPeriods = 3, idvars = "id",
+                      timevars = c("Y0", "Y1", "Y2"), timevarName = "Y")
> dtTime
> 
> # Varying # of periods and intervals - need to have variables
> # called nCount and mInterval
> 
> def <- defData(varname = "xbase", dist = "normal", formula = 20, variance = 3)
> def <- defData(def,varname = "nCount", dist = "noZeroPoisson", formula = 6)
> def <- defData(def, varname = "mInterval", dist = "gamma", formula = 30, variance = .01)
> def <- defData(def, varname = "vInterval", dist = "nonrandom", formula = .07)
> 
> dt <- genData(200, def)
> dt[id %in% c(8,121)]
    id    xbase nCount mInterval vInterval
1:   8 20.87227      6  32.94064      0.07
2: 121 18.49349      5  27.77496      0.07
> 
> dtPeriod <- addPeriods(dt)
Error in `[.data.table`(dtTimes1, , `:=`(time, round(cumsum(timeElapsed))),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: addPeriods -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Loading required package: data.table
Quitting from lines 499-511 (simstudy.Rmd) 
Error: processing vignette ‘simstudy.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Found the following hidden files and directories:
  vignettes/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘abind’ ‘svUnit’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
simSummary: no visible global function definition for ‘abind’
simSummary_unitTests: no visible global function definition for
  ‘clearLog’
simSummary_unitTests: no visible global function definition for
  ‘runTest’
simSummary_unitTests: no visible global function definition for
  ‘svSuite’
simSummary_unitTests: no visible global function definition for ‘Log’
simSummary_unitTests: no visible global function definition for ‘stats’
simSummary_unitTests: no visible global function definition for
  ‘metadata’
simSummary_unitTests: no visible global function definition for
  ‘errorLog’
Undefined global functions or variables:
  Log abind clearLog errorLog metadata runTest stats svSuite
Found the following apparent S3 methods exported but not registered:
  plot.CorrAn plot.SimAn summary.CorrAn summary.SimAn
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.CorrAn : SAPplot: no visible global function definition for ‘plot’
plot.CorrAn : SAPtitle: no visible global function definition for
  ‘title’
plot.CorrAn : SAPtitle: no visible global function definition for
  ‘mtext’
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  ‘points’
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  ‘text’
plot.CorrAn: no visible global function definition for ‘dev.new’
plot.SimAn : SAPplot: no visible global function definition for ‘plot’
plot.SimAn : SAPtitle: no visible global function definition for
  ‘title’
plot.SimAn : SAPtitle: no visible global function definition for
  ‘mtext’
plot.SimAn : SAPplotpuntos: no visible global function definition for
  ‘points’
plot.SimAn : SAPplotpuntos: no visible global function definition for
  ‘text’
plot.SimAn: no visible global function definition for ‘dev.new’
plot.SimAn: no visible global function definition for ‘points’
plot.SimAn: no visible global function definition for ‘text’
plot.SimAn: no visible global function definition for ‘par’
plot.SimAn: no visible global function definition for ‘plot’
plot.SimAn: no visible global function definition for ‘title’
plot.SimAn: no visible global function definition for ‘axis’
plot.SimAn: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis dev.new mtext par plot points text title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "arrows", "axis", "mtext", "par", "plot",
             "points", "text", "title")
to your NAMESPACE file.
Running examples in ‘SIRItoGTFS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: readGTFS
> ### Title: read GTFS files from a folder into R's environment
> ### Aliases: readGTFS
> ### Keywords: iteration utilities
> 
> ### ** Examples
> 
>   require(SIRItoGTFS)
>   directory = getwd()
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/agency.csv"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/calendar.csv"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/routes.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/shapes.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/stop_times.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/stops.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/translations.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/trips.txt"))
> 
>   # now we read just the minimal tables needed for `STG`,
>   # meaning everything besides shapes and translations
>   readGTFS(directory, minimal = TRUE, extension = "BOTH")
Error in data.table::fread(input = tbl, sep = sep, nrows = nrows, header = header,  : 
  isTrueFalse(showProgress) is not TRUE
Calls: readGTFS -> <Anonymous> -> stopifnot
Execution halted
Found the following apparent S3 methods exported but not registered:
  plot.siRSM plot.siRSM.default plot.siRSM.default print.siRSM
  print.siRSM.default print.siRSM.default siRSM.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘sitreeE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: biomass.M1988
> ### Title: Biomass functions of Marklund (1988) and Petterson and
> ###   Sth<c3><a5>l (2006)
> ### Aliases: biomass.M1988
> 
> ### ** Examples
> 
> 
> res <- sitree (tree.df   = tr,
+                 stand.df  = fl,
+                 functions = list(
+                     fn.growth     = 'grow.dbhinc.hgtinc',
+                     fn.dbh.inc = "dbhi.BN2009",
+                     fn.hgt.inc =  "height.korf", 
+                     fn.mort       = 'mort.B2007',
+                     fn.recr       = 'recr.BBG2008',
+                     fn.management = 'management.prob',
+                     fn.tree.removal = 'mng.tree.removal',
+                     fn.modif      = NULL,
+                     fn.prep.common.vars = 'prep.common.vars.fun'
+                 ),
+                 n.periods = 5,
+                 period.length = 5,
+                 mng.options = NA,
+                 print.comments = FALSE,
+                 species.spruce = c(1, 2, 3),
+                 species.pine = c(10, 11, 20, 21, 29),
+                 species.harw = c(30, 31),
+                 fun.final.felling = "harv.prob",
+                 fun.thinning      = "thin.prob",
+                 'BN2009',
+                 'BBG2008', 'SBA.m2.ha', 'spp','pr.spru.ba', 'QMD.cm',
+                 per.vol.harv = 0.83
+                 )
Error in `[.data.table`(DT, , list(wret = mean(tree.age.years), w = (tree.BA.m2/sum(tree.BA.m2))),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: sitree ... do.call -> prep.common.vars.fun -> [ -> [.data.table
Execution halted
Running examples in ‘sitree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: management.prob
> ### Title: Final felling and thinning functions for Norwegian forest
> ### Aliases: harv.prob management.prob thin.prob
> 
> ### ** Examples
> 
> foo.matrix <-  matrix(0, nrow = length(tr$dbh), ncol = (5 +1))
> colnames(foo.matrix) <- paste("t", 0:5, sep = "")
> foo.dbh <- foo.height <- foo.matrix
> foo.dbh[,1] <- tr$dbh
> foo.height[,1] <- tr$height
> 
> trl <- list(
+   plot.id  = tr$plot.id,
+   treeid    = tr$treeid,
+   dbh.mm    = foo.dbh,
+   height.dm = foo.height,
+   yrs.sim   = rep(0, nrow(tr)),
+   tree.sp   = factor(tr$tree.sp)
+ )
> tr.i <- trList$new(data = trl, nperiods = as.integer(5))
> 
> common.vars <-  prep.common.vars.fun(
+   tr = tr.i,
+   fl = fl,
+   i.period       = 0,
+   this.period    = "t0",
+   common.vars    = "NULL",
+   vars.required  = c("spp", "SBA.m2.ha", "QMD.cm", "vuprha.m3.ha", "AgeTo5"),
+   period.length = 5,
+   species.spruce = c(1, 2, 3),
+   species.pine = c(10, 11, 20, 21, 29),
+   species.harw = c(30, 31)
+ )
Error in `[.data.table`(DT, , list(wret = mean(tree.age.years), w = (tree.BA.m2/sum(tree.BA.m2))),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: prep.common.vars.fun -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 98-180 (TestEquations.Rmd) 
Error: processing vignette ‘TestEquations.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
File ‘sivipm/libs/sivipm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 apparent S3 methods exported but not registered:
  logLik.PiecewiseLinear logLik.bent_cable
  plot.LocallyWeightedPolynomial plot.PiecewiseLinear plot.SiZer
  predict.PiecewiseLinear predict.bent_cable print.PiecewiseLinear
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
cvskda: no visible global function definition for ‘detectCores’
cvskda: no visible global function definition for ‘makeCluster’
cvskda: no visible global function definition for ‘clusterApplyLB’
cvskda: no visible global function definition for ‘mclapply’
cvskda: no visible global function definition for ‘stopCluster’
Undefined global functions or variables:
  clusterApplyLB detectCores makeCluster mclapply stopCluster
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.
Found the following apparent S3 methods exported but not registered:
  print.summary.skewhypFit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
dskt: no visible global function definition for ‘dt’
pskt: no visible global function definition for ‘pt’
qskt: no visible global function definition for ‘qt’
rskt: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘kmndirs’
Unavailable namespace imported from by a ':::' call: ‘kmndirs’
  See the note in ?`:::` about the use of this operator.
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.
Error in re-building vignettes:
  ...
Loading required package: magrittr
Loading required package: data.table
skm_mls: skm solver via skm_mls_cpp ...

Quitting from lines 266-276 (skm-vignettes.Rmd) 
Error: processing vignette ‘skm-vignettes.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Found the following apparent S3 methods exported but not registered:
  plot.sla print.sla print.summary.sla sla.default summary.sla
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.sla: no visible global function definition for ‘title’
plot.sla: no visible global function definition for ‘abline’
print.sla: no visible global function definition for ‘coef’
sla.default: no visible global function definition for ‘lm’
sla.default: no visible global function definition for ‘anova’
Undefined global functions or variables:
  abline anova coef lm title
Consider adding
  importFrom("graphics", "abline", "title")
  importFrom("stats", "anova", "coef", "lm")
to your NAMESPACE file.
Running examples in ‘sla-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: eqint
> ### Title: Equivalent Intercepts Data Frame - eqint
> ### Aliases: eqint
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(eqint)
> str(eqint)
'data.frame':	10 obs. of  3 variables:
 $ group: Factor w/ 2 levels "one","two": 1 1 1 1 1 2 2 2 2 2
 $ x    : int  1 2 3 4 5 1 2 3 4 5
 $ y    : num  4 7 8 11 15 1 1.1 0.9 1.1 0.9
> eqintObj <- sla(eqint)
Error in UseMethod("sla") : 
  no applicable method for 'sla' applied to an object of class "data.frame"
Calls: sla
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 601-602 (introduction-to-sla.Rnw) 
Error: processing vignette ‘introduction-to-sla.Rnw’ failed with diagnostics:
no applicable method for ‘sla’ applied to an object of class "data.frame"
Execution halted
slcestimates: no visible global function definition for ‘par’
slcestimates: no visible global function definition for ‘plot’
slcestimates: no visible global function definition for ‘abline’
slcestimates: no visible global function definition for ‘lines’
slcestimates: no visible global function definition for ‘axis’
slcestimates: no visible global function definition for ‘points’
slcestimates: no visible global function definition for ‘title’
Undefined global functions or variables:
  abline axis lines par plot points title
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "par", "plot",
             "points", "title")
to your NAMESPACE file.
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.
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.
Error in re-building vignettes:
  ...
Quitting from lines 76-80 (slim.Rmd) 
Error: processing vignette ‘slim.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
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.
File ‘smaa/libs/smaa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cvsmac: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
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.
File ‘smam/libs/smam.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘smco/R/smco.R’:
  .onAttach calls:
    cat(paste("This is smco package", version, "\n"))

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

smco: no visible global function definition for ‘runif’
smco: no visible global function definition for ‘rnorm’
smco: no visible global function definition for ‘qnorm’
smco: no visible global function definition for ‘pnorm’
smco: no visible global function definition for ‘optim’
Undefined global functions or variables:
  optim pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "optim", "pnorm", "qnorm", "rnorm", "runif")
to your NAMESPACE file.
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 ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SMCP.Rcheck/00install.out’ for details.
SMCP : fun: no visible global function definition for ‘cor’
manipulate : fun: no visible global function definition for ‘sd’
sp: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  cor sd
Consider adding
  importFrom("stats", "cor", "sd")
to your NAMESPACE file.
File ‘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/R/zzz.R’:
  .onLoad calls:
    packageStartupMessage("##\n", "## Sequential Monte Carlo Package (SMC)\n",     "##\n", "## Functionality: sequential Monte Carlo (SMC) or sequential importance\n",     "## sampling (SIS) or hidden Markov models (HMM), particle filter (PF)\n",     "## and auxiliary particle filter (APF)\n", "##\n", "## Use: \"help(package = SMC)\" at the R prompt for more info\n",     "##\n", "## Copyright (C) 2006-", this.year, " Gopi Goswami\n",     "##\n", "##    Created by: Gopi Goswami <goswami@stat.harvard.edu>\n",     "## Maintained by: Gopi Goswami <grgoswami@gmail.com>\n",     "##\n")

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

.MHUpdateFuncGen.PF : MHUpdateFunc: no visible global function
  definition for ‘runif’
MarkovSwitchingFuncGenerator : generateNextStreamsFunc: no visible
  global function definition for ‘runif’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘rnorm’
MarkovSwitchingFuncGenerator: no visible global function definition for
  ‘runif’
MarkovSwitchingFuncGenerator : logObsDensFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘dnorm’
MarkovSwitchingFuncGenerator : propagateFunc: no visible global
  function definition for ‘runif’
Undefined global functions or variables:
  dnorm rnorm runif
Consider adding
  importFrom("stats", "dnorm", "rnorm", "runif")
to your NAMESPACE file.
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.
em: no visible global function definition for ‘coxph’
em: no visible global function definition for ‘optim’
plotpredictsmcure: no visible global function definition for ‘plot’
plotpredictsmcure: no visible global function definition for ‘matplot’
plotpredictsmcure: no visible global function definition for ‘lines’
smcure: no visible binding for global variable ‘na.omit’
smcure: no visible global function definition for ‘model.frame’
smcure: no visible global function definition for ‘model.extract’
smcure: no visible global function definition for ‘model.matrix’
smcure: no visible global function definition for ‘coxph’
smcure: no visible global function definition for ‘survreg’
smcure: no visible binding for global variable ‘var’
smcure: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  coxph lines matplot model.extract model.frame model.matrix na.omit
  optim plot pnorm survreg var
Consider adding
  importFrom("graphics", "lines", "matplot", "plot")
  importFrom("stats", "model.extract", "model.frame", "model.matrix",
             "na.omit", "optim", "pnorm", "var")
to your NAMESPACE file.
branching.resample: no visible global function definition for ‘rbinom’
cov.weights: no visible global function definition for ‘var’
inverse.cdf.weights: no visible global function definition for ‘runif’
multinomial.resample: no visible global function definition for ‘runif’
stratified.resample: no visible global function definition for ‘runif’
systematic.resample: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rbinom runif var
Consider adding
  importFrom("stats", "rbinom", "runif", "var")
to your NAMESPACE file.
Rd file 'resampling.Rd':
  \usage lines wider than 90 characters:
     residual.resample(   weights, num.samples = length(weights), engine="R", rrf = "stratified")

These lines will be truncated in the PDF manual.
File ‘smcUtils/libs/smcUtils.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘proxy’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘proxy’ ‘tm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
normalize: no visible binding for global variable ‘sd’
simDic: no visible global function definition for ‘simil’
simDoc: no visible global function definition for ‘simil’
Undefined global functions or variables:
  sd simil
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Rd file 'simDic.Rd':
  \usage lines wider than 90 characters:
     simDic(docMatrix1, docMatrix2, scoreDict, breaks = seq(-1, 1, length = 11), norm = FALSE, method = "cosine", scoreFunc = mean)

These lines will be truncated in the PDF manual.
Grad.sph: no visible global function definition for ‘dist’
IMDS: no visible global function definition for ‘cmdscale’
IMDS: no visible global function definition for ‘as.dist’
IMDS: no visible global function definition for ‘runif’
IMDS: no visible global function definition for ‘optim’
idistSph: no visible global function definition for ‘dist’
obj.sph: no visible global function definition for ‘dist’
plot.imds: no visible binding for global variable ‘lines’
plot.imds: no visible global function definition for ‘plot’
plot.imds: no visible global function definition for ‘text’
plot.imds: no visible global function definition for ‘rect’
Undefined global functions or variables:
  as.dist cmdscale dist lines optim plot rect runif text
Consider adding
  importFrom("graphics", "lines", "plot", "rect", "text")
  importFrom("stats", "as.dist", "cmdscale", "dist", "optim", "runif")
to your NAMESPACE file.
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.
'library' or 'require' calls to packages already attached by Depends:
  ‘ggplot2’ ‘reshape’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘corpcor’ ‘ggplot2’ ‘reshape’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘smfsb/libs/smfsb.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘MASS’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  disparity.glm disparity.lm summary.treg
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘SMIR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: NPL.bands
> ### Title: Nonparametric likelihood confidence bands
> ### Aliases: NPL.bands
> ### Keywords: distribution
> 
> ### ** Examples
> 
> ### Empirical distribution of a gamma variable
> ### and comparing to a normal 
> library(lattice)
> y <- round(rgamma(100,shape=1.4,scale=20))
> meany <- mean(y)
> sdy <- sd(y)
> print(xyplot(qnorm(lower)+qnorm(upper)~x,data=NPL.bands(y),
+ panel=function(x,y,...){
+ panel.xyplot(x,y,...)
+ panel.curve(qnorm(pnorm(x,mean=meany,sd=sdy)))}))
Error in if (conf.level == 0.95) { : the condition has length > 1
Calls: print -> xyplot -> xyplot.formula -> eval -> NPL.bands
Execution halted
lines.SmithWilsonYieldCurve: no visible global function definition for
  ‘lines’
plot.SmithWilsonYieldCurve: no visible global function definition for
  ‘plot’
points.SmithWilsonYieldCurve: no visible global function definition for
  ‘points’
Undefined global functions or variables:
  lines plot points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
Fourier2d: no visible global function definition for ‘fft’
kernel2dsmooth: no visible global function definition for ‘fft’
Undefined global functions or variables:
  fft
Consider adding
  importFrom("stats", "fft")
to your NAMESPACE file.
Found the following significant warnings:
  ./Scythe_IDE.cpp:70:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:107:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:108:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:109:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:147:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:148:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:149:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:189:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:211:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:212:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:262:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:265:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:266:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/smoothSurv.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  pairs.mod plot.glm.diag
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'plot.glm.diag.Rd':
  \usage lines wider than 90 characters:
     plot(x, glmdiag = glm.diag(x), subset = NULL, iden = FALSE, labels = NULL, ret = FALSE, ...)

Rd file 'poi.beta.laplace.Rd':
  \usage lines wider than 90 characters:
     poi.beta.laplace(data, alpha = get.alpha(data), phi = 1, nu = 0.1, beta = seq(from = 0, to = 7, length = 1000))

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/sm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
'library' or 'require' calls in package code:
  ‘akima’ ‘misc3d’ ‘rgl’ ‘rpanel’ ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘sm/libs/sm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dNMR: no visible global function definition for ‘pnorm’
dNMR: no visible global function definition for ‘dnorm’
pNMR: no visible global function definition for ‘pnorm’
pNMR: no visible global function definition for ‘dnorm’
rMR: no visible global function definition for ‘rnorm’
rMR: no visible global function definition for ‘rchisq’
Undefined global functions or variables:
  dnorm pnorm rchisq rnorm
Consider adding
  importFrom("stats", "dnorm", "pnorm", "rchisq", "rnorm")
to your NAMESPACE file.
SMVar.paired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.paired: no visible global function definition for ‘var’
SMVar.paired: no visible global function definition for ‘pt’
SMVar.paired: no visible global function definition for ‘p.adjust’
SMVar.paired: no visible global function definition for ‘write.table’
SMVar.unpaired : <anonymous>: no visible global function definition for
  ‘var’
SMVar.unpaired: no visible global function definition for ‘var’
SMVar.unpaired: no visible global function definition for ‘pt’
SMVar.unpaired: no visible global function definition for ‘p.adjust’
SMVar.unpaired: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  p.adjust pt var write.table
Consider adding
  importFrom("stats", "p.adjust", "pt", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'SMVar.paired.Rd':
  \usage lines wider than 90 characters:
     SMVar.paired(geneNumbers, logratio, fileexport = NULL, minrep = 2, method = "BH", threshold = 0.05)

Rd file 'SMVar.unpaired.Rd':
  \usage lines wider than 90 characters:
     SMVar.unpaired(geneNumbers, listcond, fileexport = NULL, minrep = 2, method = "BH", threshold = 0.05)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  /usr/include/python2.7/unicodeobject.h:534:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:553:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:575:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:593:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:173:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:174:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:175:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SnakeCharmR.Rcheck/00install.out’ for details.
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.
sclust: no visible global function definition for ‘var’
snipEM: no visible global function definition for ‘cov’
stEM: no visible global function definition for ‘cov’
stEM: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  cov quantile var
Consider adding
  importFrom("stats", "cov", "quantile", "var")
to your NAMESPACE file.
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 ‘snowboot/libs/snowboot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 in Depends field not imported from: ‘snow’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  [.cluster
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
KS.test: no visible global function definition for ‘quantile’
KS.test : Fgaus: no visible global function definition for ‘pnorm’
KS.test: no visible global function definition for ‘setNames’
cs.test: no visible global function definition for ‘pbinom’
cs.test: no visible global function definition for ‘pnorm’
cs.test: no visible global function definition for ‘setNames’
kde: no visible global function definition for ‘quantile’
kde : Fgaus: no visible global function definition for ‘pnorm’
kde: no visible global function definition for ‘par’
kre: no visible global function definition for ‘quantile’
kre: no visible global function definition for ‘lines’
ns.test: no visible global function definition for ‘complete.cases’
ns.test: no visible global function definition for ‘qnorm’
ns.test: no visible global function definition for ‘pnorm’
ns.test: no visible global function definition for ‘pchisq’
ns.test: no visible global function definition for ‘setNames’
ns.test: no visible global function definition for ‘qt’
quant.test: no visible global function definition for ‘complete.cases’
quant.test: no visible global function definition for ‘pbinom’
quant.test: no visible global function definition for ‘pnorm’
quant.test: no visible global function definition for ‘setNames’
quant.test: no visible global function definition for ‘quantile’
quant.test: no visible global function definition for ‘phyper’
runs.test: no visible global function definition for ‘median’
runs.test: no visible global function definition for ‘setNames’
runs.test: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  complete.cases lines median par pbinom pchisq phyper pnorm qnorm qt
  quantile setNames
Consider adding
  importFrom("graphics", "lines", "par")
  importFrom("stats", "complete.cases", "median", "pbinom", "pchisq",
             "phyper", "pnorm", "qnorm", "qt", "quantile", "setNames")
to your NAMESPACE file.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘mvtnorm’ ‘combinat’
A package should be listed in only one of these fields.
chisq.test.a: no visible global function definition for ‘chisq.test’
maxsel: no visible global function definition for ‘complete.cases’
maxsel.asymp.test: no visible global function definition for
  ‘complete.cases’
Undefined global functions or variables:
  chisq.test complete.cases
Consider adding
  importFrom("stats", "chisq.test", "complete.cases")
to your NAMESPACE file.
prepare_Rd: maxsel.rd:27-29: Dropping empty section \details
prepare_Rd: transf.inter.rd:23-25: Dropping empty section \details
MDSplot: no visible global function definition for ‘par’
MDSplot: no visible global function definition for ‘rainbow’
MDSplot: no visible global function definition for ‘plot’
MDSplot: no visible global function definition for ‘pairs’
classCenter : <anonymous>: no visible binding for global variable
  ‘median’
grow.snpRF: no visible global function definition for ‘update’
na.roughfix.data.frame : roughfix: no visible global function
  definition for ‘median’
na.roughfix.default: no visible global function definition for ‘median’
outlier.default: no visible global function definition for ‘median’
outlier.default: no visible global function definition for ‘mad’
plot.margin: no visible global function definition for
  ‘installed.packages’
plot.margin: no visible global function definition for ‘rainbow’
plot.margin: no visible global function definition for ‘plot.default’
plot.snpRF: no visible global function definition for ‘matplot’
tuneSnpRF: no visible global function definition for ‘axis’
varImpPlot: no visible global function definition for ‘par’
varImpPlot: no visible global function definition for ‘dotchart’
varImpPlot: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis dotchart installed.packages mad matplot median mtext pairs par
  plot plot.default rainbow update
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "dotchart", "matplot", "mtext", "pairs",
             "par", "plot", "plot.default")
  importFrom("stats", "mad", "median", "update")
  importFrom("utils", "installed.packages")
to your NAMESPACE file.
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.
Packages in Depends field not imported from:
  ‘colorspace’ ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
check.args: no visible global function definition for ‘is’
write.sbams: no visible global function definition for ‘as’
write.sbams: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  as is write.table
Consider adding
  importFrom("methods", "as", "is")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
Packages in Depends field not imported from:
  ‘Biostrings’ ‘GenomicRanges’ ‘IRanges’ ‘Rsamtools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following calls to attach():
File ‘SOAR/R/SOAR.R’:
  attach(NULL, pos, basename(directory))
See section ‘Good practice’ in ‘?attach’.
Running examples in ‘socialmixr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_survey
> ### Title: Get a survey, either from its Zenodo repository, a set of files,
> ###   or a survey variable
> ### Aliases: get_survey
> 
> ### ** Examples
> 
> list_surveys()
Error in `[.data.table`(multiple_records, , .I[datestamp == max(datestamp)],  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: list_surveys ... [ -> [.data.table -> eval -> eval -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 77-78 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
calculate.areas: no visible global function definition for ‘runif’
calculate.gradedareas: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm runif
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
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.
Warning: no function found corresponding to methods exports from ‘SoDA’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Missing or unexported object: ‘base::WHAT’
Call with DUP:
   .Fortran("GEODISTV", as.double(lat1), as.double(lon1), as.double(lat2), 
       as.double(lon2), dist = double(nok), as.integer(nok), DUP = DUP, 
       PACKAGE = "SoDA")
DUP is no longer supported and will be ignored.
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.
Packages in Depends field not imported from:
  ‘MASS’ ‘magic’ ‘ppls’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
get.hnx.B.initialW: no visible global function definition for
  ‘normalize.vector’
get.hnx.B.initialW: no visible global function definition for ‘adiag’
hclust.wrap: no visible global function definition for ‘hclust’
hclust.wrap: no visible global function definition for ‘dist’
hclust.wrap: no visible global function definition for ‘cutree’
my.normdata.gen: no visible global function definition for ‘mvrnorm’
my.normdata.gen: no visible global function definition for ‘rnorm’
odc.clust: no visible binding for global variable ‘kmeans’
odc.cv: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible global function definition for ‘tr’
odc.optimallambda2: no visible global function definition for ‘ginv’
odc.optimallambda2: no visible binding for global variable ‘sd’
sodc.clust: no visible binding for global variable ‘kmeans’
Undefined global functions or variables:
  adiag cutree dist ginv hclust kmeans mvrnorm normalize.vector rnorm
  sd tr
Consider adding
  importFrom("stats", "cutree", "dist", "hclust", "kmeans", "rnorm",
             "sd")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  plot.sod_sq3
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
hsvScale: no visible global function definition for ‘hsv’
plotConcentric: no visible global function definition for ‘plot’
plotConcentric: no visible global function definition for ‘points’
plotConcentric: no visible global function definition for ‘legend’
plotPoints: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘polygon’
plotStress: no visible global function definition for ‘points’
Undefined global functions or variables:
  hsv legend plot points polygon
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "plot", "points", "polygon")
to your NAMESPACE file.
File ‘SOD/libs/SOD.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
HardKMeansDemo: no visible global function definition for
  ‘graphics.off’
HardKMeansDemo: no visible global function definition for ‘plot’
HardKMeansDemo: no visible global function definition for ‘points’
initializeMeansMatrix: no visible global function definition for
  ‘runif’
initializeMeansMatrix: no visible global function definition for ‘dist’
normalizeMatrix: no visible global function definition for ‘sd’
plotRoughKMeans: no visible global function definition for
  ‘graphics.off’
plotRoughKMeans: no visible global function definition for ‘plot’
plotRoughKMeans: no visible global function definition for ‘points’
Undefined global functions or variables:
  dist graphics.off plot points runif sd
Consider adding
  importFrom("grDevices", "graphics.off")
  importFrom("graphics", "plot", "points")
  importFrom("stats", "dist", "runif", "sd")
to your NAMESPACE file.
Ssimpute.als: no visible global function definition for ‘rnorm’
Ssvd.als: no visible global function definition for ‘rnorm’
cs.default: no visible binding for global variable ‘weighted.mean’
simpute.als: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm weighted.mean
Consider adding
  importFrom("stats", "rnorm", "weighted.mean")
to your NAMESPACE file.
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.
Packages in Depends field not imported from:
  ‘aqp’ ‘lattice’ ‘methods’ ‘munsell’ ‘splancs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  head.profile.data.frame plot.profile.data.frame
  print.profile.data.frame summary.profile.data.frame
  tail.profile.data.frame
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘soilprofile-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: soilprofile-package
> ### Title: A package for consistently drawing soil profiles and their
> ###   properties
> ### Aliases: soilprofile-package soilprofile
> ### Keywords: package
> 
> ### ** Examples
> 
> plot(example, existing_data=example.data, random=FALSE)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot -> plot.default -> xy.coords
Execution halted
'library' or 'require' calls in package code:
  ‘chemometrics’ ‘spatstat’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  plot.Spectra plot.ken.sto plot.trans predict.SpectraPoints
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.soma: no visible global function definition for ‘plot’
soma: no visible global function definition for ‘runif’
Undefined global functions or variables:
  plot runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
bm: no visible global function definition for ‘rnorm’
bm: no visible global function definition for ‘ts’
fbm: no visible global function definition for ‘fft’
fbm: no visible global function definition for ‘rnorm’
fbm: no visible global function definition for ‘ts’
gbm: no visible global function definition for ‘rnorm’
gbm: no visible global function definition for ‘ts’
Undefined global functions or variables:
  fft rnorm ts
Consider adding
  importFrom("stats", "fft", "rnorm", "ts")
to your NAMESPACE file.
getAlpha: no visible global function definition for ‘pbinom’
kfweOrd: no visible global function definition for ‘qnbinom’
Undefined global functions or variables:
  pbinom qnbinom
Consider adding
  importFrom("stats", "pbinom", "qnbinom")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from ‘someMTP’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to ‘hexbin’ which was already attached by Depends.
  Please remove these calls from your code.
hexbinpie: no visible global function definition for ‘quantile’
hexbinpie: no visible global function definition for ‘polygon’
hexbinpie: no visible global function definition for ‘text’
makehexbinplot: no visible global function definition for ‘rainbow’
makehexbinplot: no visible global function definition for ‘col2rgb’
makehexbinplot: no visible global function definition for ‘edit’
makehexbinplot: no visible global function definition for ‘dev.new’
makehexbinplot: no visible global function definition for ‘plot.new’
makehexbinplot: no visible global function definition for ‘plot.window’
makehexbinplot: no visible global function definition for ‘box’
makehexbinplot: no visible global function definition for ‘axis’
makehexbinplot: no visible global function definition for ‘legend’
som.plot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  axis box col2rgb dev.new edit legend plot.new plot.window polygon
  quantile rainbow read.table text
Consider adding
  importFrom("grDevices", "col2rgb", "dev.new", "rainbow")
  importFrom("graphics", "axis", "box", "legend", "plot.new",
             "plot.window", "polygon", "text")
  importFrom("stats", "quantile")
  importFrom("utils", "edit", "read.table")
to your NAMESPACE file.
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.
dfrag: no visible global function definition for ‘qgeom’
dfrag: no visible global function definition for ‘plogis’
dfrag: no visible global function definition for ‘dgeom’
estAbund: no visible global function definition for ‘xtabs’
mmN : <anonymous>: no visible global function definition for ‘uniroot’
pfrag: no visible global function definition for ‘qgeom’
phi.deriv.default: no visible global function definition for
  ‘model.matrix’
phi.deriv.default: no visible binding for global variable ‘sd’
phi.update.default: no visible global function definition for ‘glm’
phi.update.default: no visible binding for global variable
  ‘quasipoisson’
phi.update.default: no visible global function definition for ‘predict’
phi.update.lframe: no visible global function definition for ‘glm’
phi.update.lframe: no visible binding for global variable
  ‘quasipoisson’
phi.update.lframe: no visible global function definition for ‘predict’
pr.y.given.x : <anonymous>: no visible global function definition for
  ‘dpois’
pr.y.given.x : <anonymous> : <anonymous>: no visible global function
  definition for ‘dpois’
pr.y.given.x : <anonymous>: no visible global function definition for
  ‘convolve’
qfrag: no visible global function definition for ‘qgeom’
rfrag: no visible global function definition for ‘qgeom’
simSonic: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  convolve dgeom dpois glm model.matrix plogis predict qgeom
  quasipoisson rpois sd uniroot xtabs
Consider adding
  importFrom("stats", "convolve", "dgeom", "dpois", "glm",
             "model.matrix", "plogis", "predict", "qgeom",
             "quasipoisson", "rpois", "sd", "uniroot", "xtabs")
to your NAMESPACE file.
plot.soo_function: no visible global function definition for
  ‘terrain.colors’
plot.soo_function: no visible binding for global variable ‘image’
plot.soo_function: no visible binding for global variable ‘contour’
plot3d: no visible global function definition for ‘persp3d’
plot3d: no visible global function definition for ‘terrain.colors’
random_parameters.soo_function: no visible global function definition
  for ‘runif’
random_rotation_matrix: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  contour image persp3d runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "contour", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
Non-standard files/directories found at top level:
  ‘README.markdown’ ‘build_package.sh’ ‘upload.sh’
simdata_contaminated : <anonymous>: no visible global function
  definition for ‘rbinom’
simdata_uniform : multivariate_uniform : <anonymous>: no visible global
  function definition for ‘runif’
which_min: no visible global function definition for ‘head’
which_min: no visible global function definition for ‘tail’
Undefined global functions or variables:
  head rbinom runif tail
Consider adding
  importFrom("stats", "rbinom", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
convert_municipality_names: no visible global function definition for
  ‘read.csv’
regression_plot: no visible binding for global variable ‘loess’
regression_plot: no visible global function definition for
  ‘colorRampPalette’
regression_plot: no visible global function definition for
  ‘loess.control’
regression_plot: no visible global function definition for ‘predict’
regression_plot : <anonymous>: no visible global function definition
  for ‘quantile’
regression_plot : <anonymous>: no visible global function definition
  for ‘pnorm’
regression_plot: no visible global function definition for
  ‘flush.console’
regression_plot: no visible global function definition for ‘density’
Undefined global functions or variables:
  colorRampPalette density flush.console loess loess.control pnorm
  predict quantile read.csv
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "density", "loess", "loess.control", "pnorm",
             "predict", "quantile")
  importFrom("utils", "flush.console", "read.csv")
to your NAMESPACE file.
Non-standard files/directories found at top level:
  ‘sandbox’ ‘sos4R-Ex.R’
'library' or 'require' call to ‘rgdal’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  as.data.frame.OmMeasurement as.data.frame.OmObservation
  as.list.OmObservationCollection length.OmObservationCollection
  names.OmMeasurement names.OmObservation names.OmObservationCollection
  plot.SOS plot.SensorML plot.SosObservationOffering
  print.summary.GmlTimePeriod print.summary.OmObservation
  print.summary.OmObservationCollection print.summary.OwsRange
  print.summary.SOS print.summary.SosObservationOffering
  summary.GmlTimePeriod summary.OmObservation
  summary.OmObservationCollection summary.OwsRange summary.SOS
  summary.SosObservationOffering
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SciencesPo’
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.
Package suggested but not available for checking: ‘r2cytoscape’
analyzeSP23Design: no visible global function definition for ‘plot’
exploreSP23Design: no visible global function definition for
  ‘txtProgressBar’
exploreSP23Design: no visible global function definition for
  ‘setTxtProgressBar’
generateClinicalTrialData : <anonymous>: no visible global function
  definition for ‘runif’
generateClinicalTrialData: no visible global function definition for
  ‘rbinom’
generateClinicalTrialData: no visible global function definition for
  ‘rexp’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘pnorm’
mHP.b : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.b: no visible global function definition for ‘qnorm’
mHP.b: no visible global function definition for ‘uniroot’
mHP.c : crossingProbDiff: no visible global function definition for
  ‘Miwa’
mHP.c: no visible global function definition for ‘uniroot’
mHP.c: no visible global function definition for ‘qnorm’
performInterimLook: no visible global function definition for ‘optim’
performInterimLook: no visible global function definition for
  ‘constrOptim’
performInterimLook: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  Miwa constrOptim optim plot pnorm qnorm rbinom rexp runif
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "constrOptim", "optim", "pnorm", "qnorm", "rbinom",
             "rexp", "runif", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
SPA: no visible global function definition for ‘var’
Score.Test.Interact: no visible global function definition for ‘pchisq’
Score.Test.Overall: no visible global function definition for ‘var’
Score.Test.Overall: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq var
Consider adding
  importFrom("stats", "pchisq", "var")
to your NAMESPACE file.
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.
'library' or 'require' call to ‘Matrix’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Matrix’ ‘igraph’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'SJ.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     #Fit conditional independence graph at one lambda , using the default basis functions (cubic polynomials).
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

Rd file 'generate.dag.data.Rd':
  \usage lines wider than 90 characters:
     generate.dag.data(g, n, basesd = 1, basemean = 0, bfuns = function(x){cbind(x, x^2, x^3)}, 
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)

Rd file 'spacejam-package.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

These lines will be truncated in the PDF 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.
GenPar: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Rd file 'space.joint.Rd':
  \examples lines wider than 100 characters:
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #plot(temp, vertex.size=3, vertex.frame.color="white",layout=layout.fruchterman.reingold, vertex.label=NA, edge.color=grey(0.5))

Rd file 'space.neighbor.Rd':
  \examples lines wider than 100 characters:
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #################### view the network corresponding to the parcial correlation matrix in the simulation example
     #plot(temp, vertex.size=3, vertex.frame.color="white",layout=layout.fruchterman.reingold, vertex.label=NA, edge.color=grey(0.5))

These lines will be truncated in the PDF 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.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘colorspace’ ‘picante’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'phy.dotplot.Rd':
  \usage lines wider than 90 characters:
     phy.dotplot(sp.plot, phy, edge.width = 0.2, lab.adj = c(0, 0), tips.adj = c(0.5, 3), tips.cex = 1.0, pch = 21, print.labs = FALSE, outf ... [TRUNCATED]

Rd file 'spacodi.by.nodes.Rd':
  \usage lines wider than 90 characters:
     spacodi.by.nodes(sp.plot, phy, sp.parm = "Bst", obs.only = FALSE, return.all = TRUE, n.rep = 10, method = "1s", parm = NULL, dmat = NUL ... [TRUNCATED]

Rd file 'spacodi.calc.Rd':
  \usage lines wider than 90 characters:
     spacodi.calc(sp.plot, phy = NULL, sp.traits = NULL, all.together = TRUE, prune = TRUE, pairwise = FALSE, ...)

Rd file 'spacodi.permutplot.Rd':
  \usage lines wider than 90 characters:
       spacodi.permutplot(spacodi.permutations, cex=list(pch=1.5, rand=0.1, node=0.5, legend=0.75), transp=0.8, col = list("black", "lightgr ... [TRUNCATED]
       bg = list("white", "lightgray", "black"), all.points = TRUE, add.id = TRUE, sig.plot = TRUE, cut.off = 0.05, envelope = FALSE, outfil ... [TRUNCATED]

Rd file 'spacodi.treeplot.Rd':
  \usage lines wider than 90 characters:
     spacodi.treeplot(spacodi.permutations, phy, cex=list(pch = 1.5, tip = 0.5, legend = 0.75), transp=0.8, sig.plot = TRUE, cut.off = 0.05, ... [TRUNCATED]

These lines will be truncated in the PDF 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.
Running ‘test-all.R’ [173s/231s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  ── 1. Failure: simList object initializes correctly (@test-simList.R#17)  ──────────────────────────
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘spaero/libs/spaero.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
hausman: no visible global function definition for ‘pchisq’
span.formula: no visible global function definition for ‘model.frame’
span.formula: no visible global function definition for ‘model.matrix’
span.formula: no visible global function definition for
  ‘model.response’
spbe: no visible global function definition for ‘cor’
spbe: no visible global function definition for ‘pt’
spfe: no visible global function definition for ‘cor’
spfe: no visible global function definition for ‘pt’
sprandom: no visible global function definition for ‘cor’
sprandom: no visible global function definition for ‘pt’
summary.span: no visible global function definition for ‘printCoefmat’
Undefined global functions or variables:
  cor model.frame model.matrix model.response pchisq printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "pchisq", "printCoefmat", "pt")
to your NAMESPACE file.
plot.spa: no visible global function definition for ‘plot’
plot.spa: no visible global function definition for ‘lines’
plot.spa: no visible global function definition for ‘points’
plot.spa: no visible global function definition for ‘gray’
plot.spa: no visible global function definition for ‘box’
predict.spa: no visible global function definition for ‘fitted’
predict.spa: no visible global function definition for ‘coef’
spa.gcv: no visible global function definition for ‘density’
spa.gcv: no visible global function definition for ‘quantile’
spa.sim: no visible global function definition for ‘runif’
spa.sim: no visible global function definition for ‘rnorm’
spa.sim: no visible global function definition for ‘rbinom’
update.spa: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  box coef density fitted gray lines plot points quantile rbinom rnorm
  runif
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "box", "lines", "plot", "points")
  importFrom("stats", "coef", "density", "fitted", "quantile", "rbinom",
             "rnorm", "runif")
to your NAMESPACE file.
Rd file 'predict.spa.Rd':
  \examples lines wider than 100 characters:
     title(switch(attr(dat,"type"),moon="Two Moon Simulated Data",supervised="Supervised Border Simulated set"))

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  plot.HierarchicalSparseCluster plot.HierarchicalSparseCluster.permute
  plot.KMeansSparseCluster plot.KMeansSparseCluster.permute
  print.HierarchicalSparseCluster
  print.HierarchicalSparseCluster.permute print.KMeansSparseCluster
  print.KMeansSparseCluster.permute
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'ColorDendrogram.Rd':
  \usage lines wider than 90 characters:
     ColorDendrogram(hc, y, main = "", branchlength = 0.7, labels = NULL, xlab = NULL, sub = NULL, ylab = "", cex.main = NULL)

Rd file 'HierarchicalSparseCluster.Rd':
  \usage lines wider than 90 characters:
     HierarchicalSparseCluster(x=NULL, dists=NULL,method=c("average","complete", "single","centroid"),
     wbound=NULL,niter=15,dissimilarity=c("squared.distance","absolute.value"), uorth=NULL,silent=FALSE,
  \examples lines wider than 100 characters:
       # faster than   sparsehc <- HierarchicalSparseCluster(x=x,wbound=perm.out$bestw, method="complete")
       sparsehc <- HierarchicalSparseCluster(dists=perm.out$dists, wbound=perm.out$bestw, method="complete", dissimilarity="absolute.value")

Rd file 'HierarchicalSparseCluster.permute.Rd':
  \examples lines wider than 100 characters:
       sparsehc <- HierarchicalSparseCluster(dists=perm.out$dists, wbound=perm.out$bestw, method="complete")

Rd file 'HierarchicalSparseCluster.wrapper.Rd':
  \usage lines wider than 90 characters:
     HierarchicalSparseCluster.wrapper(file,  method=c("average", "complete", "single", "centroid"),
     "single","centroid"),output.cluster.files=TRUE,outputfile.prefix=NULL,maxnumgenes=5000,standardize.arrays=TRUE)

These lines will be truncated in the PDF manual.
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.
Packages in Depends field not imported from:
  ‘RCurl’ ‘XML’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPARQL : <anonymous>: no visible global function definition for
  ‘URLencode’
SPARQL: no visible binding for global variable ‘getURL’
SPARQL: no visible global function definition for ‘URLencode’
SPARQL: no visible binding for global variable ‘xmlParse’
SPARQL: no visible global function definition for ‘getNodeSet’
SPARQL: no visible global function definition for ‘xpathApply’
SPARQL: no visible binding for global variable ‘postForm’
get_attr: no visible global function definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘getNodeSet’
get_attr : <anonymous> : <anonymous>: no visible global function
  definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xmlDoc’
get_value: no visible global function definition for ‘xpathSApply’
get_value: no visible binding for global variable ‘xmlValue’
get_value: no visible global function definition for ‘xpathApply’
get_value: no visible binding for global variable ‘xmlGetAttr’
readCSVstring: no visible global function definition for ‘read.csv’
readTSVstring: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  URLencode getNodeSet getURL postForm read.csv read.delim xmlDoc
  xmlGetAttr xmlParse xmlValue xpathApply xpathSApply
Consider adding
  importFrom("utils", "URLencode", "read.csv", "read.delim")
to your NAMESPACE file.
f.I2.cont: no visible global function definition for ‘combn’
f.I2.dich: no visible global function definition for ‘combn’
f.pstar.cont: no visible global function definition for ‘combn’
f.pstar.dich: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn
Consider adding
  importFrom("utils", "combn")
to your NAMESPACE file.
image.matrixBC: no visible global function definition for ‘dev.new’
image.matrixBC: no visible global function definition for ‘image’
image.matrixBC: no visible global function definition for ‘heat.colors’
image.matrixBC: no visible global function definition for ‘axis’
image.matrixBC: no visible global function definition for ‘title’
image.sparseBC: no visible global function definition for ‘dev.new’
image.sparseBC: no visible global function definition for ‘image’
image.sparseBC: no visible global function definition for ‘heat.colors’
image.sparseBC: no visible global function definition for ‘axis’
image.sparseBC: no visible global function definition for ‘tail’
image.sparseBC: no visible global function definition for ‘title’
matrixBC: no visible global function definition for ‘kmeans’
sparseBC: no visible global function definition for ‘kmeans’
sparseBC.choosekr: no visible global function definition for ‘kmeans’
sparseBC.choosekr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  axis dev.new heat.colors image kmeans sd tail title
Consider adding
  importFrom("grDevices", "dev.new", "heat.colors")
  importFrom("graphics", "axis", "image", "title")
  importFrom("stats", "kmeans", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
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.
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 ‘sparseSVM/libs/sparseSVM.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 ‘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.
File ‘SpatialEpi/libs/SpatialEpi.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
gev.impute: no visible global function definition for ‘rnorm’
gev.init: no visible global function definition for ‘rbinom’
gev.init: no visible global function definition for ‘var’
gev.init: no visible global function definition for ‘optimize’
gev.logscore: no visible global function definition for ‘density’
gev.logscore: no visible global function definition for ‘splinefun’
gev.update.M: no visible global function definition for ‘runif’
gev.update.hyper: no visible global function definition for ‘rgamma’
gev.update.lambda: no visible global function definition for ‘rnorm’
gev.update.lambda: no visible global function definition for ‘dgamma’
gev.update.lambda: no visible global function definition for ‘dnorm’
gev.update.lambda: no visible global function definition for ‘runif’
gev.update.tau.kappa: no visible global function definition for ‘rnorm’
gev.update.tau.kappa: no visible global function definition for ‘dnorm’
gev.update.tau.kappa: no visible global function definition for ‘runif’
gev.update.tau.mu: no visible global function definition for ‘rnorm’
gev.update.tau.mu: no visible global function definition for ‘dnorm’
gev.update.tau.mu: no visible global function definition for ‘runif’
gev.update.tau.xi: no visible global function definition for ‘rnorm’
gev.update.tau.xi: no visible global function definition for ‘dnorm’
gev.update.tau.xi: no visible global function definition for ‘runif’
gev.update.theta: no visible global function definition for ‘rnorm’
gp.like.lambda: no visible global function definition for ‘dgamma’
Undefined global functions or variables:
  density dgamma dnorm optimize rbinom rgamma rnorm runif splinefun var
Consider adding
  importFrom("stats", "density", "dgamma", "dnorm", "optimize", "rbinom",
             "rgamma", "rnorm", "runif", "splinefun", "var")
to your NAMESPACE file.
I2BR: no visible global function definition for ‘pnorm’
I2SmD2: no visible global function definition for ‘pnorm’
IBR: no visible global function definition for ‘pnorm’
ISmD2: no visible global function definition for ‘pnorm’
MestimatorBR: no visible global function definition for ‘optim’
MestimatorSmith: no visible global function definition for ‘optim’
psidotBR: no visible global function definition for ‘dnorm’
psidotBR: no visible global function definition for ‘pnorm’
psidotSmD2: no visible global function definition for ‘dnorm’
psidotSmD2: no visible global function definition for ‘pnorm’
tailBRInt: no visible global function definition for ‘pnorm’
tailSmithInt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm optim pnorm
Consider adding
  importFrom("stats", "dnorm", "optim", "pnorm")
to your NAMESPACE file.
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.
File ‘SpatialTools/libs/SpatialTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Missing link or links in documentation object 'FeatureAxis.Rd':
  ‘bounding.box’

Missing link or links in documentation object 'FeatureProps.Rd':
  ‘bounding.box’

Missing link or links in documentation object 'locperf.Rd':
  ‘bounding.box’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Running examples in ‘SpatialVx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: MergeForce
> ### Title: Force Merges in Matched Feature Objects
> ### Aliases: MergeForce
> ### Keywords: manip
> 
> ### ** Examples
> 
> x <- y <- matrix(0, 100, 100)
> x[2:3,c(3:6, 8:10)] <- 1
> y[c(4:7, 9:10),c(7:9, 11:12)] <- 1
> 
> x[30:50,45:65] <- 1
> y[c(22:24, 99:100),c(50:52, 99:100)] <- 1
> 
> hold <- make.SpatialVx( x, y, field.type="contrived", units="none",
+     data.name = "Example", obs.name = "x", model.name = "y" )
> 
> look <- FeatureFinder(hold, smoothpar=0.5)
> 
> look2 <- centmatch( look )
> 
> look2
[1] "Matching based on centroid distances using centmatch function."
[1] "centmatch"
Distance criteria based on sum of the object sizes.
Matched objects.
     Forecast Observed
[1,]        1        1
[2,]        1        2
[3,]        3        2
[4,]        5        3
Unmatched Objects.
$X
integer(0)

$Xhat
[1] 2 4 6 7 8

Objects are not merged, but implicitly defined merges would be:
New object  1 :
     Forecast Observed
[1,]        1        1
[2,]        1        2
[3,]        3        2
New object  2 :
     Forecast Observed
[1,]        5        3
> 
> look2 <- MergeForce( look2 )
> 
> look2
[1] "Matching based on centroid distances using centmatch function. (merged) "
[1] "centmatch"  "MergeForce"
Matched objects.
     Forecast Observed
[1,]        1        1
[2,]        2        2
Unmatched Objects.
$X
integer(0)

$Xhat
[1] 3 4 5 6 7

> 
> plot( look2 )
Error in UseMethod("plot", x) : 
  no applicable method for 'plot' applied to an object of class "matchedNoMap"
Calls: plot -> plot.matched
Execution halted
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.
Non-standard file/directory found at top level:
  ‘Rd_examples’
File ‘SpatioTemporal/libs/SpatioTemporal.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
GenerateCliquesCovariance: no visible global function definition for
  ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
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.
Package suggested but not available for checking: ‘spDataLarge’
bartlett: no visible global function definition for ‘pchisq’
local.rbfdot: no visible binding for global variable ‘sd’
local.rbfdot: no visible global function definition for ‘dist’
local.rbfdot : <anonymous>: no visible global function definition for
  ‘median’
speccalt: no visible global function definition for ‘kmeans’
Undefined global functions or variables:
  dist kmeans median pchisq sd
Consider adding
  importFrom("stats", "dist", "kmeans", "median", "pchisq", "sd")
to your NAMESPACE file.
Running examples in ‘speciesgeocodeR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CalcRange
> ### Title: Calculate the Extent of Occurrence
> ### Aliases: CalcRange
> ### Keywords: spatial
> 
> ### ** Examples
> 
> data(lemurs)
> CalcRange(lemurs)
Warning in CalcRange(lemurs) :
  177 points were excluded due to duplicated coordinate
Warning in CalcRange(lemurs) :
  the following species have less than 3 occurrence, values set to NA:
 Daubentonia madagascariensis
 Eulemur collaris
 Eulemur rufifrons
 Eulemur rufus
 Eulemur sanfordi
 Lepilemur septentrionalis
 Microcebus griseorufus
 Microcebus lehilahytsara
 Microcebus ravelobensis
 Propithecus candidus
 Propithecus coronatus
 Propithecus deckenii
 Propithecus tattersalli
Error in if (value == "area") { : the condition has length > 1
Calls: CalcRange
Execution halted
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.
ChaoBunge: no visible global function definition for ‘qnorm’
ChaoLee1992: no visible global function definition for ‘qnorm’
Pmix: no visible global function definition for ‘dpois’
PmixSCon: no visible global function definition for ‘dbeta’
bootPCG: no visible global function definition for ‘flush.console’
bootPCG: no visible global function definition for ‘quantile’
bootPnpmle: no visible global function definition for ‘flush.console’
bootPnpmle: no visible global function definition for ‘quantile’
bootUnpmle: no visible global function definition for ‘flush.console’
bootUnpmle: no visible global function definition for ‘quantile’
chao1984: no visible global function definition for ‘qnorm’
jackknife: no visible global function definition for ‘dbinom’
jackknife: no visible global function definition for ‘qnorm’
pcg: no visible global function definition for ‘flush.console’
unpmle: no visible global function definition for ‘flush.console’
untrunPmix: no visible global function definition for ‘dpois’
Undefined global functions or variables:
  dbeta dbinom dpois flush.console qnorm quantile
Consider adding
  importFrom("stats", "dbeta", "dbinom", "dpois", "qnorm", "quantile")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
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.
Found the following apparent S3 methods exported but not registered:
  print.summary.specificity summary.specificity
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
randomCorrelations: no visible global function definition for ‘cor’
specGlm : <anonymous>: no visible global function definition for ‘coef’
specLm : <anonymous>: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef cor
Consider adding
  importFrom("stats", "coef", "cor")
to your NAMESPACE file.
Running examples in ‘specificity-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: specificityLm, specificityEta2, specificityGlm
> ### Title: Specificity of personality trait-outcome associations
> ### Aliases: specificity-package specificityLm specificityEta2
> ###   specificityGlm specificity dum scramble specEta2 specGlm specLm
> ###   print.summary.specificity summary.specificity
> 
> ### ** Examples
> 
> # Create random data.frame
> data = as.data.frame(matrix(ncol=63, nrow=100, sample(1:5, size=6300, replace=TRUE)))
> colnames(data) = c(paste("Per", 1:60, sep=""), c("Outcome", "Covar1", "Covar2"))
> 
> # Make the Outcome categorical
> data$OutcomeCat = as.factor(data$Outcome)  
> 
> # Create Keys
> keyWithNames <- list(start=1, end=60, scale=rep(1:5, each=12), names=c("N","E","O","A","C"))
> keyWithoutNames <- list(start=1, end=60, scale = rep(1:5, each=12))
> 
> # Run analyses
> resultLm <- specificityLm(scale(.allTraits) ~ scale(Outcome) + Covar1 + Covar2, 
+             Data=data, Key = keyWithNames, R=100)
> resultEta2 <- specificityEta2(.allTraits ~ OutcomeCat + Covar1 + Covar2, 
+               Data=data, Key = keyWithNames, R=100)
> resultGlm <- specificityGlm(Outcome ~ .allTraits + Covar1 + Covar2, 
+              Data=data, Family="gaussian", Key = keyWithoutNames, R=100)
> 
> # See results
> summary(resultLm)
         Length Class     Mode   
observed 5      -none-    list   
random   5      -none-    list   
call     5      -none-    call   
key      4      -none-    list   
nsims    1      -none-    numeric
time     5      proc_time numeric
> summary(resultEta2)$true.results
Error in summary(resultEta2)$true.results : 
  $ operator is invalid for atomic vectors
Execution halted
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.
'library' or 'require' call to ‘leaps’ which was already attached by Depends.
  Please remove these calls from your code.
modSearch: no visible global function definition for ‘glm’
modSearch: no visible binding for global variable ‘binomial’
modSearch: no visible global function definition for ‘na.omit’
modSearch: no visible global function definition for ‘as.formula’
speff: no visible binding for global variable ‘na.pass’
speff: no visible global function definition for ‘model.matrix’
speff: no visible global function definition for ‘terms’
speff: no visible global function definition for ‘model.response’
speff: no visible global function definition for ‘as.formula’
speff: no visible global function definition for ‘predict’
speff: no visible global function definition for ‘na.omit’
speff: no visible global function definition for ‘glm’
speff: no visible binding for global variable ‘na.omit’
speffSurv: no visible global function definition for ‘model.matrix’
speffSurv: no visible global function definition for ‘terms’
speffSurv: no visible global function definition for ‘model.response’
speffSurv: no visible global function definition for ‘as.formula’
speffSurv: no visible global function definition for ‘uniroot’
summary.speff: no visible global function definition for ‘qnorm’
summary.speff: no visible global function definition for ‘pnorm’
summary.speffSurv: no visible global function definition for ‘qnorm’
summary.speffSurv: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  as.formula binomial glm model.matrix model.response na.omit na.pass
  pnorm predict qnorm terms uniroot
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "model.matrix",
             "model.response", "na.omit", "na.pass", "pnorm", "predict",
             "qnorm", "terms", "uniroot")
to your NAMESPACE file.
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.
Package in Depends field not imported from: ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
pointsphere: no visible global function definition for ‘runif’
rgl.sphMW: no visible global function definition for ‘plot3d’
rgl.sphcirc: no visible global function definition for ‘rotate3d’
rgl.sphcirc: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘open3d’
rgl.sphgrid: no visible global function definition for ‘plot3d’
rgl.sphgrid: no visible global function definition for ‘lines3d’
rgl.sphgrid: no visible global function definition for ‘text3d’
rgl.sphpoints: no visible global function definition for ‘points3d’
rgl.sphsun: no visible global function definition for ‘plot3d’
rgl.sphtext: no visible global function definition for ‘text3d’
Undefined global functions or variables:
  lines3d open3d plot3d points3d rotate3d runif text3d
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘spikeSlabGAM/libs/spikeSlabGAM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 in Depends field not imported from:
  ‘lars’ ‘parallel’ ‘randomForest’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
'library' or 'require' call to ‘quadprog’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
SPIn: no visible global function definition for ‘density’
SPIn: no visible global function definition for ‘quantile’
SPIn: no visible global function definition for ‘solve.QP’
bootSPIn: no visible global function definition for ‘runif’
plot.SPIn: no visible global function definition for ‘hist’
plot.SPIn: no visible global function definition for ‘lines’
plot.SPIn: no visible global function definition for ‘text’
plot.SPIn: no visible global function definition for ‘quantile’
plot.SPIn: no visible global function definition for ‘legend’
Undefined global functions or variables:
  density hist legend lines quantile runif solve.QP text
Consider adding
  importFrom("graphics", "hist", "legend", "lines", "text")
  importFrom("stats", "density", "quantile", "runif")
to your NAMESPACE file.
spi: no visible global function definition for ‘read.table’
spi: no visible global function definition for ‘ecdf’
spi: no visible global function definition for ‘qnorm’
spi: no visible global function definition for ‘colorRampPalette’
spi: no visible global function definition for ‘filled.contour’
spi: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis colorRampPalette ecdf filled.contour qnorm read.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "filled.contour")
  importFrom("stats", "ecdf", "qnorm")
  importFrom("utils", "read.table")
to your NAMESPACE file.
prepare_Rd: spi.Rd:117-119: Dropping empty section \note
prepare_Rd: spi.Rd:123-125: Dropping empty section \seealso
Rd file 'spi.Rd':
  \examples lines wider than 100 characters:
     spi(7,"spi.txt",1963,2010,"Standardized Precipitation Index - Rio Grande do Norte State",1,"years","months")

These lines will be truncated in the PDF manual.
Running examples in ‘splitstackshape-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cSplit_f
> ### Title: Split Concatenated Cells in a data.frame or a data.table
> ### Aliases: cSplit_f
> 
> ### ** Examples
> 
> 
> ## Sample data. Change `n` to larger values to test on larger data
> set.seed(1)
> n <- 10
> mydf <- data.frame(id = sequence(n))
> mydf <- within(mydf, {
+   v3 <- do.call(paste, c(data.frame(matrix(sample(
+   letters, n*4, TRUE), ncol = 4)), sep = "_"))
+   v2 <- do.call(paste, c(data.frame(matrix(sample(
+   LETTERS, n*3, TRUE), ncol = 3)), sep = "."))
+   v1 <- do.call(paste, c(data.frame(matrix(sample(
+   10, n*2, TRUE), ncol = 2)), sep = "-"))
+ })
> mydf
   id   v1    v2      v3
1   1  4-5 V.M.X g_f_y_m
2   2  9-8 Q.W.H j_e_f_p
3   3  4-4 U.L.L o_r_q_m
4   4  4-4 O.G.I x_j_d_e
5   5  5-8 N.B.Q f_u_g_v
6   6  9-3 U.C.G x_m_k_r
7   7  9-8 A.I.M y_s_a_u
8   8  4-2 M.N.T r_z_j_c
9   9  8-3 T.R.C q_j_w_s
10 10 10-2 S.K.W b_u_i_k
> 
> cSplit_f(mydf, splitCols = c("v1", "v2", "v3"), sep = c("-", ".", "_"))
Error in fread(x, sep[i], header = FALSE) : 
  You can provide 'input=' or 'file=', not both.
Calls: cSplit_f -> fread
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.
Found the following apparent S3 methods exported but not registered:
  all.equal.list all.equal.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
R2.global: no visible global function definition for ‘var’
calculer.var.exp: no visible global function definition for ‘var’
creer.noeud: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘cov’
spodt: no visible global function definition for ‘model.frame’
spodt.tree: no visible global function definition for ‘plot.new’
spodt.tree: no visible global function definition for ‘par’
spodt.tree: no visible global function definition for ‘plot.window’
spodt.tree: no visible global function definition for ‘text’
spodt.tree: no visible global function definition for ‘segments’
test.spodt: no visible global function definition for ‘model.frame’
test.spodt: no visible global function definition for ‘hist’
test.spodt: no visible global function definition for ‘abline’
tracer.noeud: no visible global function definition for ‘text’
tracer.noeud: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
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.
Ell.Theta: no visible global function definition for ‘ell.theta’
confid.int.theta: no visible global function definition for ‘qchisq’
confid.int.theta : sim.c: no visible global function definition for
  ‘runif’
confid.int.theta: no visible global function definition for ‘quantile’
dd.est: no visible global function definition for ‘ecdf’
ks.sporm : Simul: no visible global function definition for ‘runif’
ks.stat: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘plot’
test.theta: no visible global function definition for ‘ecdf’
test.theta : sim: no visible global function definition for ‘runif’
Undefined global functions or variables:
  ecdf ell.theta plot qchisq quantile runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
prepare_Rd: H.Binv.Rd:48-50: Dropping empty section \note
prepare_Rd: V.theta.Rd:28-30: Dropping empty section \details
prepare_Rd: V.theta.Rd:43-45: Dropping empty section \note
prepare_Rd: V.theta.Rd:49-51: Dropping empty section \seealso
prepare_Rd: V.theta.Rd:52-53: Dropping empty section \examples
prepare_Rd: confid.int.theta.Rd:62-64: Dropping empty section \note
prepare_Rd: dd.est.Rd:39-41: Dropping empty section \note
prepare_Rd: dd.est.Rd:45-47: Dropping empty section \seealso
prepare_Rd: ell.theta.Rd:60-62: Dropping empty section \note
prepare_Rd: ell.theta.Rd:69-70: Dropping empty section \examples
prepare_Rd: grad.hessinv.Rd:47-49: Dropping empty section \note
prepare_Rd: ks.sporm.Rd:43-45: Dropping empty section \note
prepare_Rd: ks.stat.Rd:39-41: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:66-68: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:72-74: Dropping empty section \seealso
prepare_Rd: newton.theta.Rd:47-49: Dropping empty section \note
prepare_Rd: phi.Rd:32-38: Dropping empty section \value
prepare_Rd: phi.Rd:48-50: Dropping empty section \note
prepare_Rd: plotor.Rd:26-32: Dropping empty section \value
prepare_Rd: plotor.Rd:42-44: Dropping empty section \note
prepare_Rd: plotor.Rd:48-50: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:55-56: Dropping empty section \examples
prepare_Rd: test.theta.Rd:54-56: Dropping empty section \note
prepare_Rd: elltheta.rd:53-55: Dropping empty section \note
prepare_Rd: elltheta.rd:62-63: Dropping empty section \examples
fetch_NBAPlayerStatistics: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spp.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  coef.Lifedata.MLE coef.deglmx.MLE logLik.Lifedata.MLE plot.MICsplines
  print.Lifedata.MLE print.deglmx print.summary.Lifedata.MLE sqrt.mat
  summary.Lifedata.MLE
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'SlrArd.Rd':
  \usage lines wider than 90 characters:
     SlrArd(T, X, bias = TRUE, method = c("VB", "VBMacKay", "PX-VB"), control = list(), check.lb=TRUE, a0 = 0, b0 = 0, mu0 = 0, xi0 = 1)

These lines will be truncated in the PDF manual.
plot.SPRT: no visible global function definition for ‘par’
plot.SPRT: no visible global function definition for ‘plot’
plot.SPRT: no visible global function definition for ‘abline’
print.SPRT: no visible global function definition for ‘head’
Undefined global functions or variables:
  abline head par plot
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("utils", "head")
to your NAMESPACE file.
fssa20: no visible global function definition for ‘runif’
fssa2d: no visible global function definition for ‘runif’
fssa30: no visible global function definition for ‘runif’
fssa3d: no visible global function definition for ‘runif’
ssa20: no visible global function definition for ‘runif’
ssa2d: no visible global function definition for ‘runif’
ssa30: no visible global function definition for ‘runif’
ssa3d: no visible global function definition for ‘runif’
ssi20: no visible global function definition for ‘runif’
ssi2d: no visible global function definition for ‘runif’
ssi30: no visible global function definition for ‘runif’
ssi3d: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Rd file 'fssa30.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of anisotropic 3D clusters with (1,0)-neighborhood")

Rd file 'fssa3d.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of anisotropic 3D clusters with (1,1)-neighborhood")

Rd file 'fssi30.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of isotropic 3D clusters with (1,0)-neighborhood")

Rd file 'fssi3d.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of isotropic 3D clusters with (1,1)-neighborhood")

These lines will be truncated in the PDF manual.
File ‘SPSL/libs/SPSL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
plotThin: no visible global function definition for ‘par’
plotThin: no visible global function definition for ‘dev.interactive’
plotThin: no visible global function definition for ‘plot’
plotThin: no visible global function definition for ‘hist’
thin: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  dev.interactive hist par plot write.csv
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "hist", "par", "plot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  chaos.default chaos.spt chaos.st plot.spt plot.st print.spt print.st
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.GameSPT: no visible global function definition for ‘runif’
.GameSPT: no visible global function definition for ‘points’
.GameST: no visible global function definition for ‘runif’
.GameST: no visible global function definition for ‘points’
.arc: no visible global function definition for ‘lines’
.ptpedal: no visible global function definition for ‘polygon’
.sptpedal2: no visible global function definition for ‘segments’
.sptpedal3: no visible global function definition for ‘polygon’
.sptpedal4: no visible global function definition for ‘polygon’
chaos.spt: no visible global function definition for ‘plot’
chaos.spt: no visible global function definition for ‘polygon’
chaos.spt: no visible global function definition for ‘runif’
chaos.spt: no visible global function definition for ‘points’
chaos.st: no visible global function definition for ‘plot’
chaos.st: no visible global function definition for ‘polygon’
chaos.st: no visible global function definition for ‘runif’
chaos.st: no visible global function definition for ‘points’
plot.spt: no visible global function definition for ‘plot’
plot.spt: no visible global function definition for ‘polygon’
plot.st: no visible global function definition for ‘plot’
plot.st: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  lines plot points polygon runif segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon",
             "segments")
  importFrom("stats", "runif")
to your NAMESPACE file.
Running examples in ‘spt-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chaos
> ### Title: Chaos Games for Sierpinski (Pedal) Triangle
> ### Aliases: chaos chaos.st chaos.spt chaos.default
> ### Keywords: stats
> 
> ### ** Examples
> 
> 
> (abc1 = st(50,60))
$angles
[1] 70 60 50

$viewport
[1]   0.00000   0.00000  94.13205 100.00000

$ABC
         [,1] [,2]
[1,]  0.00000    0
[2,] 94.13205    0
[3,] 57.73503  100

$tri
$tri$A
[1] 1.047198

$tri$B
[1] 1.22173

$tri$C
[1] 0.8726646

$tri$xa
[1] 0

$tri$xb
[1] 94.13205

$tri$xc
[1] 57.73503

$tri$ya
[1] 0

$tri$yb
[1] 0

$tri$yc
[1] 100

$tri$A0
[1] 0

$tri$B0
[1] 1.919862

$tri$C0
[1] 4.18879


$Dim
[1] 1.584963

$data.name
[1] "ST(50,60,70)"

attr(,"class")
[1] "st"
> chaos(abc1, iter=2000)
Error in UseMethod("chaos") : 
  no applicable method for 'chaos' applied to an object of class "st"
Calls: chaos
Execution halted
sGda : <anonymous>: no visible global function definition for ‘cov’
sortgene: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘RJDBC’ ‘RMySQL’ ‘RODBC’ ‘RPostgreSQL’ ‘RSQLite’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for ‘read.csv’
cacheQuery: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable ‘median’
SQN: no visible global function definition for ‘quantile’
SQN.demo.data: no visible global function definition for ‘rnorm’
mix.qn: no visible global function definition for ‘ecdf’
mix.qn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
plot.srafit: no visible global function definition for ‘layout’
plot.srafit: no visible global function definition for ‘par’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘dnorm’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘pnorm’
sraData : vartruncGauss: no visible global function definition for
  ‘uniroot’
sraPlotMean: no visible global function definition for ‘axis’
sraPlotMean: no visible global function definition for ‘points’
sraPlotMean: no visible global function definition for ‘lines’
sraPlotMeanResid: no visible global function definition for ‘axis’
sraPlotMeanResid: no visible global function definition for ‘abline’
sraPlotMeanResid: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘axis’
sraPlotVar: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘lines’
sraPlotVarResid: no visible global function definition for ‘axis’
sraPlotVarResid: no visible global function definition for ‘abline’
sraPlotVarResid: no visible global function definition for ‘points’
sraPlotlegend: no visible global function definition for ‘legend’
sraStartingvalues : sraStartingvalues.mu0: no visible global function
  definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarA0: no visible global
  function definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarE0: no visible global
  function definition for ‘rnorm’
sraStartingvalues: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis dnorm layout legend lines par pnorm points rnorm uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "legend", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "pnorm", "rnorm", "uniroot")
to your NAMESPACE file.
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
File ‘sROC/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

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

AUC : TrapezInt: no visible global function definition for ‘approx’
AUC : SimpsonInt: no visible global function definition for ‘approx’
CI.CDF: no visible global function definition for ‘qnorm’
bw.CDF: no visible global function definition for ‘sd’
bw.CDF: no visible global function definition for ‘IQR’
bw.CDF.pi: no visible global function definition for ‘sd’
bw.CDF.pi: no visible global function definition for ‘bw.nrd0’
bw.CDF.pi: no visible global function definition for ‘bw.nrd’
bw.CDF.pi: no visible global function definition for ‘bw.ucv’
bw.CDF.pi: no visible global function definition for ‘bw.bcv’
bw.CDF.pi: no visible global function definition for ‘bw.SJ’
bw.CDF.pi: no visible global function definition for ‘IQR’
plot.CDF: no visible global function definition for ‘plot.default’
plot.CDF: no visible global function definition for ‘lines’
plot.CDF: no visible global function definition for ‘polygon’
plot.ROC: no visible global function definition for ‘plot.default’
plot.ROC: no visible global function definition for ‘abline’
Undefined global functions or variables:
  IQR abline approx bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv lines
  plot.default polygon qnorm sd
Consider adding
  importFrom("graphics", "abline", "lines", "plot.default", "polygon")
  importFrom("stats", "IQR", "approx", "bw.SJ", "bw.bcv", "bw.nrd",
             "bw.nrd0", "bw.ucv", "qnorm", "sd")
to your NAMESPACE file.
Rd file 'CI.CDF.Rd':
  \examples lines wider than 100 characters:
     curve(pnorm(x, mean=-2, sd=1)/2 + pnorm(x, mean=3, sd=0.8)/2, from =-6, to=6, add=TRUE, lty=2, col="blue")

Rd file 'kCDF.Rd':
  \examples lines wider than 100 characters:
     curve(pnorm(x, mean=-2, sd=1)/2 + pnorm(x, mean=3, sd=0.8)/2, from =-6, to=6, add=TRUE, lty=2, col="blue")

Rd file 'kROC.Rd':
  \usage lines wider than 90 characters:
     kROC(x, y, bw.x="pi_ucv", bw.y="pi_ucv", adjust=1, kernel=c("normal", "epanechnikov"), xgrid, 

These lines will be truncated in the PDF manual.
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.
File ‘ssa/libs/ssa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ssd : correction_method_D: no visible global function definition for
  ‘rnorm’
ssd : generate_bootstrap: no visible global function definition for
  ‘rmultinom’
ssd : bootstrap_method: no visible global function definition for
  ‘median’
ssd : bootstrap_method: no visible global function definition for
  ‘quantile’
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for ‘rmultinom’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘median’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘quantile’
ssd: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
L_hNV: no visible global function definition for ‘pnorm’
L_hNV_rho: no visible global function definition for ‘pnorm’
eff.ssfa: no visible global function definition for ‘pnorm’
plot_fitted: no visible global function definition for ‘lines’
plot_moran: no visible global function definition for ‘residuals’
print.summary.ssfa: no visible global function definition for
  ‘printCoefmat’
ssfa: no visible global function definition for ‘model.frame’
ssfa: no visible global function definition for ‘model.response’
ssfa.fit: no visible global function definition for ‘lm’
ssfa.fit: no visible global function definition for ‘var’
ssfa.fit: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pnorm’
summary.ssfa: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pchisq’
summary.ssfa: no visible binding for global variable ‘df’
u.ssfa: no visible global function definition for ‘dnorm’
u.ssfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘survey’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for ‘hadamard’
Undefined global functions or variables:
  hadamard
mem.usage: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
sslCoTrain: no visible global function definition for ‘predict’
sslSelfTrain: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
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.
Found the following apparent S3 methods exported but not registered:
  coef.heckit5rob coef.heckitrob fitted.heckit5rob fitted.heckitrob
  print.heckit5rob print.heckitrob print.summary.heckit5rob
  print.summary.heckitrob residuals.heckit5rob residuals.heckitrob
  summary.heckit5rob summary.heckitrob vcov.heckit5rob vcov.heckitrob
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
map.world: no visible global function definition for ‘par’
map.world: no visible global function definition for ‘plot.new’
map.world: no visible global function definition for ‘plot.window’
map.world: no visible global function definition for ‘lines’
map.world: no visible global function definition for ‘title’
map.world: no visible global function definition for ‘axis’
map.world: no visible global function definition for ‘box’
plot.smooth.sspline: no visible global function definition for
  ‘predict’
plot.smooth.sspline: no visible global function definition for
  ‘filled.contour’
plot.smooth.sspline: no visible binding for global variable
  ‘terrain.colors’
plot.smooth.sspline: no visible global function definition for ‘title’
plot.smooth.sspline: no visible global function definition for ‘axis’
station: no visible binding for global variable ‘WTdiff’
station: no visible global function definition for ‘points’
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
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.
SS.ID: no visible global function definition for ‘var’
SS.sim.chol: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm var
Consider adding
  importFrom("stats", "rnorm", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
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 694-697 (packageAPI.Rmd) 
Error: processing vignette ‘packageAPI.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
error.est : <anonymous>: no visible global function definition for
  ‘median’
holm.robust: no visible global function definition for ‘pnorm’
holm.robust: no visible global function definition for ‘median’
holm.robust: no visible global function definition for ‘mad’
huberize: no visible global function definition for ‘quantile’
ssvd.initial: no visible global function definition for ‘mad’
ssvd.iter.thresh: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
File ‘stable/libs/stable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.ls.objects: no visible binding for global variable ‘object.size’
Undefined global functions or variables:
  object.size
Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
.expandLevels: no visible global function definition for ‘na.omit’
.ffStack: no visible global function definition for ‘na.omit’
.ffffStack: no visible global function definition for ‘na.omit’
Stack : <anonymous>: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-data.frame: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-ffdf: no visible global function definition for ‘na.omit’
ffStack,ffdf-list: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
genericPlot: no visible global function definition for ‘dev.new’
genericPlot: no visible global function definition for ‘par’
genericPlot: no visible global function definition for ‘rainbow’
genericPlot: no visible global function definition for ‘plot’
genericPlot: no visible global function definition for ‘lines’
genericPlot: no visible global function definition for ‘legend’
genericPlot: no visible global function definition for ‘dev.copy2pdf’
genericPlot: no visible global function definition for ‘dev.copy2eps’
genericPlot: no visible global function definition for ‘dev.print’
genericPlot: no visible binding for global variable ‘png’
genericPlot: no visible binding for global variable ‘tiff’
plotStrains: no visible global function definition for ‘rainbow’
plotStrains: no visible global function definition for ‘dev.new’
plotStrains: no visible global function definition for ‘par’
plotStrains: no visible global function definition for ‘plot’
plotStrains: no visible global function definition for ‘lines’
plotStrains: no visible global function definition for ‘legend’
plotStrains: no visible global function definition for ‘dev.copy2pdf’
plotStrains: no visible global function definition for ‘dev.copy2eps’
plotStrains: no visible global function definition for ‘dev.print’
plotStrains: no visible binding for global variable ‘png’
plotStrains: no visible binding for global variable ‘tiff’
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘Licence’
'library' or 'require' calls to packages already attached by Depends:
  ‘np’ ‘sp’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘np’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.

Found the following calls to attach():
File ‘stam/R/stkde.sig.r’:
  attach(samdata)
See section ‘Good practice’ in ‘?attach’.
Rd file 'stkde.sig.rd':
  \examples lines wider than 100 characters:
     system.time(stkde.sig(d[,1],d[,2],d[,3],xgrids=20,ygrids=20,breaks=0.05,sim=3,alpha=0.05,nrowspar=1))
     #determines how much real and CPU time (in seconds) the currently running R process has already taken
     system.time(stkde.sig(d[,1],d[,2],d[,3],xgrids=20,ygrids=20,breaks=0.05,sim=3,alpha=0.05,nrowspar=2))
     #determines how much real and CPU time (in seconds) the currently running R process has already taken

These lines will be truncated in the PDF manual.
find.names: no visible global function definition for ‘na.omit’
generate.names: no visible global function definition for ‘na.omit’
standardize.countrynames: no visible global function definition for
  ‘data’
standardize.names: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Rd file 'standardize.countrynames.Rd':
  \usage lines wider than 90 characters:
     standardize.countrynames(input, input.column = NULL, standard = "default", standard.column = NULL, only.names = FALSE, na.rm = FALSE, s ... [TRUNCATED]

Rd file 'standardize.text.Rd':
  \usage lines wider than 90 characters:
     standardize.text(input, input.column = NULL, standard, standard.column = NULL, regex = NULL, codes = NULL, match = FALSE, only.names =  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
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.
'library' or 'require' call to ‘codetools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘codetools’ ‘gss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Found the following hidden files and directories:
  inst/.Renviron.d
  inst/.Rprofile.d
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Running examples in ‘statar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fill_gap
> ### Title: Add rows corresponding to gaps in some variable
> ### Aliases: fill_gap
> 
> ### ** 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(lubridate)

Attaching package: ‘lubridate’

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

    date

> df <- data_frame(
+     id    = c(1, 1, 1, 2),
+     datem  = as.monthly(mdy(c("04/03/1992", "01/04/1992", "03/15/1992", "05/11/1992"))),
+     value = c(4.1, 4.5, 3.3, 3.2)
+ )
> df %>% group_by(id) %>% fill_gap(datem)
Error in `[.data.table`(ans, , list(seq(min(datem), max(datem), by = 1L)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: %>% ... fill_gap -> lazy_eval -> eval -> eval -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘StatCharrms.tex’ failed.
LaTeX errors:
! FancyVerb Error:
  Extraneous input `	\end{}' between \end{RBox} and line end
.
\FV@Error ... {FancyVerb Error:
\space \space #1
! FancyVerb Error:
  Extraneous input `	\end{}' between \end{RBox} and line end
.
\FV@Error ... {FancyVerb Error:
\space \space #1
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘statcomp/libs/statcomp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘statcomp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: global_complexity
> ### Title: A function to compute global information and complexity measures
> ###   for time series
> ### Aliases: global_complexity
> 
> ### ** Examples
> 
> x = arima.sim(model=list(ar = 0.3), n = 10^4)
> global_complexity(x = x, ndemb = 6)
        PE    MPR_Cjs  nforbiden 
0.98413890 0.03714999 0.00000000 
> # or:
> opd = ordinal_pattern_distribution(x = x, ndemb = 6)
> global_complexity(opd = opd, ndemb = 6)
Error in if (is.na(opd)) opd = ordinal_pattern_distribution(x = x, ndemb = ndemb) : 
  the condition has length > 1
Calls: global_complexity
Execution halted
Found the following apparent S3 methods exported but not registered:
  print.corsign
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
actvspred: no visible global function definition for ‘quantile’
actvspred: no visible global function definition for ‘aggregate’
actvspred: no visible global function definition for ‘par’
actvspred: no visible global function definition for ‘plot’
actvspred: no visible global function definition for ‘lines’
auc: no visible global function definition for ‘par’
auc: no visible global function definition for ‘plot’
decile: no visible global function definition for ‘quantile’
dqcontinuous : numoutliers: no visible global function definition for
  ‘quantile’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘sd’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘quantile’
gini: no visible global function definition for ‘par’
gini: no visible global function definition for ‘plot’
gini: no visible global function definition for ‘abline’
iv: no visible global function definition for ‘quantile’
iv: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘par’
ks: no visible global function definition for ‘plot’
ks: no visible global function definition for ‘lines’
outliers: no visible global function definition for ‘quantile’
outliers: no visible global function definition for ‘na.omit’
pentile: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline aggregate lines na.omit par plot quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
inspect: no visible global function definition for ‘par’
inspect: no visible global function definition for ‘abline’
inspect: no visible global function definition for ‘lines’
inspect: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘dev.off’
plotfit: no visible global function definition for ‘par’
plotfit: no visible global function definition for ‘lines’
plotfit: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘legend’
plothill: no visible global function definition for ‘par’
plothill: no visible global function definition for ‘abline’
plothill: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘par’
plotmultifit: no visible global function definition for ‘lines’
plotmultifit: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘pexp’
plotmultifit: no visible global function definition for ‘plnorm’
plotmultifit: no visible global function definition for ‘ppois’
plotmultifit: no visible global function definition for ‘legend’
plotols: no visible global function definition for ‘dev.off’
plotols: no visible global function definition for ‘lm’
plotols: no visible global function definition for ‘par’
plotols: no visible global function definition for ‘abline’
plotols: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
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.
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.
getStp: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘plot’
plot.steeptest: no visible global function definition for ‘axis’
plot.steeptest: no visible global function definition for ‘box’
plot.steeptest: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘abline’
plot.steeptest: no visible global function definition for ‘legend’
plot.steeptest: no visible global function definition for
  ‘as.graphicsAnnot’
steeptest: no visible global function definition for ‘lm’
summary.steeptest: no visible global function definition for ‘var’
summary.steeptest: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm plot quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend", "plot")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
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.
Stem.Bootstrap: no visible global function definition for ‘runif’
filtering: no visible global function definition for ‘is.ts’
filtering: no visible global function definition for ‘ts’
filtering: no visible global function definition for ‘start’
filtering: no visible global function definition for ‘end’
filtering: no visible global function definition for ‘frequency’
kalman: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘is.ts’
smoothing: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘start’
smoothing: no visible global function definition for ‘end’
smoothing: no visible global function definition for ‘frequency’
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
Running examples in ‘stepPenal-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: StepPenal
> ### Title: Stepwise forward variable selection using penalized regression.
> ### Aliases: StepPenal
> 
> ### ** Examples
> 
> # use the StepPenal function on a simulated dataset, with given lamda and w.
> 
> set.seed(14)
> beta    <- c(3, 2, -1.6, -4)
> noise   <- 5
> simData <- SimData(N=100, beta=beta, noise=noise, corr=FALSE)
> 
> before <- Sys.time()
> stepPenal<- StepPenal(Data=simData, lamda=1.5, w=0.1)
Error in if (!is.na(useoptim)) { : the condition has length > 1
Calls: StepPenal
Execution halted
File ‘stepp/libs/stepp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
d1spectrum: no visible global function definition for ‘fft’
d2spectrum: no visible global function definition for ‘fft’
plot.d1nat: no visible global function definition for ‘plot’
plot.d1nat: no visible global function definition for ‘lines’
plot.d1nat: no visible global function definition for ‘legend’
plot.d1nat: no visible global function definition for ‘title’
plot.d1spec: no visible global function definition for ‘plot’
plot.d1spec: no visible global function definition for ‘lines’
plot.d1spec: no visible global function definition for ‘legend’
plot.d1spec: no visible global function definition for ‘title’
plot.d2spec: no visible global function definition for ‘plot’
plot.d2spec: no visible global function definition for ‘lines’
plot.d2spec: no visible global function definition for ‘legend’
plot.d2spec: no visible global function definition for ‘title’
plot.pvalign: no visible global function definition for ‘plot’
plot.pvalign: no visible global function definition for ‘lines’
plot.pvalign: no visible global function definition for ‘legend’
plot.pvalign: no visible global function definition for ‘title’
print.d1nat: no visible global function definition for ‘plot’
print.d1spec: no visible global function definition for ‘plot’
print.d2spec: no visible global function definition for ‘plot’
print.pvalign: no visible global function definition for ‘plot’
utild1bin: no visible global function definition for ‘median’
utild1bin: no visible global function definition for ‘sd’
utild1clean: no visible global function definition for ‘sd’
utild1filt: no visible global function definition for ‘convolve’
Undefined global functions or variables:
  convolve fft legend lines median plot sd title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "title")
  importFrom("stats", "convolve", "fft", "median", "sd")
to your NAMESPACE file.
Running examples in ‘Stickbreaker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim.data.from.priors.for.mod.selection
> ### Title: Simulate data from priors for doing model selection
> ### Aliases: sim.data.from.priors.for.mod.selection
> 
> ### ** Examples
> 
>  n.muts <- 4
>  n.muts <- length(Khan.data[1,])-1
>  geno.matrix <- Khan.data[,seq(1, n.muts)]
>  fit.matrix <- as.matrix(Khan.data[,(n.muts+1)])
>  outdir <- system.file("extdata",package="Stickbreaker")
>  file.name <- paste("Training_simulated_priors_fit_data_", n.muts, "muts.txt", sep="")
>  outpath <- paste(outdir, file.name, sep="/")
>  sim.data.from.priors.for.mod.selection(n.muts,
+    c(0.05, 0.5),
+    c(0, 0.25),
+    c(4),
+    1,
+    c(0.1, 10),
+    1.1,
+    1,
+    c(2,1),
+    outpath,
+    50,
+    coe.sim.model="identical",
+    coe.dist.par=NA,
+    print.interval=NA)
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/Stickbreaker/extdata/Training_simulated_priors_fit_data_5muts.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: sim.data.from.priors.for.mod.selection -> write.table -> file
Execution halted
Found the following apparent S3 methods exported but not registered:
  na.stinterp.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
na.stinterp.default: no visible global function definition for ‘time’
na.stinterp.default: no visible global function definition for
  ‘na.omit’
Undefined global functions or variables:
  na.omit time
Consider adding
  importFrom("stats", "na.omit", "time")
to your NAMESPACE file.
Running examples in ‘stinepack-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: na.stinterp
> ### Title: Replace NAs by Stineman interpolation
> ### Aliases: na.stinterp na.stinterp.default
> ### Keywords: ts
> 
> ### ** Examples
> 
> na.stinterp(c(2,NA,1,4,5,2))
Error in UseMethod("na.stinterp") : 
  no applicable method for 'na.stinterp' applied to an object of class "c('double', 'numeric')"
Calls: na.stinterp
Execution halted
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.
myQQNorm: no visible global function definition for ‘mad’
myQQNorm: no visible global function definition for ‘qnorm’
myQQNorm: no visible global function definition for ‘plot’
myQQNorm: no visible global function definition for ‘matlines’
myQQNorm: no visible global function definition for ‘points’
myQQNorm: no visible global function definition for ‘qqline’
myQQNorm: no visible global function definition for ‘box’
qqnormSim,lm: no visible global function definition for ‘resid’
Undefined global functions or variables:
  box mad matlines plot points qnorm qqline resid
Consider adding
  importFrom("graphics", "box", "matlines", "plot", "points")
  importFrom("stats", "mad", "qnorm", "qqline", "resid")
to your NAMESPACE file.
File ‘StMoSim/libs/StMoSim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Rd file 'calc.stoich.coef.Rd':
  \usage lines wider than 90 characters:
     calc.stoich.coef(alpha, name, subst, subst.norm, nu.norm = 1, constraints = list(), eps = 1e-5, verbose = TRUE)

These lines will be truncated in the PDF manual.
Packages in Depends field not imported from:
  ‘cubature’ ‘deldir’ ‘splancs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.devresid plot.gridresid plot.stpp plot.superthin plot.supresid
  plot.tessdev plot.tessresid plot.thinresid print.devresid
  print.gridresid print.stgrid print.stpp print.stwin print.superthin
  print.supresid print.tessdev print.tessresid print.thinresid
  summary.superthin summary.supresid summary.thinresid
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'gridresid.Rd':
  \usage lines wider than 90 characters:
     gridresid(X, cifunction, theta = NULL, lambda = NULL, grid = c(10, 10), gf = NULL, resid = c("raw", "pearson", "inverse"), algthm = c(" ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Running examples in ‘stppResid-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gridresid
> ### Title: Calculate grid-based residuals
> ### Aliases: gridresid
> 
> ### ** Examples
> 
> #===> load simulated data <===#
> data(simdata)
> X <- stpp(simdata$x, simdata$y, simdata$t)
stw missing - using default space-time window [0, 1]x[0, 1]
> 
> #===> define two conditional intensity functions <===#
> ci1 <- function(X, theta){theta*exp(-2*X$x - 2*X$y - 2*X$t)} #correct model
> 
> ci2 <- function(X, theta = NULL){rep(250, length(X$x))} #homogeneous Poisson model
> 
> ## Not run: 
> ##D gresiduals <- gridresid(X, ci1, theta = 3000)
> ##D plot(gresiduals)
> ## End(Not run)
> gresiduals2 <- gridresid(X, ci2)
> plot(gresiduals2)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot -> plot.default -> xy.coords
Execution halted
Running examples in ‘stranger-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: crazyfy
> ### Title: Data preparation before detection of strangers
> ### Aliases: crazyfy
> 
> ### ** Examples
> 
> library(stranger)
> data(iris)
> crazy <- crazyfy(iris[,1:4])
Error in `[.data.table`(dup, , `:=`(g, .GRP), by = cols) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: crazyfy -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Warning: Using size for a discrete variable is not advised.
Quitting from lines 85-95 (stranger_for_the_impatient.Rmd) 
Error: processing vignette ‘stranger_for_the_impatient.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
StratPhyloCongruence: no visible global function definition for ‘runif’
StratPhyloCongruence: no visible global function definition for
  ‘txtProgressBar’
StratPhyloCongruence: no visible global function definition for
  ‘setTxtProgressBar’
StratPhyloCongruence: no visible global function definition for ‘pnorm’
StratPhyloCongruence: no visible global function definition for ‘sd’
geoscalePhylo: no visible global function definition for ‘data’
geoscalePhylo: no visible global function definition for ‘par’
geoscalePhylo: no visible global function definition for ‘text’
geoscalePhylo: no visible global function definition for ‘segments’
geoscalePhylo: no visible global function definition for ‘rect’
geoscalePhylo: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  data par pnorm rect rgb runif sd segments setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "rect", "segments", "text")
  importFrom("stats", "pnorm", "runif", "sd")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
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 apparent S3 methods exported but not registered:
  plot.icweib print.icweib
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
HRatio: no visible global function definition for ‘qnorm’
icweib: no visible global function definition for ‘model.frame’
icweib: no visible binding for global variable ‘na.pass’
icweib: no visible global function definition for ‘complete.cases’
icweib: no visible global function definition for ‘model.matrix’
icweib: no visible global function definition for ‘optim’
icweib: no visible global function definition for ‘pchisq’
icweib: no visible global function definition for ‘pnorm’
plot.icweib : getstat: no visible global function definition for
  ‘qnorm’
plot.icweib: no visible global function definition for ‘plot’
plot.icweib: no visible global function definition for ‘lines’
plot.icweib: no visible global function definition for ‘legend’
print.icweib: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  complete.cases legend lines model.frame model.matrix na.pass optim
  pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "model.frame", "model.matrix",
             "na.pass", "optim", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
Running examples in ‘straweib-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.icweib
> ### Title: Plot estimated survival function
> ### Aliases: plot.icweib
> 
> ### ** Examples
> 
> data(tooth24)
> fit <- icweib(L = left, R = right, data = tooth24, strata = dmf, covariates = ~sex)
> surv <- plot(fit, Z = 1, tRange = c(1, 7), tEst=1:7, xlab = "Time", ylab = "Survival Function", 
+      main = "Estimated survival function for sex = 1 (girls)")
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/streamR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
'library' or 'require' call to ‘ROAuth’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stringr)
  > 
  > test_check("stringr")
  ── 1. Failure: special case are correct (@test-match.r#13)  ────────────────────
  str_match(NA, "(a)") not equal to matrix(NA_character_).
  Lengths differ: 2 is not 1
  
  ── 2. Failure: special case are correct (@test-match.r#14)  ────────────────────
  str_match(character(), "(a)") not equal to matrix(character(), 0, 1).
  Attributes: < Component "dim": Mean relative difference: 0.5 >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 217 SKIPPED: 0 FAILED: 2
  1. Failure: special case are correct (@test-match.r#13) 
  2. Failure: special case are correct (@test-match.r#14) 
  
  Error: testthat unit tests failed
  Execution halted
breakpoints.formula: no visible global function definition for
  ‘%dopar%’
breakpoints.formula: no visible binding for global variable ‘i’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
sctest.default: no visible global function definition for ‘tail’
Undefined global functions or variables:
  %dopar% i tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in ‘StructFDR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: StructFDR
> ### Title: False Discovery Rate (FDR) Control Integrating a General Prior
> ###   Structure
> ### Aliases: StructFDR
> ### Keywords: Multiple testing False discovery rate Genetics Metagenomics
> ###   Genomics
> 
> ### ** Examples
> 
> require(ape) 
> require(nlme)
> require(cluster)
> require(StructFDR)
> 
> # Generate a caelescence tree and partition into 10 clusters
> set.seed(1234)
> n <- 20
> p <- 200
> tree <- rcoal(p)
> # Pairwise distance matrix. 
> D <- cophenetic(tree)
> clustering <- pam(D, k=10)$clustering
> 
> # Simulate case-control data, assuming cluster 2 is differential  
> X.control <- matrix(rnorm(n*p), p, n)
> X.case <- matrix(rnorm(n*p), p, n)
> eff.size <- rnorm(sum(clustering == 2), 0.5, 0.2)     
> X.case[clustering == 2, ] <- X.case[clustering == 2, ] + eff.size
> X <- cbind(X.control, X.case)
> Y <- gl(2, n) 
> 
> # Define testing and permutation function
> test.func <- function (X, Y) {
+ 	obj <- apply(X, 1, function(x) {
+ 				ttest.obj <- t.test(x ~ Y)
+ 				c(ttest.obj$p.value, sign(ttest.obj$statistic))
+ 			})
+     return(list(p.value=obj[1, ], e.sign=obj[2, ]))
+ }
> 
> perm.func <- function (X, Y) {
+ 	return(list(X=X, Y=sample(Y)))
+ }
> 
> # Call StructFDR
> tree.fdr.obj <- StructFDR(X, Y, D, test.func, perm.func)
Warning in StructFDR(X, Y, D, test.func, perm.func) :
  Both the data matrix and the distance matrix should have labels (rownames) to avoid potential errors!

Test on original data sets  ...
Test on permuted data sets  ...
Error in if (alt.FDR == "Permutation") { : the condition has length > 1
Calls: StructFDR
Execution halted
PlotHypTree: no visible global function definition for ‘browseURL’
treePValues: no visible global function definition for ‘lm’
treePValues: no visible global function definition for ‘pf’
plot,GBH-ANY: no visible binding for global variable ‘sorted.hyp’
plot,GBH-ANY: no visible binding for global variable ‘pval’
plot,GBH-ANY: no visible binding for global variable ‘group’
plot,GBH-ANY: no visible binding for global variable ‘type’
Undefined global functions or variables:
  browseURL group lm pf pval sorted.hyp type
Consider adding
  importFrom("stats", "lm", "pf")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Running examples in ‘structSSI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EstimatedHFDRControl
> ### Title: Estimate FDR control variations for HFDR procedure
> ### Aliases: EstimatedHFDRControl
> ### Keywords: ~htest
> 
> ### ** Examples
> 
> library('igraph')

Attaching package: ‘igraph’

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

    decompose, spectrum

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

    union

> library('ape')

Attaching package: ‘ape’

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

    edges, mst, ring

> 
> alternative.indices <- sample(1:49, 30)
> unadj.p.values <- vector("numeric", length = 49)
> unadj.p.values[alternative.indices] <- runif(30, 0, 0.01)
> unadj.p.values[-alternative.indices] <- runif(19, 0, 1)
> unadj.p.values[c(1:5)] <- runif(5, 0, 0.01)
> names(unadj.p.values) <- paste("Hyp ", c(1:49))
> 
> tree <- as.igraph(rtree(25))
Error in UseMethod("as.igraph") : 
  no applicable method for 'as.igraph' applied to an object of class "phylo"
Calls: as.igraph
Execution halted
Running ‘testGBHProcedures.R’ [4s/5s]
  Running ‘testHierarchicalMethods.R’ [4s/6s]
Running the tests in ‘tests/testHierarchicalMethods.R’ failed.
Complete output:
  > ## Test the hypothesesTree creation class.
  > 
  > set.seed(130229)
  > library('structSSI')
  > library('ape')
  > library('igraph')
  
  Attaching package: 'igraph'
  
  The following objects are masked from 'package:ape':
  
      edges, mst, ring
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > tree.1 <- as.igraph(rtree(10))
  Error in UseMethod("as.igraph") : 
    no applicable method for 'as.igraph' applied to an object of class "phylo"
  Calls: as.igraph
  Execution halted
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.
Running examples in ‘strvalidator-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calculateHb
> ### Title: Calculate Heterozygote Balance
> ### Aliases: calculateHb
> 
> ### ** Examples
> 
> data(ref2)
> data(set2)
> # Calculate average balances.
> calculateHb(data=set2, ref=ref2)
'kit' not provided. Attempting auto detection.
Detected kit(s): SGMPlus
Extracting known alleles from dataset...
Using 'fast' allele filtering method.
This method discards NA alleles/loci/samples.
1 "NA" in 'Allele' converted to NA
Removed 1 rows where Allele=<NA>
Audit trail created for res in function filterProfile.
Audit trail updated by function filterProfile.
Estimating size of alleles...
Audit trail updated by function addSize.
Error in `[.data.table`(DT, !is.na(Height), `:=`(Peaks, .N), list(Sample.Name,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: calculateHb -> [ -> [.data.table
Execution halted
Warning: no function found corresponding to methods exports from ‘stsm.class’ for: ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
stsm.model: no visible global function definition for ‘is.ts’
stsm.model: no visible global function definition for ‘var’
stsm.model: no visible global function definition for ‘frequency’
stsm.model: no visible global function definition for ‘na.omit’
stsm.model: no visible global function definition for ‘fft’
stsm.model: no visible global function definition for ‘new’
stsm.sgf: no visible global function definition for ‘frequency’
char2numeric,stsm: no visible global function definition for
  ‘frequency’
set.cpar,stsm: no visible global function definition for ‘validObject’
set.nopars,stsm: no visible global function definition for
  ‘validObject’
set.pars,stsm: no visible global function definition for ‘validObject’
transPars,stsm: no visible global function definition for ‘var’
Undefined global functions or variables:
  fft frequency is.ts na.omit new validObject var
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "fft", "frequency", "is.ts", "na.omit", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
Found the following apparent S3 methods exported but not registered:
  predict.sublasso
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
SubLasso: no visible global function definition for ‘predict’
SubLasso: no visible global function definition for ‘coef’
SubLasso: no visible global function definition for ‘dev.new’
SubLasso: no visible global function definition for ‘cor’
SubLasso: no visible global function definition for ‘boxplot’
predict.sublasso: no visible global function definition for ‘predict’
Undefined global functions or variables:
  boxplot coef cor dev.new predict
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "boxplot")
  importFrom("stats", "coef", "cor", "predict")
to your NAMESPACE file.
identifyGraph: no visible global function definition for ‘phyper’
mytriangle: no visible global function definition for ‘symbols’
plotGraph: no visible global function definition for ‘par’
plotGraph: no visible global function definition for ‘plot’
updateOrgEnvir: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  par phyper plot read.table symbols
Consider adding
  importFrom("graphics", "par", "plot", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.subsemble
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
predict.subsemble: no visible global function definition for ‘predict’
predict.subsemble: no visible binding for global variable ‘family’
subsemble: no visible global function definition for ‘gaussian’
subsemble: no visible global function definition for ‘detectCores’
subsemble : .make_Z_l: no visible global function definition for
  ‘parSapply’
subsemble : .make_Z_l: no visible global function definition for
  ‘makeCluster’
subsemble : .make_Z_l: no visible global function definition for
  ‘stopCluster’
subsemble: no visible global function definition for ‘parSapply’
subsemble: no visible global function definition for ‘makeCluster’
subsemble: no visible global function definition for ‘stopCluster’
subsemble: no visible global function definition for ‘predict’
Undefined global functions or variables:
  detectCores family gaussian makeCluster parSapply predict stopCluster
Consider adding
  importFrom("stats", "family", "gaussian", "predict")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘ROCR’ ‘penalized’
  Please remove these calls from your code.
ELF: no visible global function definition for ‘pt’
ELF: no visible global function definition for ‘qnorm’
ELF: no visible global function definition for ‘lm’
ELF: no visible global function definition for ‘lowess’
ELF: no visible global function definition for ‘dnorm’
ELF: no visible global function definition for ‘approx’
subtype: no visible global function definition for ‘runif’
subtype: no visible global function definition for ‘hclust’
subtype: no visible global function definition for ‘dist’
subtype: no visible global function definition for ‘cutree’
subtype: no visible global function definition for ‘pt’
subtype: no visible global function definition for ‘heatmap’
test_subtype_only: no visible global function definition for ‘pt’
test_subtype_only: no visible global function definition for ‘survdiff’
test_subtype_only: no visible global function definition for ‘survfit’
test_subtype_only: no visible global function definition for ‘title’
ufun: no visible global function definition for ‘dnorm’
ufun: no visible global function definition for ‘lowess’
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
Rd file 'subtype.Rd':
  \usage lines wider than 90 characters:
     subtype(GEset, outcomeLabels, treatment=NULL, Npermutes=10, Nchunks = 25, minClusterSizeB = 20, NclustersASet = 100, FDRpermutation = T ... [TRUNCATED]
  \examples lines wider than 100 characters:
     summary(A,f.out=0)  ### f.out can be used for filtering out uninteresting subtypes. e.g. if f.out=2, we ignore subtypes having N01_0<=2 ... [TRUNCATED]

Rd file 'summary.Rd':
  \examples lines wider than 100 characters:
     summary(A,f.out=0)  ### f.out can be used for filtering out uninteresting subtypes. e.g. if f.out=2, we ignore subtypes having N01_0<=2 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
playSudoku : replot: no visible global function definition for ‘par’
playSudoku : replot: no visible global function definition for ‘plot’
playSudoku : replot: no visible global function definition for
  ‘segments’
playSudoku : replot: no visible global function definition for ‘text’
playSudoku: no visible global function definition for ‘tktoplevel’
playSudoku: no visible global function definition for ‘tkwm.title’
playSudoku: no visible global function definition for ‘tkrplot’
playSudoku: no visible global function definition for ‘tktext’
playSudoku: no visible global function definition for ‘tkscrollbar’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkyview’
playSudoku: no visible global function definition for ‘tkconfigure’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkset’
playSudoku: no visible global function definition for ‘tkpack’
playSudoku: no visible global function definition for ‘tcl’
playSudoku: no visible global function definition for ‘tkcget’
playSudoku : showz: no visible global function definition for
  ‘tkrreplot’
playSudoku : type: no visible global function definition for ‘tkinsert’
playSudoku : type: no visible global function definition for ‘tksee’
playSudoku : kb: no visible global function definition for ‘tkdestroy’
playSudoku: no visible global function definition for
  ‘getGraphicsEvent’
playSudoku: no visible global function definition for ‘tkbind’
playSudoku: no visible global function definition for ‘tkwait.window’
Undefined global functions or variables:
  getGraphicsEvent par plot segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "plot", "segments", "text")
to your NAMESPACE file.
SUE.fitted.values: no visible global function definition for
  ‘model.frame’
SUE.lm: no visible global function definition for ‘model.frame’
SUE.lm: no visible global function definition for ‘lm’
SUE.lm: no visible global function definition for ‘anova’
SUE.plot: no visible global function definition for ‘plot’
SUE.residuals: no visible global function definition for ‘model.frame’
parameters : para2: no visible global function definition for ‘uniroot’
parameters: no visible global function definition for ‘optimize’
parameters: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  anova lm model.frame optimize plot uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
Rd file 'SUE.lm.Rd':
  \examples lines wider than 100 characters:
     ##We analysis the well known stackloss data by using ordinary linear method and the subsampling method. 
     ##proportion of outliers in the data. The subsample size is chosen to be the default size of ns = 11.
     plot(SUE.fitted.values(a2),SUE.residuals(a2),xlab="(b) fitted values",ylab="residuals",ylim=c(-12,12))
     plot(SUE.fitted.values(a3),SUE.residuals(a3),xlab="(c) fitted values",ylab="residuals",ylim=c(-12,12))

These lines will be truncated in the PDF manual.
MCMCCV: no visible global function definition for ‘rnorm’
MLCVGauss: no visible global function definition for ‘runif’
MLCVGauss: no visible global function definition for ‘optim’
SimSunderData: no visible global function definition for ‘runif’
SimSunderData: no visible global function definition for ‘dist’
SimSunderData: no visible global function definition for ‘rnorm’
SimSunderData: no visible global function definition for ‘qgamma’
SimSunderData: no visible global function definition for ‘pnorm’
SimSunderData: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
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.
sunter: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  ‘rgamma’
supcluster : itgamma: no visible global function definition for
  ‘dgamma’
supcluster : itgamma: no visible global function definition for ‘runif’
supcluster : itbeta: no visible global function definition for ‘rnorm’
supcluster : itbeta: no visible global function definition for ‘runif’
supcluster : itj: no visible global function definition for ‘dmultinom’
supcluster: no visible global function definition for ‘kmeans’
tab1: no visible global function definition for ‘image’
tab1: no visible global function definition for ‘gray’
tab1: no visible global function definition for ‘var’
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
Call with DUP:
   .C(R_clusterer, E = as.double(E), X = as.double(X), W = as.double(W), 
       P = as.double(P), y = as.double(y), prob = as.double(prob), 
       theta = as.double(theta), lambda = as.double(lambda * n), 
       n = as.integer(n), g = as.integer(g), m = as.integer(m), 
       p = as.integer(p), critflag = as.integer(critflag), penflag = as.integer(penflag), 
       blockflag = as.integer(blockflag), valiflag = as.integer(valiflag), 
       traceflag = as.integer(trace), genliste = integer(lSize), 
       kriterium = double(lSize), DUP = FALSE)
DUP is no longer supported and will be ignored.
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.
Package which this enhances but not available for checking: ‘gputools’
HCLtree: no visible global function definition for ‘hclust’
HCLtree: no visible global function definition for ‘as.dist’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matplot’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matlines’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘axis’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matplot’
plotProfilesWithinBicluster: no visible global function definition for
  ‘title’
plotProfilesWithinBicluster: no visible global function definition for
  ‘axis’
plotProfilesWithinBicluster: no visible global function definition for
  ‘par’
plotProfilesWithinBicluster: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matlines’
plotProfilesWithinBicluster: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  as.dist axis box hclust legend matlines matplot par title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "matlines", "matplot",
             "par", "title")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘boa’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
superdiag: no visible global function definition for ‘as.mcmc.list’
superdiag: no visible global function definition for ‘as.mcmc’
superdiag: no visible global function definition for ‘runif’
superdiag: no visible global function definition for ‘geweke.diag’
superdiag: no visible global function definition for ‘heidel.diag’
superdiag: no visible global function definition for ‘raftery.diag’
superdiag: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  as.mcmc as.mcmc.list gelman.diag geweke.diag heidel.diag raftery.diag
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
TrainSuperMDS: no visible global function definition for ‘rnorm’
TrainSuperMDSOnce: no visible global function definition for ‘cmdscale’
TrainSuperMDSOnce: no visible global function definition for ‘quantile’
distmat: no visible global function definition for ‘dist’
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/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.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/copulas-concordance.tex’
   ‘vignettes/surrosurv.tex’
(Is a VignetteBuilder field missing?)
Found the following apparent S3 methods exported but not registered:
  print.SurvAM
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Est.Var.CCH.trueweights: no visible binding for global variable ‘var’
getEstimatesSP: no visible global function definition for ‘quantile’
getEstimatesSP: no visible global function definition for ‘resid’
prepareDataNP: no visible global function definition for
  ‘complete.cases’
prepareDataSP: no visible global function definition for
  ‘complete.cases’
processRawOutput: no visible global function definition for ‘qnorm’
survAM.estimate: no visible global function definition for ‘median’
survAM.estimate: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  complete.cases median qnorm quantile resid sd var
Consider adding
  importFrom("stats", "complete.cases", "median", "qnorm", "quantile",
             "resid", "sd", "var")
to your NAMESPACE file.
File ‘survAccuracyMeasures/libs/survAccuracyMeasures.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for ‘plot’
plot.survAUC: no visible global function definition for ‘lines’
plot.survErr: no visible global function definition for ‘plot’
plot.survErr: no visible global function definition for ‘lines’
schemper: no visible global function definition for ‘predict’
schemper: no visible global function definition for ‘survfit’
schemper: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx lines plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
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.
Est.PH: no visible global function definition for ‘coxph’
Inf.Cval: no visible global function definition for ‘rexp’
Inf.Cval: no visible global function definition for ‘var’
Inf.Cval.Delta: no visible global function definition for ‘rexp’
Inf.Cval.Delta: no visible global function definition for ‘var’
cvC: no visible global function definition for ‘coxph’
cvC: no visible global function definition for ‘weighted.mean’
Undefined global functions or variables:
  coxph rexp var weighted.mean
Consider adding
  importFrom("stats", "rexp", "var", "weighted.mean")
to your NAMESPACE file.
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.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/survClip.Rnw’
(Is a VignetteBuilder field missing?)
pearson: no visible global function definition for ‘cor’
plot.survcorr: no visible global function definition for ‘pnorm’
plot.survcorr: no visible global function definition for ‘par’
plot.survcorr: no visible global function definition for ‘plot’
plot.survcorr: no visible global function definition for ‘points’
survcorr: no visible global function definition for ‘model.frame’
survcorr: no visible global function definition for ‘qnorm’
survcorr: no visible global function definition for ‘runif’
survcorr: no visible global function definition for ‘pnorm’
survcorr: no visible global function definition for ‘var’
survcorr: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
Running examples in ‘SurvDisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AsympDiscSurv
> ### Title: Asymptotic Estimate of Mean and Variance of Log-hazard Ratio for
> ###   Discrete Time Survival
> ### Aliases: AsympDiscSurv
> 
> ### ** Examples
> 
> set.seed(1234)
> nsim=1
> n=250
> k=50
> trt=c(rep(0,n),rep(1,n))
> betaef=rep(0,nsim)
> varef=betaef
> betapg=betaef
> varpg=betaef
> m1=3.05
> for (i in 1:nsim){
+   x=rexp(2*n,1)
+   x[(n+1):(2*n)]=x[(n+1):(2*n)]/2
+   x=ceiling(x*(k-1)/m1)
+   x=pmin(x,k)
+   cens=rbinom(2*n,1,0.9)
+   pg1=PrenticeGloeckler.test(x,cens,trt,k)
+   betapg[i]=pg1$coefficient
+   varpg[i]=(pg1$coefficient/pg1$wald.test)^2
+   efron=survival::coxph(survival::Surv(x,cens)~trt,ties="efron")
+   betaef[i]=efron$coef
+   varef[i]=efron$var}
> 
> h0=0.9*(exp(-c(0:(k-2))*m1/(k-1))-exp(-c(1:(k-1))*m1/(k-1)))
> h0=h0/(h0+exp(-c(1:(k-1))*m1/(k-1)))
> p0=exp(-c(0:(k-1))*m1/(k-1))
> p0=(p0[1:(k-1)]*0.9+p0[2:k]*0.1)/2
> h1=0.9*(exp(-c(0:(k-2))*2*m1/(k-1))-exp(-c(1:(k-1))*2*m1/(k-1)))
> h1=h1/(h1+exp(-c(1:(k-1))*2*m1/(k-1)))
> p1=exp(-2*c(0:(k-1))*m1/(k-1))
> p1=(p1[1:(k-1)]*0.9+p1[2:k]*0.1)/2
> 
> fa=AsympDiscSurv(h0=h0, h1=h1,p0=p0,p1=p1)
Error in if (!is.element(substr(method, 1, 1), c("b", "P"))) { : 
  the condition has length > 1
Calls: AsympDiscSurv
Execution halted
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.
Running examples in ‘surveyplanning-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optsize
> ### Title: Optimal sample size allocation
> ### Aliases: optsize
> ### Keywords: surveyplanning
> 
> ### ** Examples
> 
> 
> data <- data.table(H = 1 : 3,
+                    s2h=10 * runif(3),
+                    s2h2 = 10 * runif(3),
+                    poph = 8 * 1 : 3,
+                    Rh = rep(1, 3),
+                    dd = c(1, 1, 1))
> 
> vars <- optsize(H = "H",
+                 s2h=c("s2h", "s2h2"),
+                 n = 10, poph = "poph",
+                 Rh = "Rh",
+                 fullsampleh = NULL, 
+                 dataset = data)
Error in `[.data.table`(resulth, fullsampleh == 0, `:=`(nh, nh_cor * pnh/sum(pnh)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: optsize -> [ -> [.data.table
Execution halted
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Survgini: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘survC1’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.HR.FUN: no visible global function definition for ‘coxph’
Est.HR.FUN: no visible global function definition for ‘basehaz’
Est.HR.FUN: no visible global function definition for ‘approx’
Ghat.FUN: no visible global function definition for ‘survfit’
IDI.INF: no visible global function definition for ‘kmcens’
IDI.INF: no visible global function definition for ‘quantile’
IDI.INF.GRAPH: no visible global function definition for ‘plot’
IDI.INF.GRAPH: no visible global function definition for ‘lines’
IDI.INF.GRAPH: no visible global function definition for ‘abline’
IDI.INF.GRAPH: no visible global function definition for ‘points’
IDI.INF.GRAPH: no visible global function definition for ‘title’
PTB.IDI.FUN: no visible global function definition for ‘rexp’
shade: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines plot points polygon quantile
  rexp survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points", "polygon",
             "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
Rd file 'IDI.INF.GRAPH.Rd':
  \usage lines wider than 90 characters:
     IDI.INF.GRAPH(x, main = NULL, xlab = NULL, ylab = NULL, cex.main = NULL, cex.lab = NULL, ...)

Rd file 'IDI.INF.Rd':
  \usage lines wider than 90 characters:
     IDI.INF(indata, covs0, covs1, t0, npert = 300, npert.rand = NULL, seed1 = NULL, alpha = 0.05)

These lines will be truncated in the PDF manual.
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.
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.
betaEst: no visible global function definition for ‘is’
fullKernel: no visible global function definition for ‘is’
halfKernel: no visible global function definition for ‘is’
kernelAuto: no visible global function definition for ‘quantile’
kernelAuto: no visible global function definition for ‘lm’
kernelAuto: no visible global function definition for ‘pnorm’
kernelFixed: no visible global function definition for ‘pnorm’
lastValue: no visible global function definition for ‘pnorm’
nearValue: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  is lm pnorm quantile
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "lm", "pnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: ggplot2
Loading required package: ggpubr
Loading required package: magrittr
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
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 119-122 (Specifiying_weights_in_log-rank_comparisons.Rmd) 
Error: processing vignette ‘Specifiying_weights_in_log-rank_comparisons.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Running examples in ‘survMisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ci
> ### Title: *c*onfidence *i*ntervals for survival curves.
> ### Aliases: ci ci.stratTen ci.ten
> ### Keywords: survival
> 
> ### ** Examples
> 
> ## K&M 2nd ed. Section 4.3. Example 4.2, pg 105.
> data("bmt", package="KMsurv")
> b1 <- bmt[bmt$group==1, ] # ALL patients
> ## K&M 2nd ed. Section 4.4. Example 4.2 (cont.), pg 111.
> ## patients with ALL
> t1 <- ten(Surv(t2, d3) ~ 1, data=bmt[bmt$group==1, ])
Error in `[.data.table`(x, , `:=`("ncg", rev(seq.int(length(n)))), by = cg) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: ten ... ten.data.frame -> ten -> ten.data.table -> [ -> [.data.table
Execution halted
Running examples in ‘SurvRank-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CVrankSurv_fct
> ### Title: Main function of SurvRank.
> ### Aliases: CVrankSurv_fct
> ### Keywords: SurvRank
> 
> ### ** Examples
> 
> ## Simulating a survival data set
> N=100; p=10; n=4
> x=data.frame(matrix(rnorm(N*p),nrow=N,p))
> beta=rnorm(n)
> mx=matrix(rnorm(N*n),N,n)
> fx=mx[,seq(n)]%*%beta/3
> hx=exp(fx)
> ty=rexp(N,hx)
> tcens=1-rbinom(n=N,prob=.3,size=1)
> y=Surv(ty,tcens)
> data=list()
> data$x<-x; data$y<-y
> ## Ranking the features according to their significance in the univariate cox models
> out.cox<-CVrankSurv_fct(data,2,3,3,fs.method="cox.rank")

  |                                                                            
  |==============                                                        |  20%Error in output[[i]][[3]] : subscript out of bounds
Calls: CVrankSurv_fct
Execution halted
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.
fitModel: no visible global function definition for ‘var’
fitModel: no visible global function definition for ‘cov’
svpls: no visible global function definition for ‘pt’
Undefined global functions or variables:
  cov pt var
Consider adding
  importFrom("stats", "cov", "pt", "var")
to your NAMESPACE file.
Calls with DUP:
   .C("myInversion", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, DUP = FALSE, PACKAGE = "svcm")
   .C("myTrace", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, BBenv$diag, BBenv$env, BBenv$xenv, BBenv$N, 
       BBenv$Nenv, BBenv$Nplus1, ED = ED, DUP = FALSE, PACKAGE = "svcm")
   .C("dsC2env", N, A@x, as.integer(A@i), as.integer(A@p), diagvec = diagvec, 
       env = env, xenv = as.integer(xenv), DUP = FALSE)
DUP is no longer supported and will be ignored.
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.
dlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
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 ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/svd.Rcheck/00install.out’ for details.
svd3dplot: no visible global function definition for ‘wireframe’
svd3dplot: no visible global function definition for ‘levelplot’
Undefined global functions or variables:
  levelplot wireframe
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for ‘localeToCharset’
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
.onAttach : svBrowser: no visible global function definition for
  ‘browseURL’
.onAttach: no visible global function definition for ‘loadhistory’
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
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.
processSocket: no visible global function definition for ‘URLdecode’
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
completeCol: no visible global function definition for ‘colors’
completeCol: no visible global function definition for ‘col2rgb’
completeCol: no visible global function definition for ‘palette’
Undefined global functions or variables:
  col2rgb colors palette
Consider adding
  importFrom("grDevices", "col2rgb", "colors", "palette")
to your NAMESPACE file.
.formatResult : capture.str: no visible global function definition for
  ‘str’
createLog: no visible global function definition for ‘sessionInfo’
protocol_junit.svSuiteData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svSuiteData: no visible global function definition for
  ‘addChildren’
protocol_junit.svSuiteData: no visible global function definition for
  ‘saveXML’
protocol_junit.svTestData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svTestData: no visible global function definition for
  ‘addChildren’
Undefined global functions or variables:
  addChildren saveXML sessionInfo str xmlNode
Consider adding
  importFrom("utils", "sessionInfo", "str")
to your NAMESPACE file.
svycox.calibrate: no visible global function definition for ‘quantile’
svycox.calibrate: no visible binding for global variable ‘median’
svycox.calibrate: no visible global function definition for
  ‘as.formula’
svycox.calibrate: no visible global function definition for ‘plot’
svycox.calibrate: no visible global function definition for ‘arrows’
svycox.calibrate: no visible global function definition for ‘abline’
svycox.nomogram: no visible global function definition for ‘predict’
svycox.nomogram: no visible global function definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘formula’
Undefined global functions or variables:
  abline arrows as.formula formula median plot predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows", "plot")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
additional_comp: no visible global function definition for ‘aggregate’
additional_compPV : <anonymous>: no visible global function definition
  for ‘aggregate’
cor.aux.func : <anonymous>: no visible global function definition for
  ‘cov.wt’
eta.func : <anonymous>: no visible global function definition for ‘lm’
eta.func : <anonymous>: no visible global function definition for
  ‘anova’
glm.dummy.no.std: no visible global function definition for
  ‘as.formula’
pv_by: no visible binding for global variable ‘var’
pv_perc: no visible binding for global variable ‘var’
pv_quantile: no visible binding for global variable ‘var’
svyPVcor: no visible global function definition for ‘update’
svyPVcor: no visible global function definition for ‘var’
svyPVeta: no visible global function definition for ‘update’
svyPVeta: no visible global function definition for ‘var’
svyPVglm: no visible global function definition for ‘gaussian’
svyPVglm: no visible binding for global variable ‘as.formula’
svyPVglm: no visible binding for global variable ‘var’
svyPVglm: no visible global function definition for ‘pt’
svyPVttest: no visible binding for global variable ‘as.formula’
svyPVttest: no visible global function definition for ‘var’
svyPVttest: no visible global function definition for ‘pt’
svyPVttest: no visible binding for global variable ‘var’
t.test.aux: no visible global function definition for ‘as.formula’
t.test.aux: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  aggregate anova as.formula complete.cases cov.wt gaussian lm pt
  update var
Consider adding
  importFrom("stats", "aggregate", "anova", "as.formula",
             "complete.cases", "cov.wt", "gaussian", "lm", "pt",
             "update", "var")
to your NAMESPACE file.
readSWAT: no visible global function definition for ‘read.fortran’
runSWAT2005: no visible global function definition for ‘read.fortran’
runSWAT2009: no visible global function definition for ‘read.fortran’
runSWAT2012: no visible global function definition for ‘read.fortran’
Undefined global functions or variables:
  read.fortran
Consider adding
  importFrom("utils", "read.fortran")
to your NAMESPACE file.
Rd file 'build_swat_basic.Rd':
  \examples lines wider than 100 characters:
     build_swat_basic(dirname="test", iyr="1979", nbyr=13, wsarea=40, elev=200, declat=45, declon=-72, hist_wx=hist_wx) 

Rd file 'readSWAT.Rd':
  \examples lines wider than 100 characters:
       } else { print ("You need to add your file type to this function if it is not output.sub or output.rch")}

These lines will be truncated in the PDF manual.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
  src/SWAT2005/Makefile
  src/SWAT2005/Makefile.win
  src/SWAT2009/Makefile
  src/SWAT2009/Makefile.win
  src/SWAT2012/Makefile
  src/SWAT2012/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
Packages in Depends field not imported from:
  ‘MASS’ ‘fda’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fj_pl: no visible global function definition for ‘getbasismatrix’
fj_pl: no visible global function definition for ‘create.bspline.basis’
fj_pl: no visible global function definition for ‘getbasispenalty’
forward_backward.quantities : <anonymous>: no visible global function
  definition for ‘dnorm’
function_cases1AND2: no visible global function definition for ‘dnorm’
function_cases3AND4: no visible global function definition for ‘dnorm’
pij_iid: no visible global function definition for ‘dnorm’
pilj: no visible global function definition for ‘dnorm’
updateLambda: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  create.bspline.basis dnorm getbasismatrix getbasispenalty optimize
Consider adding
  importFrom("stats", "dnorm", "optimize")
to your NAMESPACE file.
calc_MW: no visible global function definition for ‘read.table’
cfba_moment: no visible global function definition for ‘median’
cfba_moment: no visible global function definition for ‘write.csv’
cfba_moment_mr: no visible global function definition for ‘median’
cfba_moment_mr: no visible global function definition for ‘write.csv’
cfba_moment_pw: no visible global function definition for ‘median’
cfba_moment_pw: no visible global function definition for ‘write.csv’
readmodel: no visible global function definition for ‘as’
Undefined global functions or variables:
  as median read.table write.csv
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "median")
  importFrom("utils", "read.table", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:

  Warning: 'cBind' is deprecated.
  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
            user system elapsed
readTSVmod 6.376  0.056   7.684
Packages suggested but not available for checking: ‘sylly.de’ ‘sylly.es’
symbol: no visible global function definition for ‘plot.new’
symbol: no visible global function definition for ‘plot.window’
symbol: no visible global function definition for ‘axis’
symbol: no visible global function definition for ‘box’
symbol: no visible global function definition for ‘title’
symbol: no visible global function definition for ‘rainbow’
symbol: no visible global function definition for ‘hsv’
symbol: no visible global function definition for ‘rect’
symbol: no visible global function definition for ‘polygon’
symbol: no visible global function definition for ‘lines’
symbol: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
Rd file 'symbol.Rd':
  \usage lines wider than 90 characters:
     symbol(df, type="star", colin=NULL, colout=NULL, colin2=NA, colout2=1, ssize=NULL, labels=0, labelsize=0.6,
            scheme=1, sortby=0, descending=FALSE, coorx=NULL, coory=NULL, lty=1, main=NULL, sub=NULL, xlab=NULL, ylab=NULL,
            add=FALSE, xlim=NULL, ylim=NULL, facew=0.5, faceh=0.5, eyes=0.5, eyed=0.5, mouthw=0.5, mouthc=0.5, brows=0.5,
            browp=0.5, nosel=0.5, nosew=0.5, ears=0.5, pupils=0.5, body=0.5, limb1=0.5, limb2=0.5, limb3=0.5, limb4=0.5, defcol=NA)

These lines will be truncated in the PDF manual.
integrate.polynomial : f: no visible global function definition for
  ‘dmvnorm’
Undefined global functions or variables:
  dmvnorm
Package in Depends field not imported from: ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for ‘fft’
cwt_iw: no visible global function definition for ‘fft’
est_riskshrink_thresh: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
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.
'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Rd file 'SyNet-package.rd':
  \examples lines wider than 100 characters:
       # Run NAM method on the previously inferred sympatry network                                           

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

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

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

These lines will be truncated in the PDF manual.
Namespaces with empty importFrom:
  ‘Rcpp’ ‘methods’
File ‘synlik/libs/synlik.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mainNetFunction: no visible global function definition for ‘png’
mainNetFunction: no visible global function definition for ‘plot’
mainNetFunction: no visible global function definition for ‘lines’
mainNetFunction: no visible global function definition for ‘legend’
mainNetFunction: no visible global function definition for ‘dev.off’
plotPR: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘lines’
simulatedData: no visible global function definition for ‘rpois’
simulatedData : <anonymous>: no visible global function definition for
  ‘rpois’
simulatedData : rlognormpois: no visible global function definition for
  ‘rnorm’
simulatedData : rlognormpois: no visible global function definition for
  ‘rpois’
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘LowRankQP’ ‘rgenoud’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for ‘LowRankQP’
gaps.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘lines’
path.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘legend’
synth: no visible binding for global variable ‘sd’
synth: no visible binding for global variable ‘var’
synth: no visible global function definition for ‘LowRankQP’
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Found the following significant warnings:
  lib_FeasibleMatrix.cpp:53:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_FeasibleMatrix.cpp:168:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_FeasibleMatrix.cpp:176:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_sample_kcycle.cpp:141:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/systemicrisk.Rcheck/00install.out’ for details.
.checkDimAndTest: no visible global function definition for
  ‘chisq.test’
.checkDimAndTest: no visible global function definition for
  ‘fisher.test’
plotTable1Heatmap: no visible global function definition for ‘par’
plotTable1Heatmap: no visible global function definition for ‘image’
plotTable1Heatmap: no visible global function definition for ‘abline’
plotTable1Heatmap: no visible global function definition for ‘axis’
plotTable1Heatmap: no visible global function definition for ‘text’
plotTable1Heatmap: no visible global function definition for ‘legend’
plotTable1Heatmap: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box chisq.test fisher.test image legend par text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "text")
  importFrom("stats", "chisq.test", "fisher.test")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  rbind.tableList rbind.tableMatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'rbind.tableList':
  ‘rbind.tableList’

S3 methods shown with full name in documentation object 'rbind.tableMatrix':
  ‘rbind.tableMatrix’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘tableMatrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getRow.tableMatrix
> ### Title: Get or set row from the matrix attribute
> ### Aliases: getRow.tableMatrix setRow.tableMatrix
> 
> ### ** Examples
> 
> 
> data(images8By8)
> data(images10By10)
> 
> # Create tableMatrix from images8By8 and images10By10
> TM <- tableMatrix(list(images8By8, images10By10), list(1:3, 1:3),
+ list(4:ncol(images8By8),4:ncol(images10By10)))
Error in setkeyv(obj$tab, c(tmName$matN, tmName$matRow)) : 
  x is not a data.table
Calls: tableMatrix -> setkeyv
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 63-93 (tableMatrix-Overview.Rmd) 
Error: processing vignette ‘tableMatrix-Overview.Rmd’ failed with diagnostics:
x is not a data.table
Execution halted
'library' or 'require' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘perturb’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cellgram: no visible global function definition for ‘grid.rect’
cellgram: no visible global function definition for ‘gpar’
cellgram: no visible global function definition for ‘grid.segments’
cellgram: no visible global function definition for ‘grid.circle’
cellgram: no visible global function definition for ‘grid.polygon’
cellgram: no visible global function definition for ‘grid.text’
cellgram: no visible global function definition for ‘unit’
compare: no visible global function definition for ‘sd’
tableplot.colldiag: no visible global function definition for
  ‘colldiag’
tableplot.colldiag: no visible global function definition for ‘xtabs’
tableplot.default: no visible global function definition for
  ‘grid.newpage’
tableplot.default: no visible global function definition for
  ‘grid.layout’
tableplot.default: no visible global function definition for ‘unit’
tableplot.default: no visible global function definition for
  ‘pushViewport’
tableplot.default: no visible global function definition for ‘viewport’
tableplot.default: no visible global function definition for
  ‘grid.text’
tableplot.default: no visible global function definition for
  ‘upViewport’
tableplot.default: no visible global function definition for ‘gpar’
tableplot.default: no visible global function definition for
  ‘grid.rect’
tableplot.default: no visible global function definition for
  ‘popViewport’
Undefined global functions or variables:
  colldiag gpar grid.circle grid.layout grid.newpage grid.polygon
  grid.rect grid.segments grid.text popViewport pushViewport sd unit
  upViewport viewport xtabs
Consider adding
  importFrom("stats", "sd", "xtabs")
to your NAMESPACE file.
Rd file 'Linehan.Rd':
  \examples lines wider than 100 characters:
             cell.specs=list(list(0,"grey50",1,1,"red",1,"white","grey90",2,.7,"black",FALSE,"black",99)),
             cell.specs=list(list(0,c("black","blue"),1,1,c("black","blue"),1,"white","grey80",2,.7,"black",FALSE,"black",99))

Rd file 'cellgram.Rd':
  \usage lines wider than 90 characters:
     cellgram(cell, shape = 0, shape.col = "black", shape.lty = 1, shape.neg = 0, shape.col.neg = "red", shape.lty.neg = 1, cell.fill = "whi ... [TRUNCATED]

Rd file 'congruence.array.Rd':
  \usage lines wider than 90 characters:
     congruence.array(X, FUN = congruence.coef, stat.name = "phi", round = FALSE, scale = 1, ref = "last")

Rd file 'make.specs0.Rd':
  \usage lines wider than 90 characters:
     make.specs0(n = NULL, as.data.frame = FALSE, shape = 0, shape.col = "black", shape.lty = 1, shape.neg = 0, shape.col.neg = "red", shape ... [TRUNCATED]
     cell.fill = "white", back.fill = "white", label = 0, label.size = 0.7, label.col = "black", ref.lines = FALSE, ref.col = "gray80",  sca ... [TRUNCATED]

Rd file 'tableplot.Rd':
  \usage lines wider than 90 characters:
             v.parts = 0, h.parts = 0, gap = 2, text.m = 0, empty.text.size = 0.8, empty.text.col = "grey30", 
             title = NULL, table.label = TRUE, label.size = 0.8, side.rot = 0, left.space = 10, top.space = 10+10*(!is.null(title)), ...)
  \examples lines wider than 100 characters:
             cell.specs = list(list(0,"grey50",1,0,"red",1,"white","grey80",1,0.7,"black",FALSE,"black",93)),

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  print.plist
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
TCRsink: no visible global function definition for ‘head’
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
itabplot : <anonymous>: no visible global function definition for
  ‘capture.output’
itabplot: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL capture.output
Consider adding
  importFrom("utils", "browseURL", "capture.output")
to your NAMESPACE file.
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.
Found the following apparent S3 methods exported but not registered:
  proj.data proj.dir proj.dir2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
NANOVA.test: no visible global function definition for ‘ecdf’
NANOVA.test2: no visible global function definition for ‘ecdf’
NANOVA.test3: no visible global function definition for ‘ecdf’
fdr.table: no visible global function definition for ‘median’
fdr.table: no visible global function definition for ‘quantile’
gene.classifier1: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  ecdf median quantile write.table
Consider adding
  importFrom("stats", "ecdf", "median", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'NANOVA.test.Rd':
  \usage lines wider than 90 characters:
     NANOVA.test2(data,f1,f2,type,time.course,equal.size=FALSE,B=100,robustify=FALSE,eb=FALSE,df=0)

Rd file 'tanova.Rd':
  \usage lines wider than 90 characters:
     tanova(data, f1, f2, tp, B=100, FDR=0.05,robustify=FALSE, equal.size=FALSE, qt=-1, longitudinal=TRUE, test.type=0,eb=FALSE,df=0)
     gene.classifier1(data, f1, f2, B=100,FDR=0.05, robustify=FALSE, equal.size=FALSE, eb=FALSE,qt=-1)
     gene.classifier2(data, f1, f2, B=100,FDR=0.05, robustify=FALSE, equal.size=FALSE, time.course, qt=-1,eb=FALSE,df=1)

These lines will be truncated in the PDF manual.
Found the following significant warnings:
  clean_trade.cpp:22:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  clean_trade.cpp:23:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  clean_trade_ms.cpp:22:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  clean_trade_ms.cpp:23:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  gzipdec.cpp:16:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  gzipdec.cpp:17:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  gzipdec_ms.cpp:59:20: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  gzipdec_ms.cpp:61:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  gzipdec_ms.cpp:63:21: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  trstdev.cpp:6:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TAQMNGR.Rcheck/00install.out’ for details.
File ‘TAQMNGR/libs/TAQMNGR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  as.matrix.by stack.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘taRifx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stack.list
> ### Title: Stack lists into data.frames
> ### Aliases: stack.list
> 
> ### ** Examples
> 
> dat <- replicate(10, data.frame(x=runif(2),y=rnorm(2)), simplify=FALSE)
> str(dat)
List of 10
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.266 0.372
  ..$ y: num [1:2] 0.184 -0.836
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.945 0.661
  ..$ y: num [1:2] 0.33 -0.82
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.687 0.384
  ..$ y: num [1:2] 0.738 0.576
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.38 0.777
  ..$ y: num [1:2] 1.51 0.39
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.267 0.386
  ..$ y: num [1:2] -2.21 1.12
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.482 0.6
  ..$ y: num [1:2] -0.0162 0.9438
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.794 0.108
  ..$ y: num [1:2] 0.594 0.919
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.783 0.553
  ..$ y: num [1:2] 0.0746 -1.9894
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.732 0.693
  ..$ y: num [1:2] -0.0561 -0.1558
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.0707 0.0995
  ..$ y: num [1:2] -0.478 0.418
> stack(dat)
Error in stack.default(dat) : at least one vector element is required
Calls: stack -> stack.default
Execution halted
AnalyzeLVZ: no visible global function definition for ‘approx’
ConvP2Vdepthinv: no visible global function definition for ‘approx’
DistSummary: no visible global function definition for ‘heat.colors’
Earthplot: no visible global function definition for ‘heat.colors’
Earthplot: no visible global function definition for ‘par’
Earthplot: no visible global function definition for ‘plot’
Earthplot: no visible global function definition for ‘approx’
Earthplot: no visible global function definition for ‘image’
Earthplot: no visible binding for global variable ‘lines’
FindRoots: no visible global function definition for ‘uniroot’
InterpModel: no visible global function definition for ‘approx’
LinInterp: no visible global function definition for ‘approx’
PolarPlot: no visible binding for global variable ‘plot’
Rayfan: no visible binding for global variable ‘lines’
polaraxis: no visible global function definition for ‘text’
Undefined global functions or variables:
  approx heat.colors image lines par plot text uniroot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "lines", "par", "plot", "text")
  importFrom("stats", "approx", "uniroot")
to your NAMESPACE file.
Rd file 'DistSummary.Rd':
  \usage lines wider than 90 characters:
     DistSummary(delta, h, model, phaselist = 'default', prop = "vp", image.col = heat.colors(500), n = 200, ...)

Rd file 'Rayfan.Rd':
  \usage lines wider than 90 characters:
     Rayfan(phaselist, h, model, deltalist = 1:17 * 20, minp = 0.5, plot = TRUE, add = TRUE, col = rep("black", length(phaselist)), verbose  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
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.
BootTree: no visible global function definition for ‘hclust’
BootTree: no visible global function definition for ‘dist’
BootTree: no visible global function definition for ‘as.dist’
BootTree: no visible global function definition for ‘cor’
BootTree: no visible binding for global variable ‘var’
Pgpd: no visible global function definition for ‘optim’
Pgpd : <anonymous>: no visible global function definition for ‘optim’
Pgpd: no visible global function definition for ‘var’
Pgpd: no visible global function definition for ‘rnorm’
Pgpd: no visible global function definition for ‘quantile’
Pvalue: no visible global function definition for ‘rnorm’
SigTree: no visible global function definition for ‘data’
TreeStat: no visible global function definition for ‘hclust’
TreeStat: no visible global function definition for ‘as.dist’
TreeStat: no visible global function definition for ‘dist’
TreeStat: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘hclust’
plot.best: no visible global function definition for ‘as.dist’
plot.best: no visible global function definition for ‘dist’
plot.best: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘plot’
treetext: no visible global function definition for ‘par’
treetext: no visible global function definition for ‘text’
Undefined global functions or variables:
  as.dist cor data dist hclust optim par plot quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: sn
Loading required package: stats4

Attaching package: 'sn'

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

    sd

Loading required package: mclust
Package 'mclust' version 5.4
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: cluster
Warning in .tkmeans.warn(O, ret) :
  Clusters with size < n * 0.02 found - try reducing k.
Warning in .tclust.warn(O, O$ret) :
  The result is artificially constrained due to restr.fact = 12.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘tclust.tex’ failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.

Error: processing vignette ‘tcpl_Overview.Rnw’ failed with diagnostics:
 chunk 4 
Error in result_create(conn@ptr, statement) : 
  attempt to write a readonly database
Execution halted
Found the following apparent S3 methods exported but not registered:
  slice.fun
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'top.fun':
  ‘slice.fun’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘tcR/libs/tcR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for ‘hist’
mapper1D: no visible global function definition for ‘dist’
mapper1D: no visible global function definition for ‘as.dist’
mapper1D: no visible global function definition for ‘hclust’
mapper1D: no visible global function definition for ‘cutree’
mapper2D: no visible global function definition for ‘dist’
mapper2D: no visible global function definition for ‘as.dist’
mapper2D: no visible global function definition for ‘hclust’
mapper2D: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
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.
Packages in Depends field not imported from:
  ‘RSEIS’ ‘pracma’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
tdt.quad: no visible global function definition for ‘runif’
tdt.rr: no visible global function definition for ‘pf’
tdt.rr: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  pf qbeta runif
Consider adding
  importFrom("stats", "pf", "qbeta", "runif")
to your NAMESPACE file.
File ‘tdthap/libs/tdthap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
E.2SI: no visible binding for global variable ‘var’
E.2SI: no visible global function definition for ‘var’
E.BE: no visible global function definition for ‘var’
E.Beta: no visible global function definition for ‘var’
E.PO: no visible global function definition for ‘var’
E.PPS: no visible global function definition for ‘var’
E.SI: no visible global function definition for ‘var’
E.STPPS: no visible global function definition for ‘var’
E.STSI: no visible global function definition for ‘var’
E.STpiPS: no visible global function definition for ‘var’
E.SY: no visible global function definition for ‘var’
E.WR: no visible global function definition for ‘var’
E.piPS: no visible global function definition for ‘var’
GREG.SI: no visible global function definition for ‘var’
S.BE: no visible global function definition for ‘runif’
S.PO: no visible global function definition for ‘runif’
S.PPS: no visible global function definition for ‘runif’
S.SI: no visible global function definition for ‘runif’
S.STPPS: no visible global function definition for ‘runif’
S.WR: no visible global function definition for ‘rbinom’
S.piPS: no visible global function definition for ‘runif’
p.WR: no visible global function definition for ‘dmultinom’
Undefined global functions or variables:
  dmultinom rbinom runif var
Consider adding
  importFrom("stats", "dmultinom", "rbinom", "runif", "var")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.Weights predict.Weights2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
TeachNet: no visible global function definition for ‘predict’
createWeights1: no visible global function definition for ‘rnorm’
createWeights2: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  predict rnorm
Consider adding
  importFrom("stats", "predict", "rnorm")
to your NAMESPACE file.
aniplotevents: no visible global function definition for ‘plot’
aniplotevents: no visible global function definition for ‘lines’
cbfs: no visible global function definition for ‘rnorm’
cbfs: no visible global function definition for ‘runif’
cbfs_red: no visible global function definition for ‘arima.sim’
cbfs_red: no visible global function definition for ‘runif’
eventCluster: no visible global function definition for ‘princomp’
eventCluster: no visible global function definition for ‘kmeans’
measures: no visible global function definition for ‘sd’
measures: no visible global function definition for ‘var’
measures: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘Box.test’
noiseTests: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘ar’
plotevents: no visible global function definition for ‘plot’
plotevents: no visible global function definition for ‘lines’
ur.za.fast : roll: no visible global function definition for ‘coef’
ur.za.fast : roll: no visible global function definition for ‘lm’
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  $.tensor ^.tensor as.contravariate.character as.covariate.character
  as.tensor.default as.tensor.tensor is.contravariate.character
  is.contravariate.numeric is.contravariate.tensor
  is.covariate.character is.covariate.numeric is.covariate.tensor
  mean.tensor |.tensor
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Calls with DUP:
   .C(tensoraCmulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.complex(X[xtidx]), as.complex(Y[ytidx]), 
       erg = complex(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
   .C(tensoramulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.numeric(X[xtidx]), as.numeric(Y[ytidx]), 
       erg = numeric(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
DUP is no longer supported and will be ignored.
S3 methods shown with full name in documentation object 'mean.tensor':
  ‘mean.tensor’

S3 methods shown with full name in documentation object 'solve.tensor':
  ‘solve.tensor’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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.
Running examples in ‘tensorA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.tensor
> ### Title: Coercion to a tensor
> ### Aliases: as.tensor as.tensor.default as.tensor.tensor
> ### Keywords: arith
> 
> ### ** Examples
> 
> A <- diag(5)
> as.tensor(A)
Error in UseMethod("as.tensor") : 
  no applicable method for 'as.tensor' applied to an object of class "c('matrix', 'double', 'numeric')"
Calls: as.tensor
Execution halted
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for global variable ‘ID’
TER.deesc.1.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B: no visible binding for global variable ‘ID’
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A3.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A2.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : B1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B: no visible binding for global variable ‘ID’
Undefined global functions or variables:
  ID
Found the following apparent S3 methods exported but not registered:
  plot.df_curves plot.dyntermstrc_nss plot.dyntermstrc_param
  plot.dyntermstrc_yields plot.error plot.fwr_curves plot.ir_curve
  plot.s_curves plot.spot_curves plot.spsearch plot.termstrc_cs
  plot.termstrc_nss plot.zeroyields print.couponbonds
  print.dyncouponbonds print.dyntermstrc_nss print.dyntermstrc_yields
  print.summary.dyntermstrc_nss print.summary.dyntermstrc_param
  print.summary.dyntermstrc_yields print.summary.termstrc_cs
  print.summary.termstrc_nss print.termstrc_cs print.termstrc_nss
  print.zeroyields summary.dyntermstrc_nss summary.dyntermstrc_param
  summary.dyntermstrc_yields summary.termstrc_cs summary.termstrc_nss
  summary.zeroyields
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘termstrc/libs/termstrc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Depends: includes the non-default packages:
  ‘grid’ ‘quadprog’ ‘maps’ ‘maptools’ ‘mapdata’ ‘dichromat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘dichromat’ ‘grid’ ‘mapdata’ ‘maps’ ‘maptools’ ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.tverify tverify.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘ternvis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: foot
> ### Title: Football betting dataset
> ### Aliases: foot
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(foot)
> # see the distribution of forecasts
> tplot(foot$p,main="Bookmaker forecasts of \n football matches",
+       dimnames=c("Home Win","Draw","Away Win"))
>       
> # see how well forecasts compare with results
> # create object of class tverify
> foot.verify <- tverify(p=foot$p,o=foot$o) 
Error in UseMethod("tverify") : 
  no applicable method for 'tverify' applied to an object of class "c('matrix', 'double', 'numeric')"
Calls: tverify
Execution halted
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.
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.
File which contains pragma(s) suppressing diagnostics:
  ‘inst/include/testthat/vendor/catch.h’
Running examples in ‘TeXCheckR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: parse_tex
> ### Title: Parse LaTeX lines
> ### Aliases: parse_tex
> 
> ### ** Examples
> 
> parse_tex(c("A{}", "B[a]{b{c}{d}}z"))
Error in `[.data.table`(out, tex_group == j, `:=`((GROUP_IDj), .GRP),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: parse_tex -> [ -> [.data.table
Execution halted
Found the following apparent S3 methods exported but not registered:
  print.tepAssign print.tepBADA print.tepDICA print.tepGPLS
  print.tepGraphs print.tepPLS print.tepPLSCA print.texpoOutput
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
              user system elapsed
we8there    12.693  0.091  15.866
congress109  5.836  0.020   6.874
phyper_right: no visible global function definition for ‘dhyper’
progression: no visible global function definition for ‘density’
progression: no visible global function definition for ‘plot’
progression: no visible global function definition for ‘points’
progression: no visible global function definition for ‘legend’
progression: no visible global function definition for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘dhyper’
specificities.distribution.plot: no visible global function definition
  for ‘plot’
specificities.distribution.plot: no visible global function definition
  for ‘Axis’
specificities.distribution.plot: no visible global function definition
  for ‘arrows’
specificities.distribution.plot: no visible global function definition
  for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘title’
specificities.probabilities.vector: no visible global function
  definition for ‘phyper’
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
Running examples in ‘textrank-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: textrank_candidates_lsh
> ### Title: Use locality-sensitive hashing to get combinations of sentences
> ###   which contain words which are in the same minhash bucket
> ### Aliases: textrank_candidates_lsh
> 
> ### ** Examples
> 
> library(textreuse)
> lsh_probability(h = 1000, b = 500, s = 0.1) # A 10 percent Jaccard overlap will be detected well
[1] 0.9934295
> 
> minhash <- minhash_generator(n = 1000, seed = 123456789)
> 
> data(joboffer)
> terminology <- subset(joboffer, upos %in% c("NOUN", "ADJ"), select = c("sentence_id", "lemma"))
> candidates <- textrank_candidates_lsh(x = terminology$lemma, sentence_id = terminology$sentence_id,
+                                       minhashFUN = minhash, bands = 500)
Error in `[.data.table`(buckets, , list(bucket = digest::digest(object = list(hashes = hash,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: textrank_candidates_lsh -> mapply -> <Anonymous> -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
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 140-149 (textrank.Rmd) 
Error: processing vignette ‘textrank.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
File ‘textreg/libs/textreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
.dea_create_model: no visible global function definition for
  ‘getSrcFilename’
.wMean: no visible global function definition for ‘weighted.mean’
Undefined global functions or variables:
  getSrcFilename weighted.mean
Consider adding
  importFrom("stats", "weighted.mean")
  importFrom("utils", "getSrcFilename")
to your NAMESPACE file.
transfer: no visible global function definition for ‘rgamma’
transfer: no visible global function definition for ‘rnorm’
transfer: no visible global function definition for ‘rnbinom’
transfer: no visible global function definition for ‘rpois’
transfer: no visible global function definition for ‘rbinom’
transfer: no visible global function definition for ‘runif’
plot,transfer: no visible global function definition for ‘barplot’
plot,transfer: no visible global function definition for ‘axis’
plot,transfer: no visible global function definition for ‘par’
plot,transfer: no visible global function definition for ‘hist’
Undefined global functions or variables:
  axis barplot hist par rbinom rgamma rnbinom rnorm rpois runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "rbinom", "rgamma", "rnbinom", "rnorm", "rpois",
             "runif")
to your NAMESPACE file.
File ‘TFMPvalue/libs/TFMPvalue.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ParseTrueFX: no visible global function definition for ‘read.csv’
TrueFXRef: no visible global function definition for ‘download.file’
TrueFXRef: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
File ‘tgcd/libs/tgcd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
Package unavailable to check Rd xrefs: ‘dada2’
Thinknum: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
File ‘ThreeArmedTrials/libs/ThreeArmedTrials.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
coef_traceplot: no visible global function definition for ‘rainbow’
coef_traceplot: no visible global function definition for ‘plot’
coef_traceplot: no visible global function definition for ‘abline’
coef_traceplot : <anonymous>: no visible global function definition for
  ‘lines’
coef_traceplot: no visible global function definition for ‘text’
ee.GEE.aux : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for ‘printCoefmat’
threesls: no visible global function definition for ‘cor’
threesls: no visible global function definition for ‘pt’
tsls.formula: no visible global function definition for ‘model.matrix’
tsls.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
.LoadTickDataHK: no visible global function definition for ‘read.csv’
.LoadTickDataSHSZ: no visible global function definition for ‘read.csv’
DrawDown: no visible global function definition for ‘na.omit’
PerformanceReport: no visible global function definition for
  ‘aggregate’
PerformanceReport: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
newTiddler: no visible global function definition for ‘new’
twImage: no visible global function definition for ‘new’
twLink: no visible global function definition for ‘new’
twList: no visible global function definition for ‘new’
twTable: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘TideTables-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TideTable
> ### Title: Compute tide tables
> ### Aliases: TideTable
> 
> ### ** Examples
> 
> TideTable(dataInput=observation, asdate=observation$observation_date[1], 
+ astime=observation$observation_time[1], 
+ aedate="1991/05/01", aetime="21:00:00", ssdate="1995/01/01", 
+ sstime="00:00:00", sedate="1995/01/31", setime="21:00:00")
Error in `[.data.table`(input, , `:=`(n_mhist, .N), by = mhist) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: TideTable -> EstimateTmhwi -> [ -> [.data.table
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyinftheo)
  > 
  > test_check("tidyinftheo")
  ── 1. Error: right number of columns given (@test-errors.R#10)  ────────────────
  argument "expr" is missing, with no default
  1: expect_length(tab %>% select(vs) %>% shannon_entropy(), 1) at testthat/test-errors.R:10
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tab %>% select(vs) %>% shannon_entropy()
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: withVisible(function_list[[k]](value))
  11: function_list[[k]](value)
  12: shannon_entropy(.)
  13: reduce_data(.data, !!enquo(X), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !!!quos(...))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Found the following apparent S3 methods exported but not registered:
  plot.tight.clust
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.tight.clust: no visible global function definition for ‘hclust’
plot.tight.clust: no visible global function definition for ‘dist’
plot.tight.clust: no visible global function definition for ‘image’
plot.tight.clust: no visible global function definition for
  ‘colorRampPalette’
plot.tight.clust: no visible global function definition for ‘axis’
plot.tight.clust: no visible global function definition for ‘lines’
tight.clust : find.candidates : kmeans.classify: no visible global
  function definition for ‘kmeans’
write.tight.clust: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  axis colorRampPalette dist hclust image kmeans lines write.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "image", "lines")
  importFrom("stats", "dist", "hclust", "kmeans")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'tight.clust.Rd':
  \usage lines wider than 90 characters:
     tight.clust(x, target, k.min, alpha = 0.1, beta = 0.6, top.can = 7, seq.num = 2, resamp.num = 10, samp.p = 0.7, nstart = 1, remain.p =  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Running examples in ‘tightClust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tight.clust
> ### Title: Tight Clustering
> ### Aliases: tight.clust
> ### Keywords: cluster
> 
> ### ** Examples
> 
> ## load the test dataset
> data(tclust.test.data)
> ## find 10 tight clusters
> ptm<-proc.time()
> ## k.min=25, tighter clusters will be found
> ## target=1 is used to save time, target=10 is recommended
> tclust1<-tight.clust(tclust.test.data$Data, target=1, k.min=25, random.seed=12345)
Number of points: 1100 	Dimension: 75 

Looking for tight cluster 1 ...
k = 25
k = 26
1 tight cluster(s) found!
Cluster size: 43 	Remaining number of points: 1057 

> proc.time()-ptm
   user  system elapsed 
  3.637   0.103   6.392 
> ## plot the heat map of cluster result
> plot(tclust1)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
'library' or 'require' call to ‘shiny’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
timeline: no visible global function definition for ‘ggplot’
timeline: no visible global function definition for ‘geom_segment’
timeline: no visible global function definition for ‘aes_string’
timeline: no visible global function definition for ‘geom_rect’
timeline: no visible global function definition for ‘geom_text’
timeline: no visible global function definition for ‘theme’
timeline: no visible global function definition for ‘element_blank’
timeline: no visible global function definition for ‘xlab’
timeline: no visible global function definition for ‘ylab’
timeline: no visible global function definition for ‘xlim’
timeline: no visible global function definition for
  ‘scale_y_continuous’
timeline: no visible global function definition for ‘geom_point’
timeline: no visible global function definition for ‘scale_color_grey’
timeline: no visible global function definition for ‘geom_hline’
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TimeMachine.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  density.tm mean.tm print.tm quantile.tm summary.tm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
density.tm: no visible global function definition for ‘density’
mu.mle: no visible global function definition for ‘optimize’
pophistory.tm: no visible binding for global variable ‘quantile’
quantile.tm: no visible global function definition for ‘quantile’
sample.pop: no visible global function definition for ‘runif’
summary.tm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  density optimize quantile runif
Consider adding
  importFrom("stats", "density", "optimize", "quantile", "runif")
to your NAMESPACE file.
File ‘TimeMachine/libs/TimeMachine.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘TimeMachine-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pophistory
> ### Title: History of Population Size
> ### Aliases: pophistory pophistory.tm
> 
> ### ** Examples
> 
> # Load example dataset
> data(pdm)
> 
> transitions <- full.transitions(pdm$unitary.transitions, pdm$loci)
> pi <- stationary.dist(transitions)
> n <- 10
> mu <- 1
> samples <- 10
> est.res <- tm(transitions, pi, pdm$population, n, mu, samples)
> 
> # Plot minimum, median and maximum SEN as a function of population size
> h <- pophistory(est.res, probs=c(0, 0.5, 1))
Error in UseMethod("pophistory") : 
  no applicable method for 'pophistory' applied to an object of class "tm"
Calls: pophistory -> pophistory
Execution halted
generatelatencies: no visible binding for global variable ‘allNames’
generatetimedeltas: no visible global function definition for ‘head’
generatetimedeltas: no visible global function definition for ‘tail’
generatevertexedgelist : <anonymous>: no visible global function
  definition for ‘head’
generatevertexedgelist : <anonymous>: no visible global function
  definition for ‘tail’
plotnetworkslices: no visible global function definition for ‘par’
plotnetworkslices: no visible global function definition for ‘text’
plottanet: no visible global function definition for ‘plot’
plottonet: no visible global function definition for ‘plot’
shortesttimepath : <anonymous>: no visible global function definition
  for ‘tail’
Undefined global functions or variables:
  allNames head par plot tail text
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("methods", "allNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘plyr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘lubridate’ ‘timeDate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
is.Bizday: no visible global function definition for ‘isWeekday’
plotCalendarHeatmap: no visible global function definition for ‘ddply’
plotCalendarHeatmap: no visible global function definition for ‘.’
plotCalendarHeatmap: no visible binding for global variable ‘year’
plotCalendarHeatmap: no visible binding for global variable ‘month’
plotCalendarHeatmap: no visible binding for global variable ‘week’
plotCalendarHeatmap: no visible global function definition for ‘ggplot’
plotCalendarHeatmap: no visible global function definition for ‘aes’
plotCalendarHeatmap: no visible binding for global variable ‘monthweek’
plotCalendarHeatmap: no visible binding for global variable ‘weekday’
plotCalendarHeatmap: no visible global function definition for
  ‘geom_tile’
plotCalendarHeatmap: no visible global function definition for
  ‘facet_grid’
plotCalendarHeatmap: no visible global function definition for
  ‘scale_fill_gradientn’
projectDate: no visible global function definition for ‘holidayNYSE’
projectDate: no visible global function definition for
  ‘sparse.model.matrix’
Undefined global functions or variables:
  . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month
  monthweek scale_fill_gradientn sparse.model.matrix week weekday year
boot_autocov: no visible global function definition for ‘is.ts’
boot_autocov: no visible global function definition for ‘tsboot’
boot_autocov: no visible global function definition for ‘quantile’
boot_autocov: no visible global function definition for ‘par’
boot_autocov: no visible global function definition for ‘frequency’
boot_autocov: no visible global function definition for ‘polygon’
boot_autocov: no visible global function definition for ‘lines’
boot_autocov: no visible global function definition for ‘abline’
boot_autocov: no visible global function definition for ‘acf’
boot_spec: no visible global function definition for ‘is.ts’
boot_spec: no visible global function definition for ‘tsboot’
boot_spec: no visible global function definition for ‘spec.pgram’
boot_spec: no visible global function definition for ‘quantile’
boot_spec: no visible global function definition for ‘polygon’
boot_spec: no visible global function definition for ‘lines’
redraw: no visible global function definition for ‘spec.pgram’
statistic: no visible global function definition for ‘acf’
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
createHstore.ts: no visible global function definition for ‘time’
exploreDb : <anonymous>: no visible global function definition for
  ‘plot’
exportTsList : <anonymous>: no visible global function definition for
  ‘time’
exportTsList: no visible global function definition for ‘write.csv2’
importTsList: no visible global function definition for ‘read.csv2’
importTsList : <anonymous>: no visible global function definition for
  ‘as.ts’
plot.tslist: no visible global function definition for ‘plot’
plot.tslist : <anonymous>: no visible global function definition for
  ‘time’
plot.tslist: no visible global function definition for ‘par’
plot.tslist: no visible global function definition for ‘legend’
readTimeSeries : <anonymous>: no visible global function definition for
  ‘ts’
resolveOverlap: no visible global function definition for ‘is.ts’
resolveOverlap: no visible global function definition for ‘frequency’
resolveOverlap: no visible global function definition for ‘time’
resolveOverlap: no visible global function definition for ‘ts’
storeTimeSeries: no visible binding for global variable ‘frequency’
zooLikeDateConvert: no visible global function definition for ‘time’
zooLikeDateConvert: no visible global function definition for
  ‘frequency’
zooLikeDateConvert: no visible global function definition for ‘cycle’
Undefined global functions or variables:
  as.ts cycle frequency is.ts legend par plot read.csv2 time ts
  write.csv2
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "as.ts", "cycle", "frequency", "is.ts", "time",
             "ts")
  importFrom("utils", "read.csv2", "write.csv2")
to your NAMESPACE file.
author.search: no visible binding for global variable ‘na.omit’
reference.list: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘plot’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
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.
File ‘TIMP/libs/TIMP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 in Depends field not imported from:
  ‘ExPosition’ ‘InPosition’ ‘TExPosition’ ‘prettyGraphs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  print.tepBADA.inference.battery print.tepDICA.inference.battery
  print.tinpoAllBoots print.tinpoBoot print.tinpoBootTests
  print.tinpoComponents print.tinpoLOO print.tinpoOmni
  print.tinpoOutput print.tinpoR2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Non-standard files/directories found at top level:
  ‘DESCRIPTION.orig’ ‘README.rst’
tipom.car: no visible global function definition for ‘abline’
tipom.car: no visible global function definition for ‘axis’
tipom.heat: no visible global function definition for ‘image’
tipom.heat: no visible global function definition for ‘gray’
tipom.lw: no visible global function definition for ‘plot’
tipom.lw: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
ls.tree: no visible global function definition for ‘lm’
ls.tree: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
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.
Packages in Depends field not imported from:
  ‘rgl’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'par3dsave.Rd':
  \usage lines wider than 90 characters:
     par3dsave(params = c("userMatrix", "scale", "zoom", "FOV"), times = FALSE, dev = rgl.cur())

These lines will be truncated in the PDF manual.
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
.my.tkdev: no visible global function definition for ‘X11’
tkpersp : draw: no visible global function definition for ‘par’
tkpersp : draw: no visible global function definition for ‘persp’
Undefined global functions or variables:
  X11 par persp
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
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.
FLXmclust.Density: no visible global function definition for ‘dmvnorm’
FLXmclust.Estimate: no visible global function definition for ‘flexmix’
FLXmclust.Estimate: no visible global function definition for
  ‘FLXmclust’
coefmclust: no visible global function definition for ‘parameters’
flexmix.Density: no visible global function definition for
  ‘model.matrix’
flexmix.Density: no visible global function definition for
  ‘model.response’
flexmix.Density: no visible global function definition for
  ‘model.frame’
flexmix.Density: no visible global function definition for ‘dnorm’
flexmix.Density: no visible global function definition for ‘dpois’
flexmix.Density: no visible global function definition for ‘dbinom’
flexmix.Estimate: no visible global function definition for ‘flexmix’
flexmix.Estimate: no visible global function definition for ‘FLXglm’
tleplot,TLE-data.frame: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EMN: no visible global function definition for ‘dmvnorm’
EMN: no visible global function definition for ‘pmvnorm’
EMT: no visible global function definition for ‘GenzBretz’
EMT: no visible global function definition for ‘dmvt’
EMT: no visible global function definition for ‘pmvt’
MomemNT: no visible global function definition for ‘pnorm’
MomemNT: no visible global function definition for ‘dnorm’
MomemNT: no visible global function definition for ‘pmvnorm’
MomemNT: no visible global function definition for ‘dmvnorm’
TT.moment: no visible global function definition for ‘GenzBretz’
TT.moment: no visible global function definition for ‘pmvt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dmvt’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
inits: no visible global function definition for ‘lm’
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
Rd file 'UTIdata.Rd':
  \examples lines wider than 100 characters:
     x = cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

These lines will be truncated in the PDF manual.
search_collection: no visible global function definition for
  ‘URLencode’
search_company: no visible global function definition for ‘URLencode’
search_keyword: no visible global function definition for ‘URLencode’
search_list: no visible global function definition for ‘URLencode’
search_movie: no visible global function definition for ‘URLencode’
search_multi: no visible global function definition for ‘URLencode’
search_person: no visible global function definition for ‘URLencode’
search_tv: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
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 ‘tmlenet/libs/tmlenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
extractContentDOM: no visible global function definition for
  ‘capture.output’
extractHTMLStrip: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘tm.lexicon.GeneralInquirer’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tmuxr)
  > 
  > test_check("tmuxr")
  ── 1. Error: a session can be renamed (@test-session.R#28)  ────────────────────
  tmux: no current client
  1: expect_equal(rename_session(attach_session("foo"), "bar")$name, "bar") at testthat/test-session.R:28
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: rename_session(attach_session("foo"), "bar")
  5: tmux_rename_session("-t", session$name, as.character(new_name))
  6: stop(stringr::str_c("tmux: ", result, collapse = " "))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 7 SKIPPED: 0 FAILED: 1
  1. Error: a session can be renamed (@test-session.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Package suggested but not available for checking: ‘corpus.JSS.papers’
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.
Tosls.formula: no visible global function definition for ‘model.matrix’
Tosls.formula: no visible global function definition for
  ‘model.response’
summary: no visible global function definition for ‘coef’
summary: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘TeachingDemos’ ‘ash’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘rmongodb’
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'tcpl'
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.
toxboot 0.1.1
MongoDB settings (?toxbootConf):
  TOXBOOT_HOST: NA
  TOXBOOT_DBNS: NA
  TOXBOOT_USER: NA
  TOXBOOT_DB: NA
MySQL settings:
  Host: Not Configured
  Database: Not Configured
  User: Not Configured
Loading required package: DBI
Quitting from lines 197-204 (toxboot.Rmd) 
Error: processing vignette ‘toxboot.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
ConfA: no visible global function definition for ‘qf’
EstM2Sn: no visible global function definition for ‘nlm’
EstM2Sn: no visible global function definition for ‘qnorm’
TV.model: no visible global function definition for ‘dev.new’
TV.model: no visible global function definition for ‘points’
betaBino: no visible global function definition for ‘pbinom’
doseD: no visible global function definition for ‘lm’
doseD: no visible global function definition for ‘dev.new’
doseD: no visible global function definition for ‘par’
doseD: no visible global function definition for ‘plot’
doseD: no visible global function definition for ‘axTicks’
doseD: no visible global function definition for ‘axis’
doseD: no visible global function definition for ‘lines’
doseD: no visible global function definition for ‘abline’
doseD: no visible global function definition for ‘legend’
setD: no visible global function definition for ‘dev.new’
setD: no visible global function definition for ‘par’
setD: no visible global function definition for ‘pbinom’
setD: no visible global function definition for ‘abline’
setD: no visible global function definition for ‘axis’
setD: no visible global function definition for ‘rect’
setD: no visible global function definition for ‘lines’
setD: no visible global function definition for ‘text’
setD: no visible global function definition for ‘axTicks’
setD: no visible global function definition for ‘legend’
spoD : spoD_A: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
align1d : obj: no visible global function definition for ‘dist’
align2d : obj: no visible global function definition for ‘dist’
align2d : pen: no visible global function definition for ‘dist’
align2d: no visible global function definition for ‘dist’
sumt: no visible global function definition for ‘optim’
tpe1d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘cmdscale’
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tpr.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘track/R/track.attach.R’:
  attach(what = NULL, pos = pos, name = name)
See section ‘Good practice’ in ‘?attach’.
DeadReckoning: no visible global function definition for ‘filter’
DeadReckoning: no visible global function definition for ‘approx’
DeadReckoning: no visible global function definition for ‘lm’
Mapper: no visible global function definition for ‘colorRampPalette’
Mapper: no visible global function definition for ‘terrain.colors’
Mapper: no visible global function definition for ‘points’
Mapper: no visible global function definition for ‘axis’
Standardize: no visible global function definition for ‘lm’
Undefined global functions or variables:
  approx axis colorRampPalette filter lm points terrain.colors
Consider adding
  importFrom("grDevices", "colorRampPalette", "terrain.colors")
  importFrom("graphics", "axis", "points")
  importFrom("stats", "approx", "filter", "lm")
to your NAMESPACE file.
File ‘TransferEntropy/libs/TransferEntropy.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
microsoftTranslate: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Running examples in ‘translateSPSS2R-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xpssFlip
> ### Title: Flips variables
> ### Aliases: xpssFlip
> 
> ### ** Examples
> 
> data(fromXPSS)
> xpssFlip(x=fromXPSS,variables=c("V4","V5","V6"),names="V1")
Error in if (variables == "all") { : the condition has length > 1
Calls: xpssFlip
Execution halted
rtrapezoid: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
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.
File ‘treeclim/libs/treeclim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Build_JTree: no visible global function definition for ‘flush.console’
Run_JTree: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Running examples in ‘treemap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: random.hierarchical.data
> ### Title: Create random hierarchical data
> ### Aliases: random.hierarchical.data
> 
> ### ** Examples
> 
> d <- random.hierarchical.data(200)
> treemap(d, index=names(d)[1:(ncol(d)-1)], vSize="x")
Error in `[.data.table`(dtfDT, , list(s = fn(s), c = do.call("fun", c(list(c),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: treemap ... tmAggregate -> tmAggregateStep -> [ -> [.data.table
Execution halted
LikAge: no visible global function definition for ‘read.table’
bd.ME.optim: no visible global function definition for ‘optim’
bd.ME.optim.rho: no visible global function definition for ‘optim’
bd.ME.optim.rho.all: no visible global function definition for ‘optim’
bd.MEyule.optim: no visible global function definition for ‘optimize’
bd.MEyule.optim: no visible global function definition for ‘optim’
bd.age.optim.matlab: no visible global function definition for
  ‘read.table’
bd.groups.conf: no visible global function definition for ‘uniroot’
bd.shifts.plot: no visible global function definition for ‘plot’
bd.shifts.plot: no visible global function definition for ‘lines’
bdsky.stt.optim: no visible global function definition for ‘optim’
create.mat: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines optim optimize plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for ‘hist’
plot.treeperm: no visible global function definition for ‘points’
plot.treeperm: no visible global function definition for ‘text’
treeperm.formula: no visible global function definition for
  ‘model.frame’
treeperm.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
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 ‘trelliscope-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: applyCogFn
> ### Title: Apply Cognostics Function to a Key-Value Pair
> ### Aliases: applyCogFn
> 
> ### ** Examples
> 
> # create a division with a between-subset variable
> d <- divide(iris, by = "Species",
+   bsvFn = function(x) list(msl = mean(x$Sepal.Length)))
Error in `[.data.table`(d, , ff(.SD), by = key(d), .SDcols = nms) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: divide -> getDivideDF -> [ -> [.data.table
Execution halted
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("trelliscope")
  Loading required package: trelliscope
  Loading required package: datadr
  Note: trelliscope will eventually be superseded by trelliscopejs: https://github.com/hafen/trelliscopejs
  ── 1. Error: (unknown) (@test-1-simple-display.R#13)  ──────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: datadr::divide(barley, by = "site") at testthat/test-1-simple-display.R:13
  2: getDivideDF(data, by = by, postTransFn = postTransFn, bsvFn = bsvFn, update = update)
  3: d[, ff(.SD), by = key(d), .SDcols = nms]
  4: `[.data.table`(d, , ff(.SD), by = key(d), .SDcols = nms)
  
  ── 2. Error: find globals (@test-2-globals.R#10)  ──────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: datadr::divide(barley, by = "site") at testthat/test-2-globals.R:10
  2: getDivideDF(data, by = by, postTransFn = postTransFn, bsvFn = bsvFn, update = update)
  3: d[, ff(.SD), by = key(d), .SDcols = nms]
  4: `[.data.table`(d, , ff(.SD), by = key(d), .SDcols = nms)
  
  ── 3. Error: (unknown) (@test-3-globals-by-hand.R#10)  ─────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: datadr::divide(barley, by = "site") at testthat/test-3-globals-by-hand.R:10
  2: getDivideDF(data, by = by, postTransFn = postTransFn, bsvFn = bsvFn, update = update)
  3: d[, ff(.SD), by = key(d), .SDcols = nms]
  4: `[.data.table`(d, , ff(.SD), by = key(d), .SDcols = nms)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test-1-simple-display.R#13) 
  2. Error: find globals (@test-2-globals.R#10) 
  3. Error: (unknown) (@test-3-globals-by-hand.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Found the following apparent S3 methods exported but not registered:
  plot.trifield
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.trifield: no visible global function definition for ‘topo.colors’
plot.trifield: no visible global function definition for ‘plot’
plot.trifield: no visible global function definition for ‘image’
plot.trifield: no visible global function definition for ‘contour’
plot.trifield: no visible global function definition for ‘text’
ternary.legend: no visible global function definition for ‘arrows’
ternary.legend: no visible global function definition for ‘text’
triaxes: no visible global function definition for ‘lines’
tribox: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  arrows contour image lines plot polygon text topo.colors
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "arrows", "contour", "image", "lines", "plot",
             "polygon", "text")
to your NAMESPACE file.
Rd file 'plot.trifield.Rd':
  \usage lines wider than 90 characters:
     plot(x, contours = TRUE, col = topo.colors(256), lab1 = "A = 0", lab2 = "B = 0", lab3 = "C = 0", tribox = TRUE, axis.lines = TRUE, ...)

Rd file 'ternary.legend.Rd':
  \usage lines wider than 90 characters:
     ternary.legend(x0 = 0.2, y0 = 0.8, radius = 0.1, lab1 = "A", lab2 = "B", lab3 = "C", infl = 1.5, cex = 0.75, length = 0.05, ...)

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘fpc’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  plot.tkm print.tkm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.tkm: no visible global function definition for ‘plotcluster’
plot.tkm: no visible global function definition for ‘plot’
plot.tkm: no visible global function definition for ‘points’
plot.tkm: no visible global function definition for ‘lines’
plot.tkm: no visible global function definition for ‘discrcoord’
Undefined global functions or variables:
  discrcoord lines plot plotcluster points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
cinbag: no visible global function definition for ‘var’
trimTrees: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
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.
'library' or 'require' calls to packages already attached by Depends:
  ‘gtools’ ‘mgcv’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘gtools’ ‘mgcv’ ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for ‘odd’
HtoGp: no visible global function definition for ‘even’
plot.pirls.gam: no visible global function definition for ‘par’
plot.pirls.gam: no visible global function definition for ‘plot’
plot.pirls.gam: no visible global function definition for ‘title’
plot.pirls.gam: no visible global function definition for ‘lines’
plot.pirls.gam: no visible global function definition for ‘rug’
plot.pirls.gam: no visible global function definition for ‘mtext’
test.trioGxE: no visible global function definition for ‘write.table’
trioGxE: no visible global function definition for ‘quantile’
trioGxE: no visible global function definition for ‘qtnorm’
trioplot: no visible global function definition for ‘quantile’
trioplot: no visible global function definition for ‘formula’
trioplot: no visible global function definition for ‘gam’
trioplot: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
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.
Found the following apparent S3 methods exported but not registered:
  Ops.VectorAddr print.VectorAddr update.VectorAddr
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘TRSbook/libs/TRSbook.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.
DrawMargin: no visible global function definition for ‘qnorm’
DrawProbability: no visible global function definition for ‘pnorm’
Factor: no visible global function definition for ‘new’
Gaussian: no visible global function definition for ‘new’
LikelihoodFactor: no visible global function definition for ‘new’
Parameters: no visible global function definition for ‘new’
Player: no visible global function definition for ‘new’
PriorFactor: no visible global function definition for ‘new’
SumFactor: no visible global function definition for ‘new’
TruncateFactor: no visible global function definition for ‘new’
Variable: no visible global function definition for ‘new’
Vdraw: no visible global function definition for ‘dnorm’
Vdraw: no visible global function definition for ‘pnorm’
Vwin: no visible global function definition for ‘dnorm’
Vwin: no visible global function definition for ‘pnorm’
Wdraw: no visible global function definition for ‘dnorm’
Wdraw: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cdens: no visible global function definition for ‘head’
dplot: no visible global function definition for ‘knots’
dplot: no visible global function definition for ‘median’
dplot: no visible global function definition for ‘par’
dplot: no visible global function definition for ‘plot.stepfun’
dplot: no visible global function definition for ‘abline’
edf: no visible global function definition for ‘approxfun’
mctest : rdist: no visible global function definition for ‘runif’
mctest : S: no visible global function definition for ‘optim’
qplot: no visible global function definition for ‘plot’
qplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approxfun head knots median optim par plot plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
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.
Non-standard file/directory found at top level:
  ‘changes’
'library' or 'require' calls to packages already attached by Depends:
  ‘leaps’ ‘locfit’ ‘mgcv’
  Please remove these calls from your code.
':::' calls which should be '::':
  ‘stats:::ARMAacf’ ‘stats:::acf’ ‘stats:::arima’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  fitted.Arima plot.Arima plot.armasubsets predict.TAR rstandard.Arima
  summary.armasubsets tsdiag.Arima tsdiag.TAR
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘TSA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.Arima
> ### Title: Compute and Plot the Forecasts Based on a Fitted Time Series
> ###   Model
> ### Aliases: plot.Arima
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(oil.price)
> oil.IMA11alt=arima(log(oil.price),order=c(0,1,1),
+ # create the design matrix of the covariate for prediction
+ xreg=data.frame (constant=seq(oil.price)))
> n=length(oil.price)
> n.ahead=24
> newxreg=data.frame(constant=(n+1):(n+n.ahead))
> # do the prediction and plot the results
> plot(oil.IMA11alt,n.ahead=n.ahead,newxreg=newxreg,
+ ylab='Log(Oil Price)',xlab='Year',n1=c(2000,1))
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
dmvnb: no visible global function definition for ‘dbinom’
drvts: no visible global function definition for ‘dnorm’
drvts: no visible global function definition for ‘dbinom’
dsvts: no visible global function definition for ‘dnorm’
rescale: no visible global function definition for ‘qlogis’
rescale: no visible global function definition for ‘plogis’
tslogl: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dbinom dnorm plogis qlogis
Consider adding
  importFrom("stats", "dbinom", "dnorm", "plogis", "qlogis")
to your NAMESPACE file.
Found the following significant warnings:
  ./tsBSS.h:10:22: warning: 'varExx_k' has C-linkage specified, but returns user-defined type 'arma::mat' (aka 'Mat<double>') which is incompatible with C [-Wreturn-type-c-linkage]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tsBSS.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  print.tsbugs
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'ar.bugs.Rd':
  \examples lines wider than 100 characters:
     ar2 <- ar.bugs(y = diff(LH), ar.order = 2, ar.prior = "dunif(-1,1)", var.prior = "dgamma(0.001,0.001)")

Rd file 'rv.bugs.Rd':
  \usage lines wider than 90 characters:
                     rv.tol0.prior = "dgamma(0.000001,0.000001)", rv.eps.prior = "dbeta(1, 100)", 
  \examples lines wider than 100 characters:
       plot(NULL, type = "n", xlim = tsp(sigma.pn)[1:2], ylim = range(sigma.pn[, 1:95]), main = "sigma_t")

Rd file 'sv.bugs.Rd':
  \examples lines wider than 100 characters:
       plot(NULL, type = "n", xlim = tsp(sigma.pn)[1:2], ylim = range(sigma.pn[, 1:95]), main = "sigma_t")

These lines will be truncated in the PDF manual.
tfDetails: no visible global function definition for ‘start’
tfDetails: no visible global function definition for ‘end’
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for ‘pnorm’
plrt: no visible global function definition for ‘uniroot’
plrt: no visible global function definition for ‘optimize’
simulatedata: no visible global function definition for ‘rnorm’
tsc.test: no visible global function definition for ‘shapiro.test’
tsc.test: no visible global function definition for ‘p.adjust’
tsc.test: no visible global function definition for ‘glm’
tsc.test : f: no visible global function definition for ‘pnorm’
tsc.test: no visible global function definition for ‘uniroot’
tsc.test: no visible global function definition for ‘optimize’
variance: no visible global function definition for ‘density’
variance: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
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.
Running examples in ‘tsDyn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: selectHyperParms
> ### Title: Automatic selection of model hyper-parameters
> ### Aliases: selectLSTAR selectNNET
> ### Keywords: ts
> 
> ### ** Examples
> 
> llynx <- log10(lynx)
> selectLSTAR(llynx, m=2)
Error in if (!is.na(start.con$candidates)) { : 
  the condition has length > 1
Calls: selectLSTAR -> lstar
Execution halted
Package in Depends field not imported from: ‘deSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.ami plot.d2 plot.false.nearest print.d2 print.false.nearest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'sim.cont.Rd':
  \examples lines wider than 100 characters:
     rossler.ts <- sim.cont(rossler.syst, start=0, end=650, dt=0.1, start.x=c(0,0,0), parms=c(0.15, 0.2, 10))

These lines will be truncated in the PDF manual.
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.
vintageMap: no visible global function definition for ‘read.table’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘frequency’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘frequency’
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for ‘cov’
FAfitStats.TSFmodel: no visible global function definition for ‘cov’
FAfitStats.default: no visible global function definition for ‘cor’
FAfitStats.default: no visible global function definition for
  ‘factanal’
FAfitStats.default: no visible global function definition for ‘pchisq’
FAmodelFitStats: no visible global function definition for ‘pchisq’
checkResiduals.TSFmodel: no visible global function definition for
  ‘cov’
distribution.factorsEstEval: no visible global function definition for
  ‘par’
distribution.factorsEstEval: no visible binding for global variable
  ‘par’
distribution.factorsEstEval: no visible global function definition for
  ‘density’
distribution.factorsEstEval: no visible global function definition for
  ‘matplot’
distribution.factorsEstEval: no visible global function definition for
  ‘title’
summary.TSFmodel: no visible global function definition for ‘start’
summary.TSFmodel: no visible global function definition for ‘end’
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
Func.SAX: no visible global function definition for ‘sd’
Func.SAX: no visible global function definition for ‘qnorm’
Func.matrix: no visible global function definition for ‘qnorm’
Func.motif: no visible global function definition for ‘sd’
Func.motif: no visible global function definition for ‘na.omit’
Func.motif: no visible global function definition for ‘combn’
Func.motif.multivariate: no visible global function definition for
  ‘txtProgressBar’
Func.motif.multivariate: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
dLag : dlag.f: no visible global function definition for
  ‘complete.cases’
distmat: no visible global function definition for ‘dist’
fitCity: no visible global function definition for ‘glm.control’
fitCity: no visible global function definition for ‘terms’
ldmvnorm: no visible global function definition for ‘mahalanobis’
lspline: no visible global function definition for ‘quantile’
plot.tsdecomp: no visible global function definition for ‘par’
plot.tsdecomp: no visible global function definition for ‘plot’
setupFormula: no visible global function definition for ‘as.formula’
spatialgibbs: no visible global function definition for ‘rnorm’
spatialgibbs: no visible global function definition for ‘rgamma’
spatialgibbs: no visible global function definition for ‘runif’
tsdecomp: no visible global function definition for ‘fft’
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
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.
Running examples in ‘TSstudio-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EURO_Brent
> ### Title: Crude Oil Prices: Brent - Europe
> ### Aliases: EURO_Brent
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ts.plot_ly(EURO_Brent)
[1] "The ts.plot_ly function will be deprecated on the next release, please use ts_plot instead"
Error in `[.data.table`(dt, , c(.I, NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: <Anonymous> ... plotly_build.plotly -> lapply -> FUN -> group2NA -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: TTR
Version 0.4-0 included new data defaults. See ?getSymbols.
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.


WARNING: There have been significant changes to Yahoo Finance data.
Please see the Warning section of '?getSymbols.yahoo' for details.

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
Quitting from lines 37-64 (TSstudio_Intro.Rmd) 
Error: processing vignette ‘TSstudio_Intro.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
TT.GS : TT.GS.sp: no visible global function definition for ‘qt’
TT.GS : TT.GS.sp: no visible global function definition for ‘runif’
TT.GS : TT.GS.sp: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
ttScreening: no visible global function definition for ‘gaussian’
ttScreening: no visible global function definition for ‘glm.control’
ttScreening: no visible global function definition for ‘model.response’
ttScreening: no visible global function definition for ‘is.empty.model’
ttScreening: no visible global function definition for ‘model.matrix’
ttScreening: no visible global function definition for ‘na.omit’
ttScreening: no visible global function definition for ‘terms’
ttScreening: no visible global function definition for ‘capture.output’
ttScreening: no visible global function definition for ‘glm’
ttScreening: no visible binding for global variable ‘gaussian’
ttScreening: no visible global function definition for ‘pt’
ttScreening: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  capture.output gaussian glm glm.control is.empty.model model.matrix
  model.response na.omit p.adjust pt terms
Consider adding
  importFrom("stats", "gaussian", "glm", "glm.control", "is.empty.model",
             "model.matrix", "model.response", "na.omit", "p.adjust",
             "pt", "terms")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
.saveDevice: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
ttwa: no visible global function definition for ‘aggregate’
ttwa: no visible global function definition for ‘txtProgressBar’
ttwa: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Running examples in ‘tuckerR.mmgg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot
> ### Title: Plot an interactive Biplot
> ### Aliases: plot plot.marta
> 
> ### ** Examples
> 
> data(maize_pop,package = "tuckerR.mmgg")
> prueba1 <- tucker2R(maize_pop, amb=2, stand=TRUE, nc1=3, nc2=3)
> plot(prueba1)
Error in UseMethod("plot") : 
  no applicable method for 'plot' applied to an object of class "c('double', 'numeric')"
Calls: plot -> plot.marta -> plot
Execution halted
http.connection: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘gsl’ ‘igraph’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  predict.TuneParetoModel print.TuneParetoClassifier
  print.TuneParetoModel print.TuneParetoResult
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘TunePareto/libs/TunePareto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
turf: no visible global function definition for ‘read.table’
turf: no visible global function definition for ‘flush.console’
turf.combos: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
File ‘TUWmodel/libs/TUWmodel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
TwoCop: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
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.
Found the following apparent S3 methods exported but not registered:
  print.twoStageGwasPower print.twoStageNull
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
condnorm: no visible global function definition for ‘pnorm’
condnorm: no visible global function definition for ‘dnorm’
find.p.joint: no visible global function definition for ‘integrate’
find.p.joint.alt: no visible global function definition for ‘integrate’
termsInt: no visible global function definition for ‘pnorm’
termsInt.alt: no visible global function definition for ‘pnorm’
twoStageNull: no visible global function definition for ‘qnorm’
twoStageNull: no visible global function definition for ‘optimize’
twoStagePower: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm integrate optimize pnorm qnorm
Consider adding
  importFrom("stats", "dnorm", "integrate", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
Rd file 'twoStageGwasPower.Rd':
  \usage lines wider than 90 characters:
     twoStageGwasPower(pD, pG, grr, inheritance = "multiplicative", pi.samples, pi.markers, alpha.marker, n.cases, n.controls)

These lines will be truncated in the PDF manual.
txtacf: no visible binding for global variable ‘na.fail’
txtacf: no visible global function definition for ‘acf’
txtboxplot : <anonymous>: no visible global function definition for
  ‘boxplot.stats’
txtboxplot: no visible global function definition for ‘boxplot.stats’
txtdensity: no visible global function definition for ‘density’
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
Crm: no visible global function definition for ‘integrate’
Crm : <anonymous>: no visible global function definition for
  ‘integrate’
Crm: no visible global function definition for ‘optimize’
ail1: no visible global function definition for ‘uniroot’
ail2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ail2: no visible global function definition for ‘uniroot’
aip : fu : <anonymous>: no visible global function definition for
  ‘integrate’
aip: no visible global function definition for ‘uniroot’
ait1: no visible global function definition for ‘uniroot’
ait2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ait2: no visible global function definition for ‘uniroot’
sim3p3: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘palette’
simCrm: no visible global function definition for ‘gray’
simCrm: no visible global function definition for ‘plot’
simCrm: no visible global function definition for ‘abline’
simCrm: no visible global function definition for ‘lines’
ssim3p3: no visible global function definition for ‘txtProgressBar’
ssim3p3: no visible global function definition for ‘setTxtProgressBar’
ssimCrm: no visible global function definition for ‘txtProgressBar’
ssimCrm: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
rmd2pdf: no visible global function definition for ‘tail’
rnw2pdf: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
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.
Running examples in ‘udpipe-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.data.frame.udpipe_connlu
> ### Title: Convert the result of udpipe_annotate to a tidy data frame
> ### Aliases: as.data.frame.udpipe_connlu
> 
> ### ** Examples
> 
> x <- udpipe_download_model(language = "dutch-lassysmall")
Downloading udpipe model from https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.0/master/inst/udpipe-ud-2.0-170801/dutch-lassysmall-ud-2.0-170801.udpipe to /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/udpipe.Rcheck/dutch-lassysmall-ud-2.0-170801.udpipe
trying URL 'https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.0/master/inst/udpipe-ud-2.0-170801/dutch-lassysmall-ud-2.0-170801.udpipe'
Content type 'application/octet-stream' length 9208258 bytes (8.8 MB)
==================================================
downloaded 8.8 MB

> ud_dutch <- udpipe_load_model(x$file_model)
> txt <- c("Ik ben de weg kwijt, kunt u me zeggen waar de Lange Wapper ligt? Jazeker meneer", 
+          "Het gaat vooruit, het gaat verbazend goed vooruit")
> x <- udpipe_annotate(ud_dutch, x = txt)
> x <- as.data.frame(x)
Error in `[.data.table`(out, , `:=`(paragraph_id, cumsum(is_newparagraph)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: as.data.frame ... as.data.frame.udpipe_connlu -> read_connlu -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Downloading udpipe model from https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.0/master/inst/udpipe-ud-2.0-170801/dutch-ud-2.0-170801.udpipe to /home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/udpipe.Rcheck/vign_test/udpipe/vignettes/dutch-ud-2.0-170801.udpipe
trying URL ‘https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.0/master/inst/udpipe-ud-2.0-170801/dutch-ud-2.0-170801.udpipe’
Content type 'application/octet-stream' length 19992491 bytes (19.1 MB)
==================================================
downloaded 19.1 MB

Quitting from lines 93-99 (udpipe-annotation.Rmd) 
Error: processing vignette ‘udpipe-annotation.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
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.
Rd file 'dataItemExplorer.Rd':
  \usage lines wider than 90 characters:
       apiurl = "http://marketinformation.natgrid.co.uk/MIPIws-public/public/publicwebservice.asmx")

These lines will be truncated in the PDF manual.
ubRacing : predCandidate: no visible global function definition for
  ‘predict’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘pchisq’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘qt’
ubRacing : aux.friedman.edit: no visible global function definition for
  ‘wilcox.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘t.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘p.adjust’
ubRacing : idFolds: no visible global function definition for
  ‘quantile’
ubRacing: no visible binding for global variable ‘sd’
ubSmoteExs: no visible global function definition for ‘runif’
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for ‘quantile’
uh: no visible global function definition for ‘mad’
uh.bu: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.uniCox print.uniCoxCVFit print.uniCoxFit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
permute.rows: no visible global function definition for ‘runif’
uniCox: no visible global function definition for ‘quantile’
uniCoxCV: no visible global function definition for ‘quantile’
uniCoxCV: no visible global function definition for ‘coxph’
uniCoxCV: no visible binding for global variable ‘var’
Undefined global functions or variables:
  coxph quantile runif var
Consider adding
  importFrom("stats", "quantile", "runif", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'predict.uniCox':
  ‘predict.uniCox’

S3 methods shown with full name in documentation object 'uniCox-internal':
  ‘print.uniCoxCVFit’ ‘print.uniCoxFit’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘uniCox/libs/uniCox.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dudewicz.unif.test: no visible global function definition for ‘runif’
frosini.unif.test: no visible global function definition for ‘runif’
hegazy.unif.test: no visible global function definition for ‘runif’
kolmogorov.unif.test: no visible global function definition for ‘runif’
kuiper.unif.test: no visible global function definition for ‘runif’
neyman.unif.test: no visible global function definition for ‘runif’
quesenberry.unif.test: no visible global function definition for
  ‘runif’
sarkadi.unif.test: no visible global function definition for ‘runif’
sherman.unif.test: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cumcount: no visible global function definition for ‘setNames’
uniqtag: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
File ‘unsystation/libs/unsystation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 apparent S3 methods exported but not registered:
  plot.upclassfit print.upclassfit summary.upclassfit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.upclassfit: no visible global function definition for ‘frame’
plot.upclassfit: no visible global function definition for ‘par’
plot.upclassfit: no visible global function definition for ‘axis’
plot.upclassfit: no visible global function definition for ‘matplot’
plot.upclassfit: no visible global function definition for ‘legend’
plot.upclassfit: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis frame legend matplot par title
Consider adding
  importFrom("graphics", "axis", "frame", "legend", "matplot", "par",
             "title")
to your NAMESPACE file.
Running examples in ‘upclass-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.upclassfit
> ### Title: Plot for upclassfit
> ### Aliases: plot.upclassfit plot
> ### Keywords: Classification
> 
> ### ** Examples
> 
> data(wine, package = "gclus")
> X <- as.matrix(wine[, -1])
> cl <- unclass(wine[, 1])
> indtrain <- sort(sample(1:178, 120))
> indtest <- setdiff(1:178, indtrain)
> 
> fitup <- upclassify(X[indtrain,], cl[indtrain], X[indtest,], cl[indtest])
> plot(fitup)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
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.
Package suggested but not available for checking: ‘USAboundariesData’
readSEER: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000cdp/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000tract/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000tract\").\n")
    cat("Type help(package=\"UScensus2000tract\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
'library' or 'require' call to ‘rgdal’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'MSA.Rd':
  \usage lines wider than 90 characters:
     MSA(msafips = NULL, msaname = NULL, state=NULL , statefips=FALSE, level = c("tract", "blk", "blkgrp"), proj = NULL)

Rd file 'areaPoly.Rd':
  \examples lines wider than 100 characters:
     choropleth(oregon.county10,"den00",color = list(fun = "rainbow", attr = list(4)),main="2010 US Counties \n Oregon",type="plot",border=" ... [TRUNCATED]

Rd file 'choropleth.Rd':
  \usage lines wider than 90 characters:
     choropleth(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, 0.6, 0 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     choropleth(oregon.county10,"P0010001",color = list(fun = "rainbow", attr = list(4)),main="2010 Counties \n Oregon",type="plot",border=" ... [TRUNCATED]
     choropleth(oregon.county10,"P0010001",main="2010 Counties \n Oregon",border="transparent",type="spplot")

Rd file 'choropleth.plot.Rd':
  \usage lines wider than 90 characters:
     choropleth.plot(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, 0 ... [TRUNCATED]

Rd file 'choropleth.spplot.Rd':
  \usage lines wider than 90 characters:
     choropleth.spplot(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, ... [TRUNCATED]

Rd file 'county.Rd':
  \usage lines wider than 90 characters:
     county(fips = NULL, name = NULL, state, level = c("tract", "blk", "blkgrp"), statefips = FALSE, sp.object=NULL, proj=NULL)

These lines will be truncated in the PDF manual.
Running examples in ‘useful-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.kmeans
> ### Title: plot.kmeans
> ### Aliases: plot.kmeans
> 
> ### ** Examples
> 
> 
> k1 <- kmeans(x=iris[, 1:4], centers=3)
> plot(k1)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
File ‘utf8latex/libs/utf8latex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
histw: no visible global function definition for ‘plot.new’
histw: no visible global function definition for ‘plot.window’
histw: no visible global function definition for ‘axis’
histw: no visible global function definition for ‘rect’
histw: no visible global function definition for ‘lines’
uwham.boot: no visible binding for global variable ‘var’
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 92-93 (regress_intro.Rmd) 
Error: processing vignette ‘regress_intro.Rmd’ failed with diagnostics:
object ‘ttodth’ not found
Execution halted
Packages suggested but not available for checking: ‘vaers’ ‘vaersND’
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.
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.
Mammen: no visible global function definition for ‘runif’
PR2: no visible global function definition for ‘ar.burg’
PR2: no visible global function definition for ‘pt’
PR2: no visible global function definition for ‘pf’
PR3: no visible global function definition for ‘ar.burg’
PR3: no visible global function definition for ‘pt’
PR3: no visible global function definition for ‘pf’
VAR.FOR: no visible global function definition for ‘qnorm’
VAR.ForeB: no visible global function definition for ‘runif’
VAR.LRtest: no visible global function definition for ‘pchisq’
VAR.LRtest: no visible global function definition for ‘pf’
VAR.PI: no visible global function definition for ‘quantile’
VAR.Waldtest: no visible global function definition for ‘pf’
VAR.irf: no visible global function definition for ‘par’
VAR.irf: no visible global function definition for ‘plot’
VAR.irf: no visible global function definition for ‘abline’
VAR1.sim: no visible global function definition for ‘rnorm’
resamp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘Todo’
Packages in Depends field not imported from:
  ‘MASS’ ‘strucchange’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
black_scholes: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for ‘density’
burdenPlot: no visible global function definition for ‘axis’
burdenPlot: no visible global function definition for ‘points’
burdenPlot: no visible global function definition for ‘lines’
burdenPlot: no visible global function definition for ‘abline’
burdenPlot: no visible global function definition for ‘text’
burdenPlot: no visible global function definition for ‘sd’
burdenPlot: no visible global function definition for ‘segments’
vbdm: no visible global function definition for ‘var’
vbdm: no visible global function definition for ‘pchisq’
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for ‘var’
vbdmR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
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.
compute_KL : rtnorm: no visible global function definition for ‘runif’
compute_KL : rtnorm: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘qnorm’
compute_KL: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘pnorm’
compute_KL: no visible global function definition for ‘var’
compute_KL: no visible global function definition for ‘rbinom’
compute_KL: no visible global function definition for ‘rnorm’
compute_KL: no visible global function definition for ‘sd’
vbsr: no visible global function definition for ‘qchisq’
vbsr: no visible global function definition for ‘var’
vbsr: no visible global function definition for ‘pchisq’
vbsr: no visible global function definition for ‘sd’
vbsr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
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.
cv.vda.le.default: no visible global function definition for ‘predict’
cv.vda.r.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘VDA/libs/VDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Compare2FDS: no visible global function definition for ‘runif’
Compare2FDS: no visible global function definition for ‘lm’
Compare2FDS: no visible global function definition for ‘model.matrix’
Compare2FDS: no visible global function definition for ‘plot’
Compare2FDS: no visible global function definition for ‘abline’
Compare2FDS: no visible global function definition for ‘lines’
Compare2FDS: no visible global function definition for ‘text’
Compare2Vdg: no visible global function definition for ‘par’
Compare2Vdg: no visible global function definition for ‘plot’
Compare2Vdg: no visible global function definition for ‘lines’
Compare2Vdg: no visible global function definition for ‘legend’
FDSPlot: no visible global function definition for ‘runif’
FDSPlot: no visible global function definition for ‘lm’
FDSPlot: no visible global function definition for ‘model.matrix’
FDSPlot: no visible global function definition for ‘plot’
FDSPlot: no visible global function definition for ‘abline’
Vdgraph: no visible global function definition for ‘par’
Vdgraph: no visible global function definition for ‘plot’
Vdgraph: no visible global function definition for ‘lines’
Vdgraph: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
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.
calculateParameters,AffineTransformation: no visible global function
  definition for ‘lm’
calculateParameters,AffineTransformation: no visible global function
  definition for ‘coef’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘lm’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘coef’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘points’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘legend’
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘stats’ which was already attached by Depends.
  Please remove these calls from your code.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of ‘arg’ to
  ‘args’
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
prepare_Rd: H.Rd:41-42: Dropping empty section \note
prepare_Rd: M.homog.Rd:19-21: Dropping empty section \details
prepare_Rd: M.homog.Rd:35-36: Dropping empty section \note
prepare_Rd: Rel.homog.Rd:24-25: Dropping empty section \note
prepare_Rd: bootstrap.Rd:34: Dropping empty section \note
prepare_Rd: d.Rd:35-36: Dropping empty section \note
prepare_Rd: normalize.rows.Rd:26-27: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:23-24: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:26: Dropping empty section \examples
prepare_Rd: sim.groups.Rd:27-28: Dropping empty section \note
prepare_Rd: sim.table.Rd:25-26: Dropping empty section \note
prepare_Rd: similarity.Rd:25-26: Dropping empty section \note
prepare_Rd: turnover.Rd:17-18: Dropping empty section \details
prepare_Rd: turnover.Rd:29-30: Dropping empty section \note
plot.VennDiagram : <anonymous>: no visible global function definition
  for ‘hcl’
plot.VennDiagram: no visible global function definition for ‘plot.new’
plot.VennDiagram: no visible global function definition for
  ‘plot.window’
plot.VennDiagram: no visible global function definition for ‘col2rgb’
plot.VennDiagram: no visible global function definition for ‘rgb’
plot.VennDiagram: no visible global function definition for ‘polygon’
plot.VennDiagram: no visible global function definition for ‘text’
plot.VennDiagram: no visible global function definition for ‘title’
Undefined global functions or variables:
  col2rgb hcl plot.new plot.window polygon rgb text title
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rgb")
  importFrom("graphics", "plot.new", "plot.window", "polygon", "text",
             "title")
to your NAMESPACE file.
File ‘vertexenum/libs/vertexenum.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 ‘VideoComparison/libs/VideoComparison.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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.
vif: no visible global function definition for ‘sd’
vif: no visible global function definition for ‘lm’
vif: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
Rd file 'vif.Rd':
  \usage lines wider than 90 characters:
             vif(y, x, w0 = 0.05, dw = 0.05, subsize = 200, trace = TRUE, mode = c("dense", "sparse"))
  \examples lines wider than 100 characters:
             vif.sel <- vif(housingexp$y, housingexp$x, w0 = 0.0005, dw = 0.005, subsize = 300, trace = FALSE);

These lines will be truncated in the PDF manual.
hyperpara: no visible binding for global variable ‘var’
hyperpara: no visible global function definition for ‘hist’
Undefined global functions or variables:
  hist var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "var")
to your NAMESPACE file.
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.
Running examples in ‘VIM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hotdeck
> ### Title: Hot-Deck Imputation
> ### Aliases: hotdeck
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
> data(sleep)
> sleepI <- hotdeck(sleep)
> sleepI2 <- hotdeck(sleep,ord_var="BodyWgt",domain_var="Pred")
Error in `[.data.table`(x, , imputeHD(.SD, variableX = variable, varTypeX = varType,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: hotdeck ... hotdeck.data.frame -> hotdeck_work -> [ -> [.data.table
Execution halted
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.
panel.meansdplot : meansdplot.stats: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
prepare_Rd: panel.meansdplot.Rd:42-45: Dropping empty section \value
prepare_Rd: panel.meansdplot.Rd:49-51: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:40-42: Dropping empty section \details
prepare_Rd: panel.violinm.Rd:43-49: Dropping empty section \value
prepare_Rd: panel.violinm.Rd:53-55: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:50-52: Dropping empty section \author
prepare_Rd: violinmplot.Rd:34-36: Dropping empty section \details
prepare_Rd: violinmplot.Rd:48-50: Dropping empty section \note
Package in Depends field not imported from: ‘sm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
vioplot: no visible global function definition for ‘quantile’
vioplot: no visible global function definition for ‘median’
vioplot: no visible global function definition for ‘plot.new’
vioplot: no visible global function definition for ‘plot.window’
vioplot: no visible global function definition for ‘axis’
vioplot: no visible global function definition for ‘box’
vioplot: no visible global function definition for ‘polygon’
vioplot: no visible global function definition for ‘lines’
vioplot: no visible global function definition for ‘rect’
vioplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis box lines median plot.new plot.window points polygon quantile
  rect
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "points", "polygon", "rect")
  importFrom("stats", "median", "quantile")
to your NAMESPACE file.
viopoints.default: no visible global function definition for ‘par’
viopoints.default: no visible global function definition for ‘plot.new’
viopoints.default: no visible global function definition for
  ‘plot.window’
viopoints.default: no visible global function definition for ‘axis’
viopoints.default: no visible global function definition for ‘arrows’
viopoints.default: no visible global function definition for
  ‘getFromNamespace’
viopoints.default: no visible global function definition for ‘title’
viopoints.default: no visible global function definition for ‘box’
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 157-163 (using_visdat.Rmd) 
Error: processing vignette ‘using_visdat.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
          user system elapsed
ViSiElse 6.668  0.032   8.667
Running examples in ‘vistime-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vistime
> ### Title: vistime
> ### Aliases: vistime vistime-package vistime
> ### Keywords: gantt plotly timeline vistime
> 
> ### ** Examples
> 
> # presidents and vice presidents
> pres <- data.frame(Position=c(rep("President", 3), rep("Vice", 3)),
+                   Name = c("Washington", "Adams", "Jefferson", "Adams", "Jefferson", "Burr"),
+                   start = rep(c("1789-03-29", "1797-02-03", "1801-02-03"), 2),
+                   end = rep(c("1797-02-03", "1801-02-03", "1809-02-03"), 2),
+                   color = c('#cbb69d', '#603913', '#c69c6e'),
+                   rep(c("black", "white", "black"), 2))
> 
> vistime(pres, events="Position", groups="Name", title="Presidents of the USA",
+               lineInterval = 60*60*24*365*5)
Error in `[.data.table`(dt, , c(.I, NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: vistime ... plotly_build.plotly -> lapply -> FUN -> group2NA -> [ -> [.data.table
Execution halted
Running examples in ‘vitality-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vitality
> ### Title: Fitting routines for the Vitality family of mortality models.
> ### Aliases: vitality vitality-package
> 
> ### ** Examples
> 
> # vitality.k
> data(daphnia)
> time <- daphnia$days
> survival_fraction <- daphnia$lx
> 
> results.modk <- vitality.k(time = time,
+                            sdata = survival_fraction,
+                            rc.data=TRUE, 
+                            se=FALSE,
+                            gfit=FALSE, 
+                            datatype="CUM", 
+                            ttol=.000001, 
+                            init.params=FALSE, 
+                            lower=c(0,-1,0), upper=c(100,50,50), 
+                            pplot=TRUE, 
+                            tlab="days", 
+                            lplot=TRUE, 
+                            cplot=TRUE, 
+                            Iplot=TRUE, 
+                            silent=TRUE)
Error in if (rc.data != F) { : the condition has length > 1
Calls: vitality.k -> plotting.k
Execution halted
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.
Decile.Plot: no visible global function definition for ‘barplot’
Decile.Plot: no visible global function definition for ‘axis’
Sliding.Window: no visible global function definition for ‘plot’
Sliding.Window: no visible global function definition for ‘lines’
Sliding.Window: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
RCplot: no visible global function definition for ‘residuals’
RCplot: no visible global function definition for ‘predict’
RCplot: no visible global function definition for ‘par’
RCplot: no visible global function definition for ‘plot.new’
RCplot: no visible global function definition for ‘plot.window’
RCplot: no visible global function definition for ‘strwidth’
RCplot: no visible global function definition for ‘plot’
RCplot: no visible global function definition for ‘abline’
RCplot: no visible global function definition for ‘text’
RCplot: no visible global function definition for ‘mtext’
fitted.vlmc: no visible global function definition for ‘predict’
print.vlmc: no visible global function definition for ‘AIC’
residuals.vlmc: no visible global function definition for ‘predict’
simulate.vlmc: no visible global function definition for ‘runif’
summary.vlmc: no visible global function definition for ‘predict’
vlmc: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  AIC abline mtext par plot plot.new plot.window predict qchisq
  residuals runif strwidth text
Consider adding
  importFrom("graphics", "abline", "mtext", "par", "plot", "plot.new",
             "plot.window", "strwidth", "text")
  importFrom("stats", "AIC", "predict", "qchisq", "residuals", "runif")
to your NAMESPACE file.
File ‘VLMC/libs/VLMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘vortexR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Nadults
> ### Title: Calculate the harmonic mean of the total number of adults
> ### Aliases: Nadults
> 
> ### ** Examples
> 
> # Using Pacioni et al. example data. See ?pac.yr for more details.
> data(pac.yr)
> NadultAll <- Nadults(data=pac.yr[[2]], scenarios='all', gen=2.54, yr0=50,
+                      yrt=120, save2disk=FALSE)
Calculating the harmonic means of total number of individuals and number of adults from year 50 to year 117
NOTE: The last year used in the calculations is adjusted using the generation time provided (yrt - gen). See documentation for more information.
Error in `[.data.table`(slcensusMeans, , lapply(.SD, HarmMean), .SDcols = c("Nad",  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: Nadults -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 187-190 (vortexRguide.Rmd) 
Error: processing vignette ‘vortexRguide.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
voss1d: no visible global function definition for ‘approx’
voss1d: no visible global function definition for ‘rnorm’
voss1g: no visible global function definition for ‘dchisq’
voss1g: no visible global function definition for ‘approx’
voss1g: no visible global function definition for ‘rnorm’
voss2d: no visible global function definition for ‘rnorm’
voss2g: no visible global function definition for ‘dchisq’
voss2g: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘raster’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
level: no visible global function definition for ‘quantile’
obj.rec: no visible global function definition for ‘txtProgressBar’
obj.rec: no visible global function definition for ‘setTxtProgressBar’
project: no visible global function definition for ‘aggregate’
raster.proj: no visible global function definition for ‘quantile’
raster.proj: no visible global function definition for ‘rasterFromXYZ’
raster.proj: no visible global function definition for ‘plot.new’
raster.proj: no visible global function definition for ‘plot’
raster.proj: no visible global function definition for ‘legend’
sub.obj: no visible global function definition for ‘aggregate’
sub.obj: no visible global function definition for ‘txtProgressBar’
sub.obj: no visible global function definition for ‘setTxtProgressBar’
surface: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate legend plot plot.new quantile rasterFromXYZ
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "plot", "plot.new")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' call to ‘misc3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.vscc: no visible global function definition for ‘rainbow’
plot.vscc: no visible global function definition for ‘pairs’
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘vwr-Ex.R’
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’ ‘stringdist’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for ‘detectCores’
ald: no visible global function definition for ‘mclapply’
coltheart.N: no visible global function definition for ‘detectCores’
coltheart.N: no visible global function definition for ‘mclapply’
hamming.distance: no visible global function definition for
  ‘stringdist’
ldknn: no visible global function definition for ‘detectCores’
ldknn: no visible global function definition for ‘mclapply’
ldknn.odds: no visible global function definition for ‘glm’
ldknn.odds: no visible binding for global variable ‘binomial’
ldknn.odds: no visible global function definition for ‘coefficients’
levenshtein.damerau.distance: no visible global function definition for
  ‘stringdist’
levenshtein.distance: no visible global function definition for
  ‘stringdist’
plot.ldknn.run: no visible global function definition for ‘histogram’
plot.ldknn.run: no visible global function definition for
  ‘theEconomist.theme’
plot.ldknn.run: no visible global function definition for ‘xyplot’
plot.ldknn.run: no visible global function definition for ‘as.layer’
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'waffect-package.Rd':
  \examples lines wider than 100 characters:
     ## Not run: Typical usage to simulate case/control phenotypes under H1 (in this example: 5 individuals, 2 cases, 3 controls, the probab ... [TRUNCATED]
     ## Not run: Simulation of phenotypes in the multiclass case (in this example: 4 individuals and  3 classes, 1 individual in class 1, 2  ... [TRUNCATED]

Rd file 'waffect.Rd':
  \examples lines wider than 100 characters:
     ## Not run: Typical usage to simulate case/control phenotypes under H1 (in this example: 12 individuals, 7 cases, 5 controls, the proba ... [TRUNCATED]
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=c(7,5), label=c(1,0))
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=c(7,5), label=c(1,0))
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=7, label=c(1,0))
     ## Not run: If prob is not specified then a constant vector of probabilities is assumed by default. This is equivalent to simulate phen ... [TRUNCATED]

These lines will be truncated in the PDF manual.
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.
summary.whc: no visible global function definition for ‘printCoefmat’
wahc.fit: no visible global function definition for ‘pt’
wahc.fit: no visible global function definition for ‘cor’
whc: no visible global function definition for ‘model.frame’
whc: no visible global function definition for ‘model.matrix’
whc: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
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.
Rd file 'p.storage.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]
     d.meas.all<-read.table("weisseritz/ww100-rh.txt",header=TRUE, na.strings ="999", skip=4)  # gemessene Daten einlesen

Rd file 'read.results.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]

Rd file 'wasim-package.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]
     d.meas.all<-read.table("weisseritz/ww100-rh.txt",header=TRUE, na.strings ="999", skip=4)  # gemessene Daten einlesen

These lines will be truncated in the PDF manual.
Foreign function call to a different package:
  .C("comwr", ..., PACKAGE = "wavethresh")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.wvd summary.wvd
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'FWaveD.Rd':
  \usage lines wider than 90 characters:
     FWaveD(y, g = 1, L = 3, deg = 3, F = (log2(length(y)) - 1), thr = rep(0, log2(length(y))), SOFT = FALSE)

Rd file 'WaveD.Rd':
  \usage lines wider than 90 characters:
     WaveD(yobs, g = c(1, rep(0, (length(yobs) - 1))), MC = FALSE, SOFT = FALSE, F = find.j1(g, scale(yobs))[2], L = 3, deg = 3, eta = sqrt( ... [TRUNCATED]

Rd file 'multires.Rd':
  \usage lines wider than 90 characters:
     multires(wcUntrimmed, lowest = 3, coarse = 3, highestplot = NULL, descending = FALSE, sc = 1)

These lines will be truncated in the PDF manual.
Running examples in ‘waved-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.wvd
> ### Title: Plot wvd objects
> ### Aliases: plot.wvd
> ### Keywords: internal
> 
> ### ** Examples
> 
> library(waved)
> data=waved.example(TRUE,FALSE)
> doppler.wvd=WaveD(data$doppler.noisy,data$g)
> plot(doppler.wvd)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
Found the following apparent S3 methods exported but not registered:
  plot.dwt plot.dwt.multiple plot.modwt print.dwt print.modwt
  print.wt.filter summary.dwt summary.modwt summary.wt.filter
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
Found the following apparent S3 methods exported but not registered:
  plot.dwt.2d
See section ‘Registering S3 methods’ 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.
changepoints.sbs: no visible global function definition for ‘mad’
changepoints.wbs: no visible global function definition for ‘var’
changepoints.wbs: no visible global function definition for ‘quantile’
plot.sbs: no visible global function definition for ‘ts.plot’
plot.sbs: no visible global function definition for ‘lines’
plot.sbs: no visible global function definition for ‘title’
random.intervals: no visible global function definition for ‘runif’
sbs.default: no visible global function definition for ‘var’
wbs.default: no visible global function definition for ‘var’
Undefined global functions or variables:
  lines mad quantile runif title ts.plot var
Consider adding
  importFrom("graphics", "lines", "title")
  importFrom("stats", "mad", "quantile", "runif", "ts.plot", "var")
to your NAMESPACE file.
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.
Found the following apparent S3 methods exported but not registered:
  knots.WCE
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘WCE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: knots.WCE
> ### Title: Obtain the placement of the knots used for splines in WCE models
> ### Aliases: knots.WCE knots
> 
> ### ** Examples
> 
> 
> wce <- WCE(drugdata, "Cox", 1, 90, constrained = "R", id = "Id", event = "Event",
+ 		   start = "Start", stop = "Stop", expos = "dose", 
+ 		   covariates = c("age", "sex"))
> knots(wce)
Error in UseMethod("knots") : 
  no applicable method for 'knots' applied to an object of class "WCE"
Calls: knots
Execution halted
onesamplemeantest: no visible global function definition for ‘pnorm’
twosamplemeantest: no visible global function definition for ‘pnorm’
wcq: no visible global function definition for ‘var’
wcq: no visible global function definition for ‘pnorm’
wcq.fdrc: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
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.
Malformed Title field: should not end in a period.
Deprecated license: BSD
Non-standard file/directory found at top level:
  ‘webvis_0.0.1.tar.gz’
Found the following apparent S3 methods exported but not registered:
  +.webvis
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘webvis/R/zzz.R’:
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

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

[1] "Welcome to the webvis pacakge."
render.webvis: no visible global function definition for ‘browseURL’
unfold.webvis : <anonymous>: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  browseURL runif
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plot.webvis':
  ‘plot.webvis’

S3 methods shown with full name in documentation object '"+.webvis"':
  ‘+.webvis’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘webvis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pv.area
> ### Title: Add a bar to the visualization.
> ### Aliases: pv.area
> ### Keywords: hplot
> 
> ### ** Examples
> # line example 1 (using layers)
> wv <- pv.panel(width=150, height=150)
> render.webvis(wv + pv.area(wv=wv, data=c(1, 1.2, 1.7, 1.5, .7, .5, .2), bottom=0, height.name="y", left.name="x", height.scale="linear.y.y", left.scale="linear.x.x"))
Error in wv + pv.area(wv = wv, data = c(1, 1.2, 1.7, 1.5, 0.7, 0.5, 0.2),  : 
  non-numeric argument to binary operator
Calls: render.webvis
Execution halted
Weighted.Box.test: no visible global function definition for ‘acf’
Weighted.Box.test: no visible binding for global variable ‘na.pass’
Weighted.Box.test: no visible global function definition for ‘pgamma’
Weighted.Box.test: no visible global function definition for ‘pchisq’
Weighted.LM.test: no visible global function definition for ‘acf’
Weighted.LM.test: no visible binding for global variable ‘na.pass’
Weighted.LM.test: no visible global function definition for ‘pgamma’
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
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.
Package in Depends field not imported from: ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Z.value: no visible global function definition for ‘sd’
Z.value: no visible global function definition for ‘pnorm’
pairtest: no visible global function definition for ‘is’
pairtest: no visible global function definition for ‘new’
pairtest: no visible global function definition for ‘rbind2’
pairtest: no visible global function definition for ‘p.value’
pairtest: no visible global function definition for ‘single.snp.tests’
scoretest: no visible global function definition for ‘pchisq’
varplot : <anonymous>: no visible global function definition for ‘var’
varplot: no visible global function definition for ‘plot’
varplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline is new p.value pchisq plot pnorm rbind2 sd single.snp.tests
  var
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "is", "new", "rbind2")
  importFrom("stats", "pchisq", "pnorm", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: Matrix
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 488 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘wgsea.tex’ failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 252.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
'library' or 'require' call to ‘markdown’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested 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 ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
dlog.norm: no visible global function definition for ‘rnorm’
fun.load.hals.a: no visible global function definition for ‘sfExport’
fun.load.hals.a: no visible global function definition for ‘sfLibrary’
fun.load.hals.fill: no visible global function definition for
  ‘sfExport’
fun.load.hals.fill: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.a: no visible global function definition for ‘sfExport’
fun.load.widals.a: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.fill: no visible global function definition for
  ‘sfExport’
fun.load.widals.fill: no visible global function definition for
  ‘sfLibrary’
unif.mh: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif sfExport sfLibrary
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
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.
'library' or 'require' calls in package code:
  ‘genefilter’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for
  ‘packageDescription’
.relax.cvcompute: no visible binding for global variable
  ‘weighted.mean’
.relax.widenet.cv.elnet: no visible global function definition for
  ‘predict’
.relax.widenet.cv.elnet: no visible binding for global variable
  ‘weighted.mean’
.relax.widenet.cv.lognet: no visible global function definition for
  ‘predict’
.relax.widenet.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
.widenet.cv.elnet: no visible global function definition for ‘predict’
.widenet.cv.elnet: no visible binding for global variable
  ‘weighted.mean’
.widenet.cv.lognet: no visible global function definition for ‘predict’
.widenet.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
predict.widenet: no visible global function definition for ‘predict’
screen.cor : <anonymous>: no visible global function definition for
  ‘var’
screen.cor : <anonymous>: no visible global function definition for
  ‘cor.test’
screen.ttest: no visible global function definition for ‘colttests’
widenet: no visible global function definition for ‘mc.reset.stream’
widenet: no visible global function definition for ‘mclapply’
widenet: no visible global function definition for ‘predict’
Undefined global functions or variables:
  colttests cor.test mc.reset.stream mclapply packageDescription
  predict var weighted.mean
Consider adding
  importFrom("stats", "cor.test", "predict", "var", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
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.
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.

Found the following calls to data() loading into the global environment:
File ‘wikibooks/R/Bundesliga.Mannschaft.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.Tabelle.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.XML.R’:
  data(Bundesliga)
See section ‘Good practice’ in ‘?data’.
wilcox.selection.split: no visible global function definition for
  ‘pnorm’
wilcox.test2: no visible global function definition for ‘wilcox.test’
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Cs: no visible global function definition for ‘wilcox.test’
Don: no visible global function definition for ‘points’
Don: no visible global function definition for ‘chisq.test’
Lixn: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  chisq.test pchisq points wilcox.test
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "chisq.test", "pchisq", "wilcox.test")
to your NAMESPACE file.
plotTrait: no visible global function definition for ‘plot’
plotTrait: no visible global function definition for ‘points’
plotTrait: no visible global function definition for ‘legend’
test.windex: no visible global function definition for ‘hist’
test.windex: no visible global function definition for ‘abline’
test.windex: no visible global function definition for ‘legend’
windex: no visible global function definition for ‘sd’
windex: no visible global function definition for ‘var’
windex: no visible global function definition for ‘dist’
windex: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
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.
File ‘wle/libs/wle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘wle-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anova.wle.glm.root
> ### Title: Robust Analysis of Deviance for Generalized Linear Model Fits
> ### Aliases: anova.wle.glm.root anova.wleglmlist
> ### Keywords: robust models regression
> 
> ### ** Examples
> 
> ## --- Continuing the Example from  '?wle.glm':
> ## Don't show: 
> require(utils)
> example("wle.glm", echo = FALSE)
  treatment outcome counts
1         1       1     18
2         1       2     17
3         1       3     15
4         2       1     20
5         2       2     10
6         2       3     20
7         3       1     25
8         3       2     13
9         3       3     12
Warning in predict.lm(object, newdata, se.fit, scale = 1, type = ifelse(type ==  :
  calling predict.lm(<fake-lm-object>) ...
Error in if (class(object) != "wle.glm.root") stop("Use 'extractRoot(object)' to extract a single root from a wle.glm object") : 
  the condition has length > 1
Calls: example ... withVisible -> eval -> eval -> anova -> anova.wle.glm.root
Execution halted
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.
dbayes: no visible global function definition for ‘mahalanobis’
dbayes: no visible global function definition for ‘var’
wmd: no visible global function definition for ‘cor’
wmd: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for ‘lm’
plotfit,Leader: no visible global function definition for ‘par’
plotfit,Leader: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
'library' or 'require' call to ‘tm’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘wordcloud/libs/wordcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 in Depends field not imported from:
  ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for ‘llply’
wordmatch : <anonymous>: no visible global function definition for
  ‘llply’
wordmatch: no visible global function definition for ‘melt’
wordmatch: no visible global function definition for ‘count’
Undefined global functions or variables:
  count llply melt
pickList : <anonymous>: no visible global function definition for
  ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
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.
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.
simul.wsvm: no visible binding for global variable ‘mixture.example’
wsvm.boost: no visible global function definition for ‘plot’
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Rd file 'simul.wsvm.Rd':
  \usage lines wider than 90 characters:
         simul.wsvm(set.seeds = 123, obs.num = 1000, mu = c(0,0), cov.mat = 0.2*diag(2), X = NULL, Y = NULL)

Rd file 'wsvm.boost.Rd':
  \usage lines wider than 90 characters:
         wsvm.boost(X, Y, new.X, new.Y, c.n, B = 50, kernel.type = list(type = "rbf", par= 0.5), C = 4, eps = 1e-10, plotting = FALSE)

These lines will be truncated in the PDF manual.
Running examples in ‘wtest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: w.diagnosis
> ### Title: Plots for w values diagnosis
> ### Aliases: w.diagnosis
> 
> ### ** Examples
> 
> data(mydata)
> # Please note that parameter B is recommended to be greater than 400.
> hf1<-hf.calculation(data = mydata, w.order = 1, B = 100)
> hf2<-hf.calculation(data = mydata, w.order = 2, B = 50)
> w.diagnosis(mydata, w.order = 1, n.rep = 100, hf1 = hf1, main=NULL, xlab=NULL, ylab=NULL)
Error in if (hf1 == "default.hf1") { : the condition has length > 1
Calls: w.diagnosis
Execution halted
Running examples in ‘WVPlots-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotlyROC
> ### Title: Use 'plotly' to produce a ROC plot.
> ### Aliases: plotlyROC
> 
> ### ** Examples
> 
> 
> 
> d <- data.frame(x= 1:5, y= c(TRUE, FALSE , TRUE, TRUE, TRUE))
> plotlyROC(d, 'x', 'y', TRUE, 'example plot')
Error in `[.data.table`(dt, , c(.I, NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: <Anonymous> ... plotly_build.plotly -> lapply -> FUN -> group2NA -> [ -> [.data.table
Execution halted
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘CONTENTS’
Rd file 'classroom.Rd':
  \examples lines wider than 100 characters:
     {boxplot(classroom.first8$mathgain[classroom.first8$schoolid==i] ~ classroom.first8$classid[classroom.first8$schoolid==i],ylab="Mathgai ... [TRUNCATED]

These lines will be truncated in the PDF manual.
quadplot: no visible global function definition for ‘median’
xgobi: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
XHWE: no visible global function definition for ‘read.table’
result: no visible global function definition for ‘pchisq’
result: no visible global function definition for ‘rbinom’
result: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  +.CellStyle CellBlock.default CellStyle.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.xssfcolor: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
to your NAMESPACE file.
Running examples in ‘xlsx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CellBlock
> ### Title: Create and style a block of cells.
> ### Aliases: CellBlock CellBlock.default CB.setColData CB.setRowData
> ###   CB.setMatrixData CB.setFill CB.setFont CB.setBorder is.CellBlock
> 
> ### ** Examples
> 
> 
>   wb <- createWorkbook()
>   sheet  <- createSheet(wb, sheetName="CellBlock")
> 
>   cb <- CellBlock(sheet, 7, 3, 1000, 60)
Error in UseMethod("CellBlock") : 
  no applicable method for 'CellBlock' applied to an object of class "jobjRef"
Calls: CellBlock
Execution halted
R5.value.default: no visible binding for global variable ‘data.table’
R5.value.default: no visible global function definition for
  ‘as.data.table’
R5.value.parse: no visible binding for global variable ‘data.table’
R5.value.parse: no visible global function definition for
  ‘is.data.table’
R5.value.parse: no visible global function definition for
  ‘as.data.table’
stampme: no visible global function definition for ‘flush.console’
stampmsg: no visible global function definition for ‘flush.console’
write.data.table: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
File ‘xml2/libs/xml2.so’:
  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.
Non-standard files/directories found at top level:
  ‘Bug.R’ ‘Bugs.html’ ‘Check’ ‘CodeDetails’ ‘DESCRIPTION.in’ ‘Docs’
  ‘FAQ.html’ ‘FIXME_NOW’ ‘GNUmakefile’ ‘GNUmakefile.admin’
  ‘Makevars.in’ ‘MemoryBug.R’ ‘NAMESPACE.in’ ‘NodeFuns’ ‘Notes’
  ‘QuestionSolutions’ ‘README.windows’ ‘Rsamples’ ‘TAGS’
  ‘Todo-orig.html’ ‘Todo.xml’ ‘VersionInfo’ ‘addFinalizer’ ‘checkLinks’
  ‘dotCalls’ ‘expat’ ‘index.html’ ‘index.html.in’ ‘libxml’
  ‘libxml2.9.R’ ‘scrapingData.xml’ ‘testRemoveFinalizers.R’
  ‘testRemoveFinalizers.c’ ‘xpathPointer.xml’
newXMLDoc: no visible binding for global variable ‘doc’
source: no visible binding for global variable ‘use_file’
xmlFlatListTree : f: no visible binding for global variable ‘nodeNames’
xmlFlatListTree : f: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘parentCount’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘parentCount’
xmlFlatListTree : <anonymous>: no visible binding for global variable
  ‘e’
xmlFlatTree : <anonymous>: no visible binding for global variable ‘e’
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_file
Rd file 'makeClassTemplate.Rd':
  \examples lines wider than 100 characters:
     "<doc><part><name>ABC</name><type>XYZ</type><cost>3.54</cost><status>available</status></part></doc>"

Rd file 'xmlClone.Rd':
  \examples lines wider than 100 characters:
     xmlParse('<doc><author id="dtl"><firstname>Duncan</firstname><surname>Temple Lang</surname></author></doc>')

Rd file 'xmlToS4.Rd':
  \examples lines wider than 100 characters:
      "<doc><part><name>ABC</name><type>XYZ</type><cost>3.54</cost><status>available</status></part></doc>"

These lines will be truncated in the PDF manual.
File ‘XML/libs/XML.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘DocParse.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.
LPGM: no visible global function definition for ‘flush.console’
PGM: no visible global function definition for ‘flush.console’
PGM.path.neighborhood: no visible global function definition for
  ‘runif’
PGMSim: no visible global function definition for ‘rpois’
PGMSim: no visible global function definition for ‘par’
WPGMSim: no visible global function definition for ‘rpois’
XMRF.Sim: no visible global function definition for ‘cov2cor’
XMRF.Sim: no visible global function definition for ‘rbinom’
XMRF.Sim: no visible global function definition for ‘rnorm’
glm.generic: no visible global function definition for ‘flush.console’
mymult: no visible global function definition for ‘rmultinom’
plot.GMS: no visible global function definition for ‘pdf’
plot.GMS: no visible global function definition for ‘dev.off’
plotNet: no visible global function definition for ‘pdf’
plotNet: no visible global function definition for ‘dev.off’
print.GMS: no visible global function definition for ‘str’
processSeq: no visible binding for global variable ‘quantile’
processSeq: no visible binding for global variable ‘var’
processSeq: no visible global function definition for ‘ks.test’
rmpois : <anonymous>: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
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.
Non-standard file/directory found at top level:
  ‘CONTRIBUTORS’
Found the following apparent S3 methods exported but not registered:
  plot.cca print.F.test.cca print.cca print.summary.cca summary.cca
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
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.
big.read.table: no visible global function definition for ‘read.table’
big.read.table: no visible global function definition for ‘object.size’
sparkline: no visible global function definition for ‘is.ts’
sparkline: no visible global function definition for ‘time’
sparkline: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
bootstrapswapcurve: no visible global function definition for ‘ts’
fitted: no visible global function definition for ‘ts’
forwardrates: no visible global function definition for ‘ts’
residuals: no visible global function definition for ‘ts’
tZC_NS: no visible global function definition for ‘cmpfun’
tZC_NS_extra: no visible global function definition for ‘cmpfun’
tZC_SV: no visible global function definition for ‘cmpfun’
tZC_SV_extra: no visible global function definition for ‘cmpfun’
ycextra: no visible global function definition for ‘new’
ycinter: no visible global function definition for ‘new’
ycplot: no visible global function definition for ‘par’
ycplot: no visible global function definition for ‘points’
ycplot: no visible global function definition for ‘abline’
ycplot: no visible global function definition for ‘hist’
ycplot: no visible global function definition for ‘lines’
ycplot: no visible global function definition for ‘density’
ycplot: no visible global function definition for ‘qqnorm’
ycplot: no visible global function definition for ‘qqline’
ycsummary: no visible global function definition for ‘shapiro.test’
ycsummary: no visible global function definition for ‘pf’
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘yCrypticRNAs/libs/yCrypticRNAs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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 ‘yCrypticRNAs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bam_to_reads
> ### Title: Convert BAM files into BED files containing the reads overlaping
> ###   the specified annotations.
> ### Aliases: bam_to_reads
> 
> ### ** Examples
> 
> bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
> data(annotations)
> bam_to_reads(bamfile, annotations)
Error in FUN(X[[i]], ...) : failed to build index
  file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Calls: bam_to_reads -> .index_bam
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-60 (yCrypticRNAs.Rmd) 
Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
failed to build index
  file: /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Execution halted
.NS.estimator: no visible global function definition for ‘lm’
.NS.estimator: no visible global function definition for ‘coef’
.NS.estimator: no visible global function definition for ‘na.omit’
.NS.estimator: no visible global function definition for ‘resid’
.NSS.estimator: no visible global function definition for ‘lm’
.NSS.estimator: no visible global function definition for ‘coef’
.NSS.estimator: no visible global function definition for ‘na.omit’
.NSS.estimator: no visible global function definition for ‘resid’
NSrates: no visible global function definition for ‘time’
Nelson.Siegel: no visible global function definition for ‘optimize’
Srates: no visible global function definition for ‘time’
Svensson: no visible global function definition for ‘median’
Svensson: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
Rd file 'ECBYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat.ECB, ECBYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

Rd file 'FedYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat, FedYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

These lines will be truncated in the PDF manual.
kmeansN: no visible global function definition for ‘kmeans’
kmeansN: no visible global function definition for ‘aggregate’
kmeansN2: no visible global function definition for ‘aggregate’
kmeansN2: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
Deprecated license: CC BY-SA 2.0 + file LICENSE
Package suggested but not available for checking: ‘zdat’
Found the following apparent S3 methods exported but not registered:
  cbind.zoocat
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'merge':
  ‘cbind.zoocat’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: reshape2

Attaching package: 'zoocat'

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

    cor

Quitting from lines 69-74 (my-vignette.Rmd) 
Error: processing vignette ‘my-vignette.Rmd’ failed with diagnostics:
no applicable method for ‘cattr’ applied to an object of class "zoo"
Execution halted
.getPath: no visible global function definition for ‘predict’
ZIClass: no visible binding for global variable ‘na.omit’
ZIClass: no visible global function definition for ‘predict’
analyzeClass: no visible global function definition for ‘plot’
calibrate : findmax: no visible global function definition for ‘lowess’
calibrate: no visible global function definition for ‘lm’
calibrate: no visible global function definition for ‘anova’
calibrate: no visible global function definition for ‘coef’
focusGraph: no visible global function definition for ‘dev.list’
getTrain: no visible global function definition for ‘na.omit’
makeClass : selectVars: no visible global function definition for
  ‘as.formula’
predict.ZIClass: no visible global function definition for ‘predict’
processSampleAll: no visible global function definition for ‘predict’
viewResults: no visible global function definition for ‘par’
viewResults: no visible global function definition for ‘plot’
viewResults: no visible global function definition for ‘points’
viewResults: no visible global function definition for ‘text’
zidbDrawVignette: no visible global function definition for ‘dev.size’
zidbDrawVignette: no visible global function definition for ‘par’
zidbDrawVignette: no visible global function definition for ‘dev.cur’
zidbDrawVignette: no visible global function definition for
  ‘rasterImage’
zidbPlotNew: no visible global function definition for ‘par’
zidbPlotNew: no visible global function definition for ‘plot’
Undefined global functions or variables:
  anova as.formula coef dev.cur dev.list dev.size lm lowess na.omit par
  plot points predict rasterImage text
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "dev.size")
  importFrom("graphics", "par", "plot", "points", "rasterImage", "text")
  importFrom("stats", "anova", "as.formula", "coef", "lm", "lowess",
             "na.omit", "predict")
to your NAMESPACE file.
File which contains pragma(s) suppressing diagnostics:
  ‘src/third_party/zstd-1.2.0/lib/dictBuilder/divsufsort.c’
Found the following apparent S3 methods exported but not registered:
  confint.zyp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
confint.zyp: no visible global function definition for ‘qnorm’
confint.zyp: no visible global function definition for ‘var’
zyp.sen: no visible global function definition for ‘terms’
zyp.sen: no visible global function definition for ‘median’
zyp.trend.csv: no visible global function definition for ‘read.csv’
zyp.trend.csv: no visible global function definition for ‘write.csv’
zyp.yuepilon: no visible global function definition for ‘acf’
zyp.yuepilon: no visible binding for global variable ‘na.pass’
zyp.yuepilon: no visible global function definition for ‘confint’
zyp.yuepilon: no visible global function definition for ‘lm’
zyp.zhang: no visible global function definition for ‘acf’
zyp.zhang: no visible binding for global variable ‘na.pass’
zyp.zhang: no visible global function definition for ‘confint’
zyp.zhang: no visible global function definition for ‘lm’
Undefined global functions or variables:
  acf confint lm median na.pass qnorm read.csv terms var write.csv
Consider adding
  importFrom("stats", "acf", "confint", "lm", "median", "na.pass",
             "qnorm", "terms", "var")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 78-85 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
subscript out of bounds
Execution halted
Found the following significant warnings:
  ADM3.c:37:12: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:37:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:54:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ADM3.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘amap.tex’ failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte 244.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Argument of \UTFviii@three@octets has an extra }.
<inserted text> 
                \par 
l.12 ...block {\em Revue de Statistique Appliqu<e9>e}
                                                  , 50(4), 2002.
! Paragraph ended before \UTFviii@three@octets was complete.
<to be read again> 
                   \par 
l.12 ...block
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  em.cpp:208:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Amelia.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/scratch/RtmpfCjpdi/RLIBS_19241d02fb87/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
  WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
  WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/scratch/RtmpfCjpdi/RLIBS_1924330885c1/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ANLP.Rcheck/00install.out’ for details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #Copyright © 2016 RTE Réseau de transport d’électricité
  > 
  > require(testthat)
  Loading required package: testthat
  > require(antaresRead)
  Loading required package: antaresRead
  > require(plyr)
  Loading required package: plyr
  > 
  > 
  > #Maybe include this in some test-file.R 
  > #is.solaris<-function(){
  > #  grepl('SunOS',Sys.info()['sysname'])
  > #}
  > 
  > #if(!is.solaris()){
  > 
  > test_check("antaresRead")
  Error in `[.data.table`(x, , mapply(function(x, f) { : 
    SETLENGTH() cannot be applied to an ALTVEC object.
  Calls: test_check ... eval -> eval -> suppressMessages -> withCallingHandlers
  Execution halted
Running examples in ‘ApacheLogProcessor-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read.multiple.apache.access.log
> ### Title: Reads multiple files of apache web server.
> ### Aliases: read.multiple.apache.access.log
> 
> ### ** Examples
> 
> path <- system.file("examples", package="ApacheLogProcessor")
> path <- paste(path, "/", sep="")
> 
> #read multiple gziped logs with the prefix m_access_log_combined_
> dfLog <- read.multiple.apache.access.log(path, "m_access_log_combined_")
[1] "Starting the log processing. This may take a long time..."
[1] "Processing file  m_access_log_combined_1.log.gz"
[1] "Unziping  m_access_log_combined_1.log.gz"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/ApacheLogProcessor/examples/m_access_log_combined_1.log': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: read.multiple.apache.access.log -> write -> cat -> file
Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  pa.c:247:2: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Running examples in ‘batchtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Tags
> ### Title: Add or Remove Job Tags
> ### Aliases: Tags addJobTags removeJobTags getUsedJobTags
> 
> ### ** Examples
> 
> tmp = makeRegistry(file.dir = NA, make.default = FALSE)
No configuration file found
Created registry in '/home/hornik/tmp/scratch/RtmpZuWK81/registry7d14a0bd9e8' using cluster functions 'Interactive'
> ids = batchMap(sqrt, x = -3:3, reg = tmp)
Adding 7 jobs ...
> 
> # Add new tag to all ids
> addJobTags(ids, "needs.computation", reg = tmp)
> getJobTags(reg = tmp)
   job.id              tags
1:      1 needs.computation
2:      2 needs.computation
3:      3 needs.computation
4:      4 needs.computation
5:      5 needs.computation
6:      6 needs.computation
7:      7 needs.computation
> 
> # Add more tags
> addJobTags(findJobs(x < 0, reg = tmp), "x.neg", reg = tmp)
> addJobTags(findJobs(x > 0, reg = tmp), "x.pos", reg = tmp)
> getJobTags(reg = tmp)
Error in `[.data.table`(reg$tags[ids, on = "job.id"], , list(tags = stri_flatten(sort(tag,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: getJobTags -> [ -> [.data.table
Execution halted
Running examples in ‘bayesQR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.bayesQR
> ### Title: Summarize the output of the 'bayesQR' function
> ### Aliases: summary.bayesQR
> 
> ### ** Examples
> 
> # Load the Prostate cancer dataset
> data(Churn)
> 
> # Estimate the model parameters with default prior
> out <- bayesQR(churn~gender+recency, data=Churn, ndraw=5000)
Current iteration :
[1] 500
Current iteration :
[1] 1000
Current iteration :
[1] 1500
Killed
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Loading required package: leaps
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘SimExperimentBICq.tex’ failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 150.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  newmat5.cpp:494:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bfp.Rcheck/00install.out’ for details.
Running examples in ‘biclique-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bi.format
> ### Title: Add number of vertices and edges to the input file
> ### Aliases: bi.format
> 
> ### ** Examples
> 
> bi.format(system.file("extdata", "example2.el", package = "biclique"))
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/biclique/extdata/example2.el': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: bi.format -> cat -> file
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/biclust.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [3s/33s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(biolink)
  > 
  > test_check("biolink")
  ── 1. Error: Reference CRAN Package URL is valid (@test-links-cran.r#7)  ───────
  Timeout was reached: Operation timed out after 10001 milliseconds with 0 out of 0 bytes received
  1: expect_equal(check_url_status(url), 200) at testthat/test-links-cran.r:7
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: check_url_status(url)
  5: httr::GET(url) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/biolink.Rcheck/tests/testthat/helper-functions.r:4
  6: request_perform(req, hu$handle$handle)
  7: request_fetch(req$output, req$url, handle)
  8: request_fetch.write_memory(req$output, req$url, handle)
  9: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 119 SKIPPED: 1 FAILED: 1
  1. Error: Reference CRAN Package URL is valid (@test-links-cran.r#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette ‘brms_overview.ltx’ failed with diagnostics:
Running ‘texi2dvi’ on ‘brms_overview.ltx’ failed.
LaTeX errors:
! Undefined control sequence.
\UseRawInputEncoding ...tencodingname \@undefined 
                                                  \let \DeclareFontEncoding@...
l.59 \begin{document}
                     
! Missing \endcsname inserted.
<to be read again> 
                   \protect 
l.59 \begin{document}
                     
! Missing \endcsname inserted.
<to be read again> 
                   \cdp@elt 
l.59 \begin{document}
                     
! Missing \endcsname inserted.
<to be read again> 
                   \cdp@elt 
l.59 \begin{document}
                     
! Extra \else.
\@changed@cmd ... #1\expandafter \endcsname \else 
                                                  \noexpand #1\fi 
l.59 \begin{document}
                     
! Missing \endcsname inserted.
<to be read again> 
                   \def 
l.59 \begin{document}
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/bsts.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Quitting from lines 1199-1209 (cjamp.Rmd) 
Error: processing vignette ‘cjamp.Rmd’ failed with diagnostics:
Complete cases matrix of predictors_Y1 doesn't have full rank.
Execution halted
Found the following significant warnings:
  exact.cpp:10:9: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  exact.cpp:125:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  exact.cpp:174:10: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  exact.cpp:204:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/clusrank.Rcheck/00install.out’ for details.
Found the following significant warnings:
  principal_balances.cpp:114:32: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  sbp.cpp:627:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  sbp.cpp:627:50: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  sbp.cpp:649:22: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/coda.base.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/23s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(codemetar)
  > 
  > test_check("codemetar")
  ── 1. Failure: we can call crosswalk (@test-crosswalk.R#12)  ───────────────────
  `v` isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 13 FAILED: 1
  1. Failure: we can call crosswalk (@test-crosswalk.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  date.cpp:173:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ConvCalendar.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bdsmatrix_stub.h:41:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:44:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:50:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:53:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:97:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:100:12: warning: return from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/coxme.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cplm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘CREAM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CREAM
> ### Title: CREAM is the main function for CORE identification
> ### Aliases: CREAM
> 
> ### ** Examples
> 
> CREAM(system.file("extdata", "A549_Chr21.bed", package = "CREAM"),
+ system.file("extdata", "A549_Chr21_COREs.bed", package = "CREAM"),
+ MinLength = 1000, peakNumMin = 2)
[1] "Please make sure there is no overlap between the input genomic regions. Overlap between the input regions may cause error."
[1] "Identifying window size for each Order"
[1] "Identifying COREs"
[1] "Filtering clusters of low order"
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/CREAM/extdata/A549_Chr21_COREs.bed': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: CREAM -> write.table -> file
Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
              user system elapsed
text_win_rqa 6.845  0.008  10.432
Found the following significant warnings:
  instabCorrection.cpp:34:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cstab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ctsem.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DatABEL.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
      user system elapsed
sdp  6.934  0.018   8.678
rgrs 3.177  0.020   5.128
Error in re-building vignettes:
  ...
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

Joining, by = "gene"
Joining, by = "cell"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Have 35 cells after filtering
Joining, by = "cell"
Have 20 genes after filtering
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "gene"
Joining, by = "cell"
Joining, by = c("cell", "capture")
Compiling model
the number of chains is less than 1; sampling not done
Saving compiled model to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/DeLorean/extdata/exact-sizes.rds
Quitting from lines 145-146 (DeLorean.Rmd) 
Error: processing vignette ‘DeLorean.Rmd’ failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=36.094994,-111.837962&zoom=12&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=24.2,-77.88&zoom=11&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=37.89,-122.28&zoom=11&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=37.81391,-122.478289&zoom=19&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=-33.857077,151.214722&zoom=17&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false
Loading required package: ggplot2
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=24.2,-77.88&zoom=11&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false
Quitting from lines 74-84 (earthtones.rmd) 
Error: processing vignette ‘earthtones.rmd’ failed with diagnostics:
cannot open URL ‘http://maps.googleapis.com/maps/api/staticmap?center=48.7709,-64.660939&zoom=9&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false’
Execution halted
Running examples in ‘EasyStrata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EasyStrata
> ### Title: Function to run EasyStrata (v8.6).
> ### Aliases: EasyStrata
> 
> ### ** Examples
> 
> extDataDir=system.file("extdata", package="EasyStrata")
> ## Example Pipeline:
> ecfPipe=paste(extDataDir,"example_pipeline.ecf",sep="/")
> EasyStrata(ecfPipe)
Warning message:
In file(fileLog, open = "a") :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/EasyStrata/extdata/example_pipeline.ecf.out': Read-only file system
Execution halted
Found the following significant warnings:
  oregMclust.cc:227:25: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  oregMclust.cc:531:31: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  oregMclust.cc:532:22: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/edci.Rcheck/00install.out’ for details.
Found the following significant warnings:
  newmat5.cpp:494:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EditImputeCont.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [10s/16s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  ── 1. Error: Zed (@test-calculators.R#169)  ────────────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: moves_calc(df) at testthat/test-calculators.R:169
  2: dt[, `:=`(moves, school_switch(.SD)), by = sid]
  3: `[.data.table`(dt, , `:=`(moves, school_switch(.SD)), by = sid)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 503 SKIPPED: 0 FAILED: 1
  1. Error: Zed (@test-calculators.R#169) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘elrm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.elrm
> ### Title: Plot Diagnostics for an elrm Object
> ### Aliases: plot.elrm
> ### Keywords: methods
> 
> ### ** Examples
> 
> # Drug dataset example with sex and treatment as the variables of interest
> data(drugDat);
> drug.elrm = elrm(formula=recovered/n~sex+treatment, interest=~sex+treatment, r=4, 
+ 	iter=50000, burnIn=1000, dataset=drugDat);
Generating the Markov chain ...
Progress:   0%  Progress:   5%  Progress:  10%  Progress:  15%  Progress:  20%  Progress:  25%  Progress:  30%  Progress:  35%  Progress:  40%  Progress:  45%  Progress:  50%  Progress:  55%  Progress:  60%  Progress:  65%  Progress:  70%  Progress:  75%  Progress:  80%  Progress:  85%  Progress:  90%  Progress:  95%  Progress: 100%  
Generation of the Markov Chain required 5 secs
Conducting inference ...
Inference required 2 secs
> 
> # Plot the sampled values of the sufficient statistic for each parameter of 
> # interest (sex and treatment)
> plot(drug.elrm,p=0.5,ask=TRUE);
Error in plot.default(drug.elrm, p = 0.5, ask = TRUE) : 
  argument 2 matches multiple formal arguments
Calls: plot
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eurostat)
  > 
  > test_check("eurostat")
  trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ftsdtr210.tsv.gz'
  downloaded 17 KB
  
  ── 1. Error: (unknown) (@test-all.R#112)  ──────────────────────────────────────
  tsdtr210 does not exist or is not readable
  1: get_eurostat("tsdtr210", type = "label", keepFlags = T, cache = FALSE) at testthat/test-all.R:112
  2: get_eurostat_raw(id)
  3: stop(id, " does not exist or is not readable")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 14 FAILED: 1
  1. Error: (unknown) (@test-all.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/eVenn.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘eVenn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: eVenn-package
> ### Title: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
> ###   Diagrams
> ### Aliases: eVenn-package eVenn
> ### Keywords: package
> 
> ### ** Examples
> 
> library(eVenn)
> YNdisplay = TRUE	# Allows commentaries and display of the main steps of the process
> 
> #	Matrix of binary data
>    data(Data_Binary_Matrix)
>    evenn(matLists=Data_Binary_Matrix, display=YNdisplay, CompName="Binary_Matrix")
        ,.-.,                                                                          
      .`     `.                                                                        
     /.-., ,.-.`            *       *                                 ****         *   
   .`    .`.    `.     ***   *     *   ***    ****   ****    *     * *    *      * *   
  / `.  /   `.  / `  *     *  *   *  *     * *    * *    *    *   *      *      *  *   
 |    ',_____,'    | ******   *   *  ******  *    * *    *     * *      *      *   *   
 `.     `   /     /  *         * *   *       *    * *    *     * *    *       *******  
   ',    '_'    ,'    *****     *     *****  *    * *    *      *    ****** *      *   
     `'-'` `'-'`                                                                       
Default results path is: 
	/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/eVenn.Rcheck/Venn.diagrams/
The results will be placed here: 
	/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/eVenn.Rcheck/Venn.diagrams//Venn_Binary_Matrix
     => Source = binary matrix
Error in if ((noms != "") & (length(noms) != nListe)) { : 
  the condition has length > 1
Calls: evenn
Execution halted
Found the following significant warnings:
  optile.c:3122:26: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3127:26: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3189:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3192:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3340:28: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3353:28: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3408:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3411:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/extracat.Rcheck/00install.out’ for details.
Running examples in ‘extRemes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ci.fevd
> ### Title: Confidence Intervals
> ### Aliases: ci.fevd ci.fevd.bayesian ci.fevd.lmoments ci.fevd.mle
> ### Keywords: htest distribution
> 
> ### ** Examples
> 
> 
> data(Fort)
> 
> fit <- fevd(Prec, Fort, threshold = 2, type = "GP",
+     units = "inches", verbose = TRUE)

 Data span  99.99452 years 
Setting up parameter model design matrices.
Parameter model design matrices set up.
Initial estimates found where necessary (not from Lmoments).  Initial value = 23.55314 
Initial estimates are:
     scale      shape 
0.70463329 0.00000001 
Beginning estimation procedure.
initial  value 23.553137 
final  value 23.553137 
converged
Time difference of 0.1157174 secs
> 
> ci(fit, type = "parameter")
Error in UseMethod("ci", x) : 
  no applicable method for 'ci' applied to an object of class "fevd.mle"
Calls: ci -> ci.fevd
Execution halted
Found the following significant warnings:
  FastRCS.cpp:152:9: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastRCS.Rcheck/00install.out’ for details.
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 ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
     user system elapsed
fcr 7.547  0.062  11.191
Running ‘testthat.R’ [7s/89s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FedData)
  Loading required package: sp
  > 
  > test_check("FedData")
  ── 1. Failure: The NHD Subregion boundaries dataset is availableat the correct U
  suppressWarnings(httr::http_error(url)) isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 26 SKIPPED: 0 FAILED: 1
  1. Failure: The NHD Subregion boundaries dataset is availableat the correct URL (@test.NHD.R#7) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In inherits(x, "factor") :
    closing unused connection 4 (ftp://ftp.ncdc.noaa.gov/pub/data/paleo/treering/chronologies/)
  Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/frailtyHL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘funcy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: funcyOutList-class
> ### Title: Class '"funcyOutList"'
> ### Aliases: funcyOutList-class funcyOutList
> ### Keywords: classes
> 
> ### ** Examples
> 
> set.seed(2808)
> ds <- sampleFuncy(obsNr=30, k=4, timeNr=7)
> data <- Data(ds)
> clusters <- Cluster(ds)
> 
> res <- funcit(data=data, clusters=clusters, seed=2808,
+               methods=1:5, k=4, parallel=TRUE)
4 : * *4 :Warning in funclustWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  It is not possible to set a seed for method funclust.
 * *
 *Loading required namespace: funHDDC
 *Warning in Funclustering::funclust(fd = fd, K = k, thd = thd, increaseDimension = increaseDimension,  :
  Convergence of the algorithm to a solution with at least one empty cluster.
            Restart or a choose a smaller value for K = 4
Warning in funHDDCWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  Clustering with 4 classes is not possible. 3 clusters are used!

Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 3 classes is not possible. 2 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 2 classes is not possible. 1 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 1 classes is not possible. 0 clusters are used!
Error in funcit(data = data, clusters = clusters, seed = 2808, methods = 1:5,  : 
  Method funHDDC : Clustering for this data not possible.
Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
      user system elapsed
fpca 5.885  0.024   9.141
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fuzzr)
  > 
  > test_check("fuzzr")
  ── 1. Failure: Multi-class returns can be handled appropriately (@test_fuzz.R#14
  fdf\[fdf\$x == "char_multiple", \]\$warnings does not match "condition has length > 1".
  Actual value: "warn 1; warn 2"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 74 SKIPPED: 0 FAILED: 1
  1. Failure: Multi-class returns can be handled appropriately (@test_fuzz.R#147) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:

  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
        user system elapsed
hockey 4.725  0.054   6.441
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GenABEL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(genomic.autocorr)
  > 
  > test_check("genomic.autocorr")
  ── 1. Error: /home/hornik/tmp/scratch/RtmpcxQOgX/R.INSTALL7a582b110b7b/genomic.a
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: block.glm(f.lhs = c("y0", "y1"), f.rhs = "x", data = data, block.size = 20, B = 200)
  2: results[, .(beta.med = median(value), beta.025 = quantile(value, 0.975), beta.975 = quantile(value, 
         0.025), se.beta = sd(value), nboot = .N), by = byvars]
  3: `[.data.table`(results, , .(beta.med = median(value), beta.025 = quantile(value, 
         0.975), beta.975 = quantile(value, 0.025), se.beta = sd(value), nboot = .N), 
         by = byvars)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: /home/hornik/tmp/scratch/RtmpcxQOgX/R.INSTALL7a582b110b7b/genomic.autocorr/man/block.glm.Rd 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Extended_Metropolis_Hastings_Sampler.cpp:1426:33: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Extended_Metropolis_Hastings_Sampler.cpp:1471:33: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Extended_Metropolis_Hastings_Sampler.cpp:1969:27: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Extended_Metropolis_Hastings_Sampler.cpp:2007:27: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:523:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:527:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:531:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:535:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:539:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:543:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:772:33: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:823:33: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GERGM.Rcheck/00install.out’ for details.
Running ‘test-add_pval.R’ [2s/2s]
Running the tests in ‘tests/test-add_pval.R’ failed.
Complete output:
  > library(ggpval)
  > library(ggplot2)
  > library(data.table)
  > A <- rnorm(200, 0, 3)
  > B <- rnorm(200, 2, 4)
  > G <- rep(c("G1", "G2"), each = 100)
  > dt <- data.table(A, B, G)
  > dt <- melt(dt, id.vars = "G")
  > dt[, G := factor(G, levels = c("G2", "G1"))]
  > 
  > plt <- ggplot(dt, aes(variable, value)) +
  +   geom_boxplot() +
  +   geom_jitter()
  > 
  > plt_facet <- ggplot(dt, aes(variable, value)) +
  +   geom_boxplot() +
  +   geom_jitter() +
  +   facet_wrap(~G)
  > 
  > add_pval(plt, pairs = list(c(1, 2)))
  > 
  > add_pval(plt_facet, pairs = list(c(1, 2)))
  Error in `[.data.table`(data_2_test, , lapply(.SD, function(i) get(test)(response ~  : 
    SETLENGTH() cannot be applied to an ALTVEC object.
  Calls: add_pval -> [ -> [.data.table
  Execution halted
Running ‘testthat.R’ [3s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ggvis)
  > 
  > test_check("ggvis")
  ── 1. Error: (unknown) (@test-specs.r#5)  ──────────────────────────────────────
  no applicable method for 'group_by_' applied to an object of class "ggvis"
  1: suppressMessages(sys.source(spec, envir = new.env(), chdir = TRUE)) at testthat/test-specs.r:5
  2: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  3: sys.source(spec, envir = new.env(), chdir = TRUE)
  4: eval(exprs[i], envir)
  5: eval(exprs[i], envir)
  6: mtcars %>% ggvis(x = ~wt, stroke = ~cyl) %>% group_by(cyl) %>% layer_freqpolys(width = 1) %>% 
         save_spec("layer/freqpoly-grouped.json")
  7: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  8: eval(quote(`_fseq`(`_lhs`)), env, env)
  9: eval(quote(`_fseq`(`_lhs`)), env, env)
  10: `_fseq`(`_lhs`)
  11: freduce(value, `_function_list`)
  12: function_list[[i]](value)
  13: group_by(., cyl)
  14: group_by.default(., cyl)
  15: group_by_(.data, .dots = compat_as_lazy_dots(...), add = add)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 447 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-specs.r#5) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  calculategphmm.cpp:217:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gphmm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rothmana.cpp:123:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/graphicalVAR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  _t_array_properties.cpp:10:13: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gRbase.Rcheck/00install.out’ for details.
Running examples in ‘happybiRthday-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: celebrate
> ### Title: Celebrating software birthdays
> ### Aliases: celebrate
> 
> ### ** Examples
> 
> celebrate("Bohdan-Khomtchouk")
Error in gh::gh("/users/:username/repos", username = github_username,  : 
  GitHub API error (403): 403 Forbidden
  API rate limit exceeded for 137.208.57.142. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)
Calls: celebrate -> <Anonymous> -> gh_process_response
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(HURDAT)
  > 
  > test_check("HURDAT")
  ── 1. Error: (unknown) (@test-hurdat.R#4)  ─────────────────────────────────────
  HTTP error 404.
  1: get_hurdat(basin = "AL") at testthat/test-hurdat.R:4
  2: purrr::map_df(.x = basin, .f = parse_hurdat)
  3: map(.x, .f, ...)
  4: .f(.x[[i]], ...)
  5: readr::read_lines(file = url)
  6: datasource(file, skip = skip)
  7: datasource_connection(file, skip, comment)
  8: datasource_raw(read_connection(path), skip, comment = comment)
  9: new_datasource("raw", text, skip = skip, comment = comment)
  10: structure(list(x, skip = skip, comment = comment, ...), class = c(paste0("source_", 
         type), "source"))
  11: read_connection(path)
  12: open(con, "rb")
  13: open.connection(con, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-hurdat.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘ibhm.tests.R’ [3s/4s]
Running the tests in ‘tests/ibhm.tests.R’ failed.
Complete output:
  > library(IBHM)
  Loading required package: compiler
  Loading required package: DEoptim
  Loading required package: parallel
  
  DEoptim package
  Differential Evolution algorithm in R
  Authors: D. Ardia, K. Mullen, B. Peterson and J. Ulrich
  
  Loading required package: cmaes
  Loading required package: Rcpp
  > source('utils.R')
  > 
  > 
  > (test.Tanh <- function(){
  +   x <- seq(-6,6,length.out=400)
  +   y <- tanh(x)
  +   
  +   set.seed(123)  
  +   m <- TrainIBHM(x,y, ConfigureIBHM(scal.candidates='dot.pr', activ.candidates='tanh'))  
  +   stopifnot(summary(m)$rmse<0.1) 
  +   cat('tanh - ok\n')
  + })()
  Error in summary(m)$rmse < 0.1 : $ operator is invalid for atomic vectors
  Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
Found the following significant warnings:
  regTree.c:317:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  regTree.c:336:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/iJRF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  transformations.cpp:274:15: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/imager.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stringr)
  > library(io)
  Loading required package: filenamer
  > 
  > test_check("io")
  ── 1. Error: (unknown) (@test_read-write-read.R#8)  ────────────────────────────
  no applicable method for 'h5write' applied to an object of class "character"
  1: test_read_write_read(f) at testthat/test_read-write-read.R:8
  2: qwrite(x, outfile) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/io.Rcheck/tests/testthat/helper.R:48
  3: .qwrite(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  4: qwrite.hdf5(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  5: .write_hdf5_array(x, file)
  6: rhdf5::h5write("array", file, "type")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_read-write-read.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
      user system elapsed
MFKM 4.568  0.027   6.186
Found the following significant warnings:
  LBLasso.c:98:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  LBlogistic.c:100:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  LBmultilogistic.c:110:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ggm.c:69:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ising.c:83:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  potts.c:99:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Libra.Rcheck/00install.out’ for details.
Running examples in ‘MAGNAMWAR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FormatMCLFastas
> ### Title: Format all raw GenBank fastas to single OrthoMCL compatible
> ###   fasta file
> ### Aliases: FormatMCLFastas
> 
> ### ** Examples
> 
> 
> dir <- system.file('extdata', 'fasta_dir', package='MAGNAMWAR')
> dir <- paste(dir,'/',sep='')
> formatted_file <- FormatMCLFastas(dir)
Warning in file.remove(outfile) :
  cannot remove file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta', reason 'Read-only file system'
Writing out to /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta 
Warning in file(description = file.out, open = open) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MAGNAMWAR/extdata/fasta_dir/MCLformatted_all.fasta': Read-only file system
Error in file(description = file.out, open = open) : 
  cannot open the connection
Calls: FormatMCLFastas -> <Anonymous> -> file
Execution halted
Error in re-building vignettes:
  ...
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 264-270 (estimaterates.Rmd) 
Error: processing vignette ‘estimaterates.Rmd’ failed with diagnostics:
cannot open the connection to 'http://info.mcmaster.ca/~udang/mp_example_data'
Execution halted
Found the following significant warnings:
  matching.cc:267:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  matching.cc:466:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  matching.cc:821:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  matching.cc:1227:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  matching.cc:1428:26: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  matching.cc:1838:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  matching.cc:2018:26: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  matching.cc:2615:26: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  matching.cc:2683:24: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Matching.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mue_nelmC.cpp:147:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nelmC.cpp:185:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nelmC.cpp:230:22: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:135:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:173:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:218:22: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mcIRT.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cHDPHMMpoisson.cc:441:18: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  cHDPHMMpoisson.cc:445:18: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  cHDPHMMpoisson.cc:449:18: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MCMCpack.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mdhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘MetaSubtract-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: meta.subtract
> ### Title: Subtracts GWAS results from one or more cohorts from the
> ###   meta-GWAS results
> ### Aliases: meta.subtract
> ### Keywords: Correct meta-GWAS results Leave-one-out
> 
> ### ** Examples
> 
> metafile="meta_results.txt"
> cohortfiles=c("cohort1_results.txt","cohort2_results.txt")
> # Subtract summary statistics of the two cohorts from the meta summary statistics in metafile.
> # Genomic control correction of the imported meta summary statistics will be undone using 
> # lambda.meta. Genomic control will be applied to the corrected meta summary statistics 
> # (gc_meta=TRUE by default) based on a lambda derived from the new meta summary statistics 
> # (calculate_lambda.meta=TRUE by default). The cohorts summary statistics will always be first 
> # corrected for genomic control before subtracting them from the meta summary statistics. By 
> # default, the lambda will be calculated from the data (calculate_lambdas.cohort=TRUE by default).
> m1<-meta.subtract(metafile=metafile, cohortfiles=cohortfiles, lambda.meta=1.046, 
+       dir=system.file("extdata", package="MetaSubtract"))
[1] "Fri May  4 16:58:35 2018"
Reading meta_results.txt 
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file 'MetaSubtract.log': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: meta.subtract -> write.table -> file
Execution halted
Found the following significant warnings:
  NMix_RJMCMCcombine.cpp:422:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mixAK.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mixCpp.cpp:122:19: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  mixCpp.cpp:167:19: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  mixCpp.cpp:399:22: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  mixCpp.cpp:444:22: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mixR.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > suppressPackageStartupMessages({
  +   library(testthat)
  +   library(data.table)
  + })
  > 
  > test_check("mknapsack")
  Loading required package: mknapsack
  ── 1. Error: group_moq: combines data provided at unit level to MOQ level (@test
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: group_moq(units) at testthat/test-packing.R:17
  2: dt[, `:=`(cnt, 1:.N), by = sku]
  3: `[.data.table`(dt, , `:=`(cnt, 1:.N), by = sku)
  
  ── 2. Error: mknapsack: Generates vector of optimal containers for a given probl
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: group_moq(units) at testthat/test-packing.R:34
  2: dt[, `:=`(cnt, 1:.N), by = sku]
  3: `[.data.table`(dt, , `:=`(cnt, 1:.N), by = sku)
  
  ── 3. Error: mknapsack: with sold vector, sold items have highest priority (@tes
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: group_moq(units) at testthat/test-packing.R:74
  2: dt[, `:=`(cnt, 1:.N), by = sku]
  3: `[.data.table`(dt, , `:=`(cnt, 1:.N), by = sku)
  
  ── 4. Error: at contains MOQ line or after: combines data provided at unit level
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: group_moq(units) at testthat/test-packing.R:161
  2: dt[, `:=`(cnt, 1:.N), by = sku]
  3: `[.data.table`(dt, , `:=`(cnt, 1:.N), by = sku)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 4
  1. Error: group_moq: combines data provided at unit level to MOQ level (@test-packing.R#17) 
  2. Error: mknapsack: Generates vector of optimal containers for a given problem (@test-packing.R#34) 
  3. Error: mknapsack: with sold vector, sold items have highest priority (@test-packing.R#74) 
  4. Error: at contains MOQ line or after: combines data provided at unit level to MOQ level (@test-packing.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  confusionMatrix_.cpp:10:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:12:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:14:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:16:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:57:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:104:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:106:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:108:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:110:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ModelMetrics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  weiszfeldIterations.cpp:195:48: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Mposterior.Rcheck/00install.out’ for details.
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MSBVAR.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(msmtools)
  > 
  > test_check("msmtools")
  ── 1. Error: a warning is printed when t_cens is the only var used  ────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: expect_warning(augment(hosp, subj, adm_number, label_3, t_start = dateIN, t_end = dateOUT, 
         t_cens = dateCENS, verbose = F))
  2: quasi_capture(enquo(object), capture_warnings, label = label)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withCallingHandlers(code, warning = function(condition) {
         out$push(condition)
         invokeRestart("muffleWarning")
     })
  5: eval_bare(get_expr(quo), get_env(quo))
  6: augment(hosp, subj, adm_number, label_3, t_start = dateIN, t_end = dateOUT, t_cens = dateCENS, 
         verbose = F)
  7: data[, .(ev = all(get(cols[[2]]) == cummax(get(cols[[2]])))), by = eval(cols[[1]])]
  8: `[.data.table`(data, , .(ev = all(get(cols[[2]]) == cummax(get(cols[[2]])))), by = eval(cols[[1]]))
  
  ── 2. Error: (unknown) (@test_dataset_return.R#18)  ────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: augment(data = hosp, data_key = subj, n_events = adm_number, pattern = label_2, t_start = dateIN, 
         t_end = dateOUT, t_cens = dateCENS, verbose = F) at testthat/test_dataset_return.R:18
  2: data[, .(ev = all(get(cols[[2]]) == cummax(get(cols[[2]])))), by = eval(cols[[1]])]
  3: `[.data.table`(data, , .(ev = all(get(cols[[2]]) == cummax(get(cols[[2]])))), by = eval(cols[[1]]))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 2
  1. Error: a warning is printed when t_cens is the only var used 
  2. Error: (unknown) (@test_dataset_return.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  evallf.c:86:23: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mvnmle.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [26s/39s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(magrittr)
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following objects are masked from 'package:magrittr':
  
      equals, is_less_than, not
  
  > test_check("NetLogoR")
  Loading required package: NetLogoR
  Loading required package: raster
  Loading required package: sp
  
  Attaching package: 'raster'
  
  The following object is masked from 'package:magrittr':
  
      extract
  
  ── 1. Error: diffuse works with 4 neighbors (@test-patch-functions.R#5)  ───────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: diffuse(world = w1, share = 0.6, nNeighbors = 4) at testthat/test-patch-functions.R:5
  2: diffuse(world = w1, share = 0.6, nNeighbors = 4)
  3: .local(world, share, nNeighbors, torus)
  4: dt[, `:=`(loose, sum(toGiveNeigh)), by = from]
  5: `[.data.table`(dt, , `:=`(loose, sum(toGiveNeigh)), by = from)
  
  ── 2. Error: diffuse works with 8 neighbors (@test-patch-functions.R#52)  ──────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: diffuse(world = w1, share = 0.6, nNeighbors = 8) at testthat/test-patch-functions.R:52
  2: diffuse(world = w1, share = 0.6, nNeighbors = 8)
  3: .local(world, share, nNeighbors, torus)
  4: dt[, `:=`(loose, sum(toGiveNeigh)), by = from]
  5: `[.data.table`(dt, , `:=`(loose, sum(toGiveNeigh)), by = from)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1138 SKIPPED: 1 FAILED: 2
  1. Error: diffuse works with 4 neighbors (@test-patch-functions.R#5) 
  2. Error: diffuse works with 8 neighbors (@test-patch-functions.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(nima)
  nima: Nima Hejazi's R Toolbox
  Version: 0.4.5
  > 
  > test_check("nima")
  ── 1. Failure: attrnames finds the names of the attributes of a data frame (@tes
  attrnames(y) not equal to c("names", "row.names", "class").
  2/3 mismatches
  x[2]: "class"
  y[2]: "row.names"
  
  x[3]: "row.names"
  y[3]: "class"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Failure: attrnames finds the names of the attributes of a data frame (@test-attribute_names.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [15s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘exporting-methods.R’ [3s/4s]
  Running ‘mahal-dist.R’ [3s/4s]
  Running ‘testthat.R’ [18s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ── 1. Failure: ISM sorting (@test.InfinitySparseMatrix.R#424)  ─────────────────
  `expect_error(sort(X, byCol = c(1, 1)))` did not produce any warnings.
  
  ── 2. Failure: BISM sorting (@test.InfinitySparseMatrix.R#505)  ────────────────
  `expect_error(sort(b, byCol = c(1, 1)))` did not produce any warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1367 SKIPPED: 0 FAILED: 2
  1. Failure: ISM sorting (@test.InfinitySparseMatrix.R#424) 
  2. Failure: BISM sorting (@test.InfinitySparseMatrix.R#505) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
       user system elapsed
optrdd 4.83  0.117   6.781
Running ‘testthat.R’ [19s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(origami)
  origami: Generalized Cross-Validation Framework
  Version: 1.0.0
  > library(data.table)
  > test_check("origami")
  ── 1. Error: (unknown) (@test-folds.R#96)  ─────────────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: validation_dt[, list(one_count = sum(strata_ids)), by = list(fold)] at testthat/test-folds.R:96
  2: `[.data.table`(validation_dt, , list(one_count = sum(strata_ids)), by = list(fold)) at testthat/test-folds.R:96
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-folds.R#96) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘pbdRPC-guide.tex’ failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 145.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte 146.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte 145.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte 146.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte 145.

See the inputenc package documentation for explanation.
Type  H <return>  for immedi
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘pbdZMQ-guide.tex’ failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [15s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("penaltyLearning")
  Loading required package: penaltyLearning
  Loading required package: data.table
  ── 1. Error: no error for finite limits (@test-errors.R#51)  ───────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: targetIntervalROC(ok3, 1:3) at testthat/test-errors.R:51
  2: target.errors[, `:=`(possible.fp, max(fp)), by = observation]
  3: `[.data.table`(target.errors, , `:=`(possible.fp, max(fp)), by = observation)
  
  ── 2. Error: no error for one col vector predictions (@test-errors.R#65)  ──────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: targetIntervalROC(ok3, cbind(foo = 1:3)) at testthat/test-errors.R:65
  2: target.errors[, `:=`(possible.fp, max(fp)), by = observation]
  3: `[.data.table`(target.errors, , `:=`(possible.fp, max(fp)), by = observation)
  
  ── 3. Error: (unknown) (@test-features.R#29)  ──────────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: featureMatrix(three, c("profile.id", "chromosome"), "logratio") at testthat/test-features.R:29
  2: data.table(data.sequences)[, list(features = list(featureVector(.SD[[data.var]]))), 
         by = problem.vars]
  3: `[.data.table`(data.table(data.sequences), , list(features = list(featureVector(.SD[[data.var]]))), 
         by = problem.vars)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 63 SKIPPED: 0 FAILED: 3
  1. Error: no error for finite limits (@test-errors.R#51) 
  2. Error: no error for one col vector predictions (@test-errors.R#65) 
  3. Error: (unknown) (@test-features.R#29) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:

  Warning: 'cBind' is deprecated.
  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
              user system elapsed
AIC.phmm     4.852  0.023   7.565
phmm-package 4.039  0.003   5.766
phmm         3.974  0.008   5.172
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/picante.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  cat_pair.c:64:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  cat_pair.c:79:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PLordprob.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: Rcpp
rstanarm (Version 2.17.4, packaged: 2018-04-13 01:51:52 UTC)
- Do not expect the default priors to remain the same in future rstanarm versions.
Thus, R scripts should specify priors explicitly, even if they are just the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())
- Plotting theme set to bayesplot::theme_default().

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: There were 18 divergent transitions after warmup. Increasing adapt_delta above 0.95 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: Markov chains did not converge! Do not analyze results!
Warning: There were 3 divergent transitions after warmup. Increasing adapt_delta above 0.95 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems


Attaching package: 'plotly'

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

    last_plot

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

    get_x, get_y

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

    filter

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

    layout

We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/ggplot2')`
Quitting from lines 503-531 (bayesian.Rmd) 
Error: processing vignette ‘bayesian.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 126-132 (Maps_and_Timeseries_Plots.Rmd) 
Error: processing vignette ‘Maps_and_Timeseries_Plots.Rmd’ failed with diagnostics:
cannot open URL ‘http://maps.google.com/maps/api/staticmap?center=47,-118&zoom=7&size=640x640&maptype=roadmap&format=png32&sensor=true’
Execution halted
Running ‘testthat.R’ [4s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pxweb)
  pxweb: R tools for PX-WEB API.
  Copyright (C) 2014 Mans Magnusson, Leo Lahti, Love Hansson
  https://github.com/ropengov/pxweb
  
  New PXWEB API(s):
   - prognos.konj.se
   - data.ssb.no
   - pxweb.asub.ax
   - makstat.stat.gov.mk
   - data.csb.gov.lv
  
  Use update_pxweb_apis() to update the api catalogue.
  > test_check("pxweb")
  ── 1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20)  ───────────────────
  NOT(success)
  
  ── 2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22)  ───────────────────
  "foo.bar" %in% unlist(lapply(api_catalogue(), function(X) X$api)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 98 SKIPPED: 16 FAILED: 2
  1. Failure: pxweb_api_class (@test-pxweb_api_class.R#20) 
  2. Failure: pxweb_api_class (@test-pxweb_api_class.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘R2GUESS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.ESS.object
> ### Title: Compiles the main input and output files from a previous run of
> ###   'R2GUESS' and creates an ESS object.
> ### Aliases: as.ESS.object
> 
> ### ** Examples
> 
> dataX <- "data-X-C-CODE.txt"
> dataY <- "data-Y-ALL-C-CODE.txt"
> 
> path.input <- system.file("Input", package="R2GUESS")
> path.output <- system.file("Output", package="R2GUESS")
> path.par <- system.file("extdata", package="R2GUESS")
> file.par <- "Par_file_example_Hopx.xml"
> root.file.output <- "Example-GUESS-Y-Hopx"
> label.Y <- c("ADR","Fat","Heart","Kidney")
> my.env <- new.env()
> data(MAP.file,envir=my.env)
> MAP.file <- my.env$MAP.file
> modelY_Hopx <-as.ESS.object(dataY=dataY,dataX=dataX,path.input=path.input,
+     path.output=path.output,root.file.output=root.file.output,label.X=NULL,
+     label.Y=label.Y,path.par=path.par,file.par=file.par,MAP.file=MAP.file)
Warning in gzfile(file, "wb") :
  cannot open compressed file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/R2GUESS/Output/Example-GUESS-Y-Hopx_output_best_visited_models.RData', probable reason 'Read-only file system'
Error in gzfile(file, "wb") : cannot open the connection
Calls: as.ESS.object -> get.best.models -> save -> gzfile
Execution halted
Error in re-building vignettes:
  ...
Loading required package: RCurl
Loading required package: bitops
Loading required package: RJSONIO

Error: processing vignette ‘rbiouml.Rnw’ failed with diagnostics:
 chunk 1 
Error in file(con, "r") : cannot open the connection
Execution halted
Running examples in ‘Rchoice-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estfun.Rchoice
> ### Title: Gradient for observations
> ### Aliases: estfun.Rchoice
> 
> ### ** Examples
> 
> ## Probit model
> data("Workmroz")
> probit <- Rchoice(lfp ~ k5 + k618 + age + wc + hc + lwg + inc,  
+                   data = Workmroz , family = binomial('probit'))
> summary(probit)

Model: binomial
Model estimated on: Fri May 04 05:23:47 PM 2018 

Call:
Rchoice(formula = lfp ~ k5 + k618 + age + wc + hc + lwg + inc, 
    data = Workmroz, family = binomial("probit"), method = "nr")


Frequencies of categories:
y
     0      1 
0.4316 0.5684 
The estimation took: 0h:0m:0s 

Coefficients:
          Estimate Std. Error z-value Pr(>|z|)    
constant  1.918422   0.380654   5.040 4.66e-07 ***
k5       -0.874711   0.113558  -7.703 1.33e-14 ***
k618     -0.038594   0.040489  -0.953 0.340488    
age      -0.037824   0.007609  -4.971 6.67e-07 ***
wc        0.488314   0.135487   3.604 0.000313 ***
hc        0.057170   0.124005   0.461 0.644776    
lwg       0.365629   0.087779   4.165 3.11e-05 ***
inc      -0.020525   0.004777  -4.297 1.73e-05 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Optimization of log-likelihood by Newton-Raphson maximisation
Log Likelihood: -452.7
Number of observations: 753
Number of iterations: 4
Exit of MLE: gradient close to zero> 
> library(sandwich)
> estfun(probit) 
Error in UseMethod("estfun") : 
  no applicable method for 'estfun' applied to an object of class "Rchoice"
Calls: estfun
Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘Rcmdr::Confint’ by ‘car::Confint’ when loading ‘RcmdrPlugin.BCA’
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RcmdrPlugin.BCA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cwb/cl/special-chars.c:1771:22: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rcqp.Rcheck/00install.out’ for details.
Running examples in ‘Rcrawler-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: LinkExtractor
> ### Title: LinkExtractor
> ### Aliases: LinkExtractor
> 
> ### ** Examples
> 
> 
> pageinfo<-LinkExtractor(url="http://www.glofile.com", ExternalLInks = TRUE)
Error in LinkExtractor(url = "http://www.glofile.com", ExternalLInks = TRUE) : 
  object 'Extlinks' not found
Execution halted
Running examples in ‘ref-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: refdata
> ### Title: subsettable reference to matrix or data.frame
> ### Aliases: refdata derefdata derefdata<- [.refdata [<-.refdata [[.refdata
> ###   [[<-.refdata $.refdata $<-.refdata dim.refdata dimnames.refdata
> ###   row.names.refdata names.refdata print.refdata
> ### Keywords: programming manip
> 
> ### ** Examples
> 
> 
>   ## Simple usage Example
>   x <- cbind(1:5, 5:1)       # take a matrix or data frame
>   rx <- refdata(x)           # wrap it into an refdata object
>   rx                         # see the autoprinting
list()
attr(,"dat")
<environment: 0x55e195f1e750>
attr(,"ind")
<environment: 0x55e195f1eb08>
attr(,"class")
[1] "refdata" "matrix" 
>   rm(x)                      # delete original to save memory
>   rx[]                       # extract all data
list()
attr(,"dat")
<environment: 0x55e195f1e750>
attr(,"ind")
<environment: 0x55e195f1eb08>
>   rx[-1, ]                   # extract part of data
Error in rx[-1, ] : incorrect number of dimensions
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/refund.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testCases.R’ [1s/2s]
Running the tests in ‘tests/testCases.R’ failed.
Complete output:
  > ## test constrained lm, rlm, glm
  > # mixing weights
  > # bootstrap standard errors
  > # models with and without intercept
  > # case weights
  > # constraints on factors and interactions
  > 
  > library(restriktor)
  This is restriktor 0.1-80.711
  restriktor is BETA software! Please report any bugs.
  > n <- 100
  > p <- 4
  > betas = c(0.1,0.2,0.3,0.4,0.5)
  > set.seed(3013073)
  > X <- cbind(mvtnorm:::rmvnorm(n, mean=rep(0,p), sigma=diag(p)), rbinom(n,1,0.5))
  > colnames(X) <- c("x1","x2","x3","x4","f1")
  > z <- X %*% betas        
  > y <- z + rnorm(n)
  > DATA <- data.frame(y, X)
  > 
  > # intercept model
  > model1 <- y ~  1 + x1 + x2 + x3 + x4
  > # no intercept model
  > model2 <- y ~ -1 + x1 + x2 + x3 + x4
  > # intercept model with interaction
  > model3 <- y ~ 1 + x1*f1 + x2*f1 + x3*f1 + x4*f1
  > # intercept model with interaction
  > model4 <- y ~ -1 + x1*f1 + x2*f1 + x3*f1 + x4*f1
  > 
  > ############################ lm #################################
  > linmod1 <- lm(model1, data = DATA)
  > linmod2 <- lm(model2, data = DATA)
  > linmod3 <- lm(model3, data = DATA)
  > linmod1wt <- lm(model1, data = DATA, weights = abs(rnorm(n)))
  > linmod2wt <- lm(model2, data = DATA, weights = abs(rnorm(n)))
  > linmod1fac <- lm(model3, data = DATA)
  > linmod2fac <- lm(model4, data = DATA)
  > 
  > constraints1 <- 'x1 > 0; x2 > 0; x3 > 0'
  > fit.restr1 <- restriktor(linmod1, constraints1)
  Error in UseMethod("conLM") : 
    no applicable method for 'conLM' applied to an object of class "lm"
  Calls: restriktor
  Execution halted
Found the following significant warnings:
  simul.cpp:82:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/revealedPrefs.Rcheck/00install.out’ for details.
Running examples in ‘RgoogleMaps-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GetMap.bbox
> ### Title: GetMap bbox
> ### Aliases: GetMap.bbox
> 
> ### ** Examples
> 
> 
> 
>  mymarkers <- cbind.data.frame(lat = c(38.898648,38.889112, 38.880940), 
+ 
+ 
+           lon = c(-77.037692, -77.050273, -77.03660), size =  c('tiny','tiny','tiny'), 
+ 
+ 
+           col = c('blue', 'green', 'red'), char = c('','',''));
> 
> 
> 
> 
> 
> ##get the bounding box:
> 
> 
>   bb <- qbbox(lat = mymarkers[,"lat"], lon = mymarkers[,"lon"]);
> 
> 
>   
> 
> 
> ##download the map:
> 
> 
>   MyMap <- GetMap.bbox(bb$lonR, bb$latR, destfile = "DC.png", GRAYSCALE =TRUE,
+ 
+ 
+                 markers = mymarkers);
Warning in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) :
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=38.889794,-77.0434365&zoom=15&size=640x640&maptype=mobile&format=png32&sensor=true&markers=size:1|col:1|char:1|38.898648,-77.037692&markers=size:1|col:2|char:1|38.889112,-77.050273&markers=size:1|col:3|char:1|38.88094,-77.0366': HTTP status was '403 Forbidden'
Error in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=38.889794,-77.0434365&zoom=15&size=640x640&maptype=mobile&format=png32&sensor=true&markers=size:1|col:1|char:1|38.898648,-77.037692&markers=size:1|col:2|char:1|38.889112,-77.050273&markers=size:1|col:3|char:1|38.88094,-77.0366'
Calls: GetMap.bbox -> GetMap -> download.file
Execution halted
Found the following significant warnings:
  atkClasses.c:1050:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1058:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1397:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1948:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1964:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8665:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11110:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RGtk2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: The javah tool is planned to be removed in the next major
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rJava.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
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:
  libjson/Source/JSONSharedString.h:297:17: warning: ‘json_shared_string::len’ will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   ‘json_shared_string::json_shared_string_internal* json_shared_string::_str’ [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:79:7: warning: ‘JSONStream::state’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   ‘void (* JSONStream::call)(void*, void*)’ [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: ‘JSONStream::err_call’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   ‘json_string JSONStream::buffer’ [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  libjson/Source/internalJSONNode.h:257:18: warning: ‘internalJSONNode::_name_encoded’ will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   ‘json_string internalJSONNode::_name’ [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Found the following significant warnings:
  PresenceAndAbsence.cpp:536:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  PresenceAndAbsence.cpp:537:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rlda.Rcheck/00install.out’ for details.
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rmixmod.Rcheck/00install.out’ for details.
Found the following significant warnings:
  npmpois.c:246:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  rmg.c:335:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rmp.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [66s/140s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("RNeXML")
  Loading required package: RNeXML
  Loading required package: ape
  Namespace prefix xhtml on div is not defined
  A nexml object representing:
   	 0 phylogenetic tree blocks, where: 
   	 block 1 contains NULL phylogenetic trees
  	 block 0 contains  phylogenetic trees 
   	 19 meta elements 
   	 0 character matrices 
   	 0 taxonomic units 
   Taxa: 	  ... 
  
   NeXML generated by RNeXML using schema version: 0.9 
   size: 23.2 Kb 
  Done simulation(s).
  ── 1. Error: we can coerce an ape::phylo tree with a 
            phytools:simmap 
  the condition has length > 1
  1: simmap_to_nexml(mtree) at testthat/test_simmap.R:21
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 176 SKIPPED: 3 FAILED: 1
  1. Error: we can coerce an ape::phylo tree with a 
            phytools:simmap extension into nexml (@test_simmap.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [4s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2015-present, Facebook, Inc.
  > # All rights reserved.
  > #
  > # This source code is licensed under the BSD-style license found in the
  > # LICENSE file in the root directory of this source tree. An additional grant
  > # of patent rights can be found in the PATENTS file in the same directory.
  > 
  > library("testthat")
  > library("DBI")
  > library("RPresto")
  > 
  > test_check("RPresto")
  -- 1. Failure: as() works (@test-src_translate_env.R#52)  ----------------------
  translate_sql(as(x, 0), con = conn[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS \"DOUBLE\")").
  1/1 mismatches
  x[1]: "AS(\"x\", 0.0)"
  y[1]: "CAST(\"x\" AS \"DOUBLE\")"
  
  -- 2. Failure: as() works (@test-src_translate_env.R#56)  ----------------------
  translate_sql(pmax(x), con = conn[["con"]]) not equal to dplyr::sql("GREATEST(\"x\")").
  1/1 mismatches
  x[1]: "MAX(\"x\")"
  y[1]: "GREATEST(\"x\")"
  
  -- 3. Failure: as() works (@test-src_translate_env.R#60)  ----------------------
  translate_sql_(...) not equal to dplyr::sql("CAST(\"x\" AS \"ARRAY<VARCHAR>\")").
  1/1 mismatches
  x[1]: "AS(\"x\", ())"
  y[1]: "CAST(\"x\" AS \"ARRAY<VARCHAR>\")"
  
  -- 4. Failure: as() works (@test-src_translate_env.R#69)  ----------------------
  translate_sql_(list(substituted.expression), con = conn[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS \"DATE\")").
  1/1 mismatches
  x[1]: "AS(\"x\", '2018-05-04')"
  y[1]: "CAST(\"x\" AS \"DATE\")"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 223 SKIPPED: 28 FAILED: 4
  1. Failure: as() works (@test-src_translate_env.R#52) 
  2. Failure: as() works (@test-src_translate_env.R#56) 
  3. Failure: as() works (@test-src_translate_env.R#60) 
  4. Failure: as() works (@test-src_translate_env.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: robustbase
Scalable Robust Estimators with High Breakdown Point (version 1.4-3)

Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[[2L]], length = arrow.len) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[[2L]], length = arrow.len) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[[2L]], length = arrow.len) :
  zero-length arrow is of indeterminate angle and so skipped
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘rrcov.tex’ failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 252.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  regTree.c:242:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RRF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
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.
Running examples in ‘RSMET-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pushSmetIntoIni
> ### Title: Pushes SMET object file into a 'meteoioini-class' object
> ### Aliases: pushSmetIntoIni
> 
> ### ** Examples
> 
> 
> ini <- as.meteoioini("test")
> 
> AA <- as.smet("test")
> BB <- as.smet("test")
> 
> 
> newini <- pushSmetIntoIni(AA,BB,ini=ini)
Warning in file(con, "w") :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/RSMET/temp/test_station.smet': Read-only file system
Error in file(con, "w") : cannot open the connection
Calls: pushSmetIntoIni -> lapply -> FUN -> print.smet -> <Anonymous> -> file
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rsunlight.Rcheck/00install.out’ for details.
Running ‘tests.R’ [0s/0s]
Running the tests in ‘tests/tests.R’ failed.
Complete output:
  > require(rtf)
  Loading required package: rtf
  > require(lattice)
  Loading required package: lattice
  > 
  > output<-"test_rtf-package.doc"
  > png.res<-300
  > 
  > rtf<-RTF(output,width=8.5,height=11,font.size=10,omi=c(1,1,1,1))
  > addHeader(rtf,title="Test",subtitle="2011-08-15\n")
  Error in UseMethod("addHeader") : 
    no applicable method for 'addHeader' applied to an object of class "c('RTF', 'Object')"
  Calls: addHeader
  Execution halted
Found the following significant warnings:
  bitmap.c:1594:29: warning: suggest parentheses around comparison in operand of ‘^’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rttf2pt1.Rcheck/00install.out’ for details.
Running examples in ‘satscanMapper-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: satscanMapper
> ### Title: Function to map Results data produced by a SaTScan (TM) cluster
> ###   analysis
> ### Aliases: satscanMapper
> 
> ### ** Examples
> 
> ######
> #
> #  These examples focus on mapping the SaTScan (TM) data after the analysis
> #  has been completed.
> #  See the section on the CreateGeo4SS function for an example of how 
> #  to build a coordinates file (.geo) that matches the satscanMapper 
> #  boundary data.
> #
> ######
> 
> ######
> #
> #  Example # 1 - Mapping existing SaTScan (TM) results - "USStateLung" result files
> #     Make sure SaTScan (TM) results files are still located in the directories
> #     documented in the session saved (.prm) file.
> #
> #     This example maps data for the US States containing circular clusters.
> #
> #   Get location of .prm file and location to write mapping output files
> #
> 
> SSMInstDir <- system.file(package="satscanMapper", "extdata")
> 
> TT =c("Contiguous US States All Lung Cancer Mortality, 2004")
> 
> satscanMapper(resDir=SSMInstDir,                # path to .prm file location for output files. 
+                      prmFile  = "stateLung.prm", 
+                      title    = TT          )
Error in pdf(file = OutputFNpdf, width = vW, height = vH) : 
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/satscanMapper/extdata/stateLung-R01.pdf'
Calls: satscanMapper -> pdf
Execution halted
Running examples in ‘sbgcop-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sbgcop.mcmc
> ### Title: Semiparametric Bayesian Gaussian copula estimation and
> ###   imputation
> ### Aliases: sbgcop.mcmc plot.psgc summary.psgc print.sum.psgc
> ### Keywords: multivariate models
> 
> ### ** Examples
> 
> fit<-sbgcop.mcmc(swiss)
10 percent done  Fri May  4 20:42:45 2018 
20 percent done  Fri May  4 20:42:45 2018 
30 percent done  Fri May  4 20:42:45 2018 
40 percent done  Fri May  4 20:42:45 2018 
50 percent done  Fri May  4 20:42:45 2018 
60 percent done  Fri May  4 20:42:46 2018 
70 percent done  Fri May  4 20:42:46 2018 
80 percent done  Fri May  4 20:42:46 2018 
90 percent done  Fri May  4 20:42:46 2018 
100 percent done  Fri May  4 20:42:46 2018 
> summary(fit)
         Length Class  Mode   
C.psamp  3600   -none- numeric
Y.pmean   282   -none- numeric
Y.impute    0   -none- NULL   
LPC       100   -none- numeric
> plot(fit)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
Running ‘globalRecoding_test.R’ [3s/4s]
  Running ‘microaggregation_test.R’ [2s/3s]
Running the tests in ‘tests/microaggregation_test.R’ failed.
Complete output:
  > require(sdcMicro)
  Loading required package: sdcMicro
  --------
  This is sdcMicro v5.2.0.
  For references, please have a look at citation('sdcMicro')
  Note: since version 5.0.0, the graphical user-interface is a shiny-app that can be started with sdcApp().
  Please submit suggestions and bugs at: https://github.com/sdcTools/sdcMicro/issues
  --------
  > ### for a data.frame
  > dat <- data.frame(x = rnorm(100))
  > microaggregation(obj = dat, variables = "x", method = "mdav", aggr = 3, measure = "mean")
  Error in `[.data.table`(xdat, , j = list(idvariableforresorting = idf(idvariableforresorting),  : 
    SETLENGTH() cannot be applied to an ALTVEC object.
  Calls: microaggregation ... mafastX -> mafastWORK -> eval -> eval -> [ -> [.data.table
  Execution halted
Running ‘testthat.R’ [6s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  > library(sentometrics)
  Loading required package: data.table
  Loading required package: ggplot2
  Loading required package: foreach
  > 
  > test_check("sentometrics")
  Compute sentiment... Done. 
  ── 1. Error: (unknown) (@test_aggregation.R#15)  ───────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: sento_measures(corpus, lex, ctr) at testthat/test_aggregation.R:15
  2: perform_agg(toAgg, ctr)
  3: agg_documents(toAgg, by = by, how = howDocs, do.ignoreZeros = do.ignoreZeros)
  4: s[, lapply(.SD, function(x) (x * word_count)/x), by = date]
  5: `[.data.table`(s, , lapply(.SD, function(x) (x * word_count)/x), by = date)
  
  Compute sentiment... Done. 
  ── 2. Error: (unknown) (@test_attribution.R#15)  ───────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: sento_measures(corpus, lex, ctr) at testthat/test_attribution.R:15
  2: perform_agg(toAgg, ctr)
  3: agg_documents(toAgg, by = by, how = howDocs, do.ignoreZeros = do.ignoreZeros)
  4: s[, list(w = word_count/sum(word_count, na.rm = TRUE)), by = date]
  5: `[.data.table`(s, , list(w = word_count/sum(word_count, na.rm = TRUE)), by = date)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test_aggregation.R#15) 
  2. Error: (unknown) (@test_attribution.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
             user system elapsed
prepScores  5.360  0.034   7.498
prepScores2 5.007  0.040   7.029
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘test-all.R’ [124s/187s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  ── 1. Failure: simList object initializes correctly (@test-simList.R#17)  ──────────────────────────
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  sparseSVM.c:367:30: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sparseSVM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  timeFuns.c:1084:34: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/splusTimeDate.Rcheck/00install.out’ for details.
Found the following significant warnings:
  wdl.cpp:184:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spp.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  points.within
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'points.within':
  ‘points.within’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  ChangePointAnalyzeNorm.cpp:49:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ChangePointAnalyzePoiss.cpp:42:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/StepSignalMargiLike.Rcheck/00install.out’ for details.
Running examples in ‘Stickbreaker-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sim.data.from.priors.for.mod.selection
> ### Title: Simulate data from priors for doing model selection
> ### Aliases: sim.data.from.priors.for.mod.selection
> 
> ### ** Examples
> 
>  n.muts <- 4
>  n.muts <- length(Khan.data[1,])-1
>  geno.matrix <- Khan.data[,seq(1, n.muts)]
>  fit.matrix <- as.matrix(Khan.data[,(n.muts+1)])
>  outdir <- system.file("extdata",package="Stickbreaker")
>  file.name <- paste("Training_simulated_priors_fit_data_", n.muts, "muts.txt", sep="")
>  outpath <- paste(outdir, file.name, sep="/")
>  sim.data.from.priors.for.mod.selection(n.muts,
+    c(0.05, 0.5),
+    c(0, 0.25),
+    c(4),
+    1,
+    c(0.1, 10),
+    1.1,
+    1,
+    c(2,1),
+    outpath,
+    50,
+    coe.sim.model="identical",
+    coe.dist.par=NA,
+    print.interval=NA)
Warning in file(file, ifelse(append, "a", "w")) :
  cannot open file '/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Stickbreaker/extdata/Training_simulated_priors_fit_data_5muts.txt': Read-only file system
Error in file(file, ifelse(append, "a", "w")) : 
  cannot open the connection
Calls: sim.data.from.priors.for.mod.selection -> write.table -> file
Execution halted
Running examples in ‘stocks-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: beta_trailing50
> ### Title: Beta for Last 50 Daily Gains
> ### Aliases: beta_trailing50
> 
> ### ** Examples
> 
> # Calculate TLT's beta based on the previous 50 daily gains
> beta_trailing50("TLT")
‘getSymbols’ currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
‘loadSymbols’ to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.


WARNING: There have been significant changes to Yahoo Finance data.
Please see the Warning section of ‘?getSymbols.yahoo’ for details.

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
Error in x[nrow(x), , drop = F] : incorrect number of dimensions
Calls: beta_trailing50 ... load_gains -> as.Date -> unlist -> lapply -> FUN -> rownames
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/streamR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stringr)
  > 
  > test_check("stringr")
  ── 1. Failure: special case are correct (@test-match.r#13)  ────────────────────
  str_match(NA, "(a)") not equal to matrix(NA_character_).
  Lengths differ: 2 is not 1
  
  ── 2. Failure: special case are correct (@test-match.r#14)  ────────────────────
  str_match(character(), "(a)") not equal to matrix(character(), 0, 1).
  Attributes: < Component "dim": Mean relative difference: 0.5 >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 217 SKIPPED: 0 FAILED: 2
  1. Failure: special case are correct (@test-match.r#13) 
  2. Failure: special case are correct (@test-match.r#14) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testGBHProcedures.R’ [3s/5s]
  Running ‘testHierarchicalMethods.R’ [3s/5s]
Running the tests in ‘tests/testHierarchicalMethods.R’ failed.
Complete output:
  > ## Test the hypothesesTree creation class.
  > 
  > set.seed(130229)
  > library('structSSI')
  > library('ape')
  > library('igraph')
  
  Attaching package: 'igraph'
  
  The following objects are masked from 'package:ape':
  
      edges, mst, ring
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > tree.1 <- as.igraph(rtree(10))
  Error in UseMethod("as.igraph") : 
    no applicable method for 'as.igraph' applied to an object of class "phylo"
  Calls: as.igraph
  Execution halted
Found the following significant warnings:

  Warning: 'cBind' is deprecated.
  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
            user system elapsed
readTSVmod 4.811  0.062   9.564
Found the following significant warnings:
  gzipdec_ms.cpp:59:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  gzipdec_ms.cpp:61:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  gzipdec_ms.cpp:63:21: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/TAQMNGR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.

Error: processing vignette ‘tcpl_Overview.Rnw’ failed with diagnostics:
 chunk 4 
Error in result_create(conn@ptr, statement) : 
  attempt to write a readonly database
Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
             user system elapsed
we8there    7.723  0.067  10.138
congress109 4.416  0.016   6.292
Running examples in ‘tightClust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tight.clust
> ### Title: Tight Clustering
> ### Aliases: tight.clust
> ### Keywords: cluster
> 
> ### ** Examples
> 
> ## load the test dataset
> data(tclust.test.data)
> ## find 10 tight clusters
> ptm<-proc.time()
> ## k.min=25, tighter clusters will be found
> ## target=1 is used to save time, target=10 is recommended
> tclust1<-tight.clust(tclust.test.data$Data, target=1, k.min=25, random.seed=12345)
Number of points: 1100 	Dimension: 75 

Looking for tight cluster 1 ...
k = 25
k = 26
1 tight cluster(s) found!
Cluster size: 43 	Remaining number of points: 1057 

> proc.time()-ptm
   user  system elapsed 
  2.872   0.112   5.483 
> ## plot the heat map of cluster result
> plot(tclust1)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'tcpl'
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.
toxboot 0.1.1
MongoDB settings (?toxbootConf):
  TOXBOOT_HOST: NA
  TOXBOOT_DBNS: NA
  TOXBOOT_USER: NA
  TOXBOOT_DB: NA
MySQL settings:
  Host: Not Configured
  Database: Not Configured
  User: Not Configured
Loading required package: DBI
Quitting from lines 197-204 (toxboot.Rmd) 
Error: processing vignette ‘toxboot.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
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.
Rd file 'ci.plot.Rd':
  \usage lines wider than 90 characters:
     ci.plot(x, y, se, level = 0.95, ylim = NULL, newplot = TRUE, fun = gaussian()$linkinv, dfun = gaussian()$mu.eta, ...)

These lines will be truncated in the PDF manual.
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.
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("trelliscope")
  Loading required package: trelliscope
  Loading required package: datadr
  Note: trelliscope will eventually be superseded by trelliscopejs: https://github.com/hafen/trelliscopejs
  ── 1. Error: (unknown) (@test-1-simple-display.R#13)  ──────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: datadr::divide(barley, by = "site") at testthat/test-1-simple-display.R:13
  2: getDivideDF(data, by = by, postTransFn = postTransFn, bsvFn = bsvFn, update = update)
  3: d[, ff(.SD), by = key(d), .SDcols = nms]
  4: `[.data.table`(d, , ff(.SD), by = key(d), .SDcols = nms)
  
  ── 2. Error: find globals (@test-2-globals.R#10)  ──────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: datadr::divide(barley, by = "site") at testthat/test-2-globals.R:10
  2: getDivideDF(data, by = by, postTransFn = postTransFn, bsvFn = bsvFn, update = update)
  3: d[, ff(.SD), by = key(d), .SDcols = nms]
  4: `[.data.table`(d, , ff(.SD), by = key(d), .SDcols = nms)
  
  ── 3. Error: (unknown) (@test-3-globals-by-hand.R#10)  ─────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: datadr::divide(barley, by = "site") at testthat/test-3-globals-by-hand.R:10
  2: getDivideDF(data, by = by, postTransFn = postTransFn, bsvFn = bsvFn, update = update)
  3: d[, ff(.SD), by = key(d), .SDcols = nms]
  4: `[.data.table`(d, , ff(.SD), by = key(d), .SDcols = nms)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test-1-simple-display.R#13) 
  2. Error: find globals (@test-2-globals.R#10) 
  3. Error: (unknown) (@test-3-globals-by-hand.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘udpipe-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.data.frame.udpipe_connlu
> ### Title: Convert the result of udpipe_annotate to a tidy data frame
> ### Aliases: as.data.frame.udpipe_connlu
> 
> ### ** Examples
> 
> x <- udpipe_download_model(language = "dutch-lassysmall")
Downloading udpipe model from https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.0/master/inst/udpipe-ud-2.0-170801/dutch-lassysmall-ud-2.0-170801.udpipe to /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/udpipe.Rcheck/dutch-lassysmall-ud-2.0-170801.udpipe
trying URL 'https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.0/master/inst/udpipe-ud-2.0-170801/dutch-lassysmall-ud-2.0-170801.udpipe'
Content type 'application/octet-stream' length 9208258 bytes (8.8 MB)
==================================================
downloaded 8.8 MB

> ud_dutch <- udpipe_load_model(x$file_model)
> txt <- c("Ik ben de weg kwijt, kunt u me zeggen waar de Lange Wapper ligt? Jazeker meneer", 
+          "Het gaat vooruit, het gaat verbazend goed vooruit")
> x <- udpipe_annotate(ud_dutch, x = txt)
> x <- as.data.frame(x)
Error in `[.data.table`(out, , `:=`(paragraph_id, cumsum(is_newparagraph)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: as.data.frame ... as.data.frame.udpipe_connlu -> read_connlu -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Downloading udpipe model from https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.0/master/inst/udpipe-ud-2.0-170801/dutch-ud-2.0-170801.udpipe to /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/udpipe.Rcheck/vign_test/udpipe/vignettes/dutch-ud-2.0-170801.udpipe
trying URL ‘https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.0/master/inst/udpipe-ud-2.0-170801/dutch-ud-2.0-170801.udpipe’
Content type 'application/octet-stream' length 19992491 bytes (19.1 MB)
==================================================
downloaded 19.1 MB

Quitting from lines 93-99 (udpipe-annotation.Rmd) 
Error: processing vignette ‘udpipe-annotation.Rmd’ failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
          user system elapsed
ViSiElse 4.885  0.023   6.665
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: Matrix
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘wgsea.tex’ failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 252.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘yCrypticRNAs-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bam_to_reads
> ### Title: Convert BAM files into BED files containing the reads overlaping
> ###   the specified annotations.
> ### Aliases: bam_to_reads
> 
> ### ** Examples
> 
> bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
> data(annotations)
> bam_to_reads(bamfile, annotations)
Error in FUN(X[[i]], ...) : failed to build index
  file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Calls: bam_to_reads -> .index_bam
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-60 (yCrypticRNAs.Rmd) 
Error: processing vignette ‘yCrypticRNAs.Rmd’ failed with diagnostics:
failed to build index
  file: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/yCrypticRNAs/extdata/wt_rep1.bam
Execution halted
Namespaces in Imports field not imported from:
  ‘httr’ ‘progress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rARPACK’ ‘sparseLDA’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  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 assignments to the global environment:
File ‘AdaptFit/R/aspm.R’:
  assign("group.vec.Handan", group.vec, pos = 1)
  assign("X.Declan", X, pos = 1)
  assign("Z.Jaida", Z, pos = 1)
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
Running examples in ‘AdhereR-Ex.R’ failed
The error most likely occurred in:

> ### Name: CMA1
> ### Title: CMA1 and CMA3 constructors.
> ### Aliases: CMA1 CMA3
> 
> ### ** Examples
> 
> cma1 <- CMA1(data=med.events,
+              ID.colname="PATIENT_ID",
+              event.date.colname="DATE",
+              event.duration.colname="DURATION",
+              followup.window.start=30,
+              observation.window.start=30,
+              observation.window.duration=365,
+              date.format="%m/%d/%Y"
+             );
OMP: Warning #96: Cannot form a team with 18 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).
Error in `[.data.table`(data, , `:=`(c(".FU.START.DATE", ".FU.END.DATE",  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: CMA1 ... compute.event.int.gaps -> .compute.function -> fnc -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
OMP: Warning #96: Cannot form a team with 18 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).
Quitting from lines 188-208 (AdhereR-overview.Rmd) 
Error: processing vignette 'AdhereR-overview.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Found the following significant warnings:
  ADM3.c:34:19: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:31: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:61: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:73: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:57: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:52:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:56: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:42: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:38: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/ADM3.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Error: processing vignette 'AccumulatedLocalEffectPlot.ltx' failed with diagnostics:
Running 'texi2dvi' on 'AccumulatedLocalEffectPlot.ltx' failed.
LaTeX errors:
! Package inputenc Error: Unicode character ̂ (U+302)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode character ̂ (U+302)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode character ̂ (U+302)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode character ̂ (U+302)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package
Execution halted
Running examples in ‘aLFQ-Ex.R’ failed
The error most likely occurred in:

> ### Name: AbsoluteQuantification
> ### Title: Absolute label-free quantification of mass spectrometry
> ###   proteomics experiments
> ### Aliases: AbsoluteQuantification AbsoluteQuantification.default
> ###   predict.AbsoluteQuantification cval cval.default
> ###   cval.AbsoluteQuantification print.AbsoluteQuantification
> ###   plot.AbsoluteQuantification hist.AbsoluteQuantification pivot
> ###   pivot.default pivot.AbsoluteQuantification export export.default
> ###   export.AbsoluteQuantification
> ### Keywords: AbsoluteQuantification absolute label-free quantification
> 
> ### ** Examples
> 
> data(UPS2MS)
> 
> UPS2_SRM<-head(UPS2_SRM,100) # Remove this line for real applications
> data_PI <- ProteinInference(UPS2_SRM)
OMP: Warning #96: Cannot form a team with 8 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).
Error in `[.data.table`(data.dt, , list(min_mean_transition_intensity = min(strictnessfilter.ProteinInference(sort(mean_transition_intensity,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: ProteinInference ... [ -> [.data.table -> eval -> eval -> [ -> [.data.table
Execution halted
Namespaces in Imports field not imported from:
  ‘rjson’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'amap.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte 244.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Argument of \UTFviii@three@octets has an extra }.
<inserted text> 
                \par 
l.12 ...block {\em Revue de Statistique Appliqu<e9>e}
                                                  , 50(4), 2002.
! Paragraph ended before \UTFviii@three@octets was complete.
<to be read again> 
                   \par 
l.12 ...block {\em Re
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Found the following significant warnings:
  matrix.c:629:8: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:631:49: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:632:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/amei.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘unmarked’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘gridExtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘magrittr’
  All declared Imports should be used.
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rgdal’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
Namespace in Imports field not imported from: ‘caret’
  All declared Imports should be used.
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #Copyright © 2016 RTE Réseau de transport d’électricité
  > 
  > require(testthat)
  Loading required package: testthat
  > require(antaresRead)
  Loading required package: antaresRead
  > require(plyr)
  Loading required package: plyr
  > 
  > 
  > #Maybe include this in some test-file.R 
  > #is.solaris<-function(){
  > #  grepl('SunOS',Sys.info()['sysname'])
  > #}
  > 
  > #if(!is.solaris()){
  > 
  > test_check("antaresRead")
  OMP: Warning #96: Cannot form a team with 4 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).
  Error in `[.data.table`(x, , mapply(function(x, f) { : 
    SETLENGTH() cannot be applied to an ALTVEC object.
  Calls: test_check ... eval -> eval -> suppressMessages -> withCallingHandlers
  Execution halted
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for ‘write.table’
runAPSIM: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/aqr.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.2Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 208-211 (data_assertion_intro.Rmd) 
Error: processing vignette 'data_assertion_intro.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.6Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
File ‘audio/libs/audio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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: ‘abind’
  All declared Imports should be used.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Running examples in ‘autoplotly-Ex.R’ failed
The error most likely occurred in:

> ### 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)
We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/ggplot2')`
Error in `[.data.table`(dt, , c(.I, .I[1], NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: autoplotly ... geom2trace.GeomPolygon -> group2NA -> [ -> [.data.table
Execution halted
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   2.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/BAMBI.Rcheck/00install.out’ for details.
installed size is 103.4Mb
  sub-directories of 1Mb or more:
    libs  102.6Mb
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.7Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Running examples in ‘batchtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: Tags
> ### Title: Add or Remove Job Tags
> ### Aliases: Tags addJobTags removeJobTags getUsedJobTags
> 
> ### ** Examples
> 
> tmp = makeRegistry(file.dir = NA, make.default = FALSE)
No configuration file found
Created registry in '/tmp/RtmpavDf9C/registrya1e03c0f4472' using cluster functions 'Interactive'
> ids = batchMap(sqrt, x = -3:3, reg = tmp)
Adding 7 jobs ...
> 
> # Add new tag to all ids
> addJobTags(ids, "needs.computation", reg = tmp)
> getJobTags(reg = tmp)
   job.id              tags
1:      1 needs.computation
2:      2 needs.computation
3:      3 needs.computation
4:      4 needs.computation
5:      5 needs.computation
6:      6 needs.computation
7:      7 needs.computation
> 
> # Add more tags
> addJobTags(findJobs(x < 0, reg = tmp), "x.neg", reg = tmp)
> addJobTags(findJobs(x > 0, reg = tmp), "x.pos", reg = tmp)
> getJobTags(reg = tmp)
Error in `[.data.table`(reg$tags[ids, on = "job.id"], , list(tags = stri_flatten(sort(tag,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: getJobTags -> [ -> [.data.table
Execution halted
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  15.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 58.0Mb
  sub-directories of 1Mb or more:
    libs  57.2Mb
Namespace in Imports field not imported from: ‘inline’
  All declared Imports should be used.
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  24.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   3.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 92.2Mb
  sub-directories of 1Mb or more:
    libs  92.1Mb
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘readxl’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 98.2Mb
  sub-directories of 1Mb or more:
    libs  96.8Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crochet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Running examples in ‘behavr-Ex.R’ failed
The error most likely occurred in:

> ### Name: bin_apply
> ### Title: Bin a variable (typically time) and compute an aggregate for
> ###   each bin
> ### Aliases: bin_apply bin_apply_all
> 
> ### ** Examples
> 
> metadata <- data.frame(id = paste0("toy_experiment|",1:5))
> dt <- toy_activity_data(metadata, duration = days(2))
> 
> # average by 30min time bins, default
> dt_binned <- bin_apply_all(dt, moving)
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).
Error in `[.data.table`(data, , bin_apply(data = .SD, ...), by = eval(data.table::key(data))) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: bin_apply_all -> [ -> [.behavr -> NextMethod -> [.data.table
Execution halted
Running examples in ‘benford.analysis-Ex.R’ failed
The error most likely occurred in:

> ### Name: MAD
> ### Title: Gets the MAD of a Benford object
> ### Aliases: MAD
> 
> ### ** Examples
> 
> data(census.2000_2010) #gets data
> c2010 <- benford(census.2000_2010$pop.2010) #generates benford object
Error in `[.data.table`(DF, , length(x) - 1, by = v) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: benford ... generate.empirical.distribution -> [ -> [.data.table
Execution halted
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
Error in re-building vignettes:
  ...
Loading required package: leaps
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SimExperimentBICq.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 150.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 144.8Mb
  sub-directories of 1Mb or more:
    include  144.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/biclust.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.5Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  28.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:172:13: warning: variable length arrays are a C99 feature [-Wvla-extension]
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:220:16: warning: variable length arrays are a C99 feature [-Wvla-extension]
See ‘/data/gannet/ripley/R/packages/tests-clang/bigrquery.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lattice’ ‘zoo’
  All declared Imports should be used.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   8.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Error in re-building vignettes:
  ...
Parsed with column specification:
cols(
  .default = col_character(),
  X1271 = col_double(),
  X1272 = col_double(),
  X1273 = col_double(),
  X1274 = col_double(),
  X1275 = col_double(),
  X1276 = col_double(),
  X1277 = col_double(),
  X1278 = col_double(),
  X1279 = col_double(),
  X1280 = col_double(),
  X1281 = col_double(),
  X1282 = col_double(),
  X1283 = col_double(),
  X1284 = col_double(),
  X1285 = col_double(),
  X1286 = col_double(),
  X1287 = col_double(),
  X1288 = col_double(),
  X1289 = col_double(),
  X1290 = col_double()
  # ... with 337 more columns
)
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(),
  UNIT_MEASURE = col_integer(),
  `Unit of measure` = 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:
Evaluation error: yearmon variable can only have one format.
Execution halted
Package suggested but not available for checking: ‘RQuantLib’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RGtk2’ ‘cairoDevice’ ‘ergm’ ‘foreign’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘haven’ ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
installed size is 43.7Mb
  sub-directories of 1Mb or more:
    libs  42.6Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Namespace in Imports field not imported from: ‘plm’
  All declared Imports should be used.
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
Found the following significant warnings:
  conditional.least.squares.c:232:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:233:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:234:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/bnlearn.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./sampling.h:84:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/BNSP.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘yaml’
  All declared Imports should be used.
installed size is 376.8Mb
  sub-directories of 1Mb or more:
    include    3.2Mb
    lib      373.3Mb
installed size is 84.6Mb
  sub-directories of 1Mb or more:
    libs  84.1Mb
Running examples in ‘BoomSpikeSlab-Ex.R’ failed
The error most likely occurred in:

> ### Name: qreg.spike
> ### Title: Quantile Regression
> ### Aliases: qreg.spike
> ### Keywords: models regression
> 
> ### ** Examples
> 
>   n <- 50
>   x <- rnorm(n)
>   y <- rnorm(n, 4 * x)
>   model <- qreg.spike(y ~ x,
+                       quantile = .8,
+                       niter = 1000,
+                       expected.model.size = 100)
=-=-=-=-= Iteration 0 Wed May  2 15:19:03 2018 =-=-=-=-=
=-=-=-=-= Iteration 100 Wed May  2 15:19:03 2018 =-=-=-=-=
=-=-=-=-= Iteration 200 Wed May  2 15:19:03 2018 =-=-=-=-=
=-=-=-=-= Iteration 300 Wed May  2 15:19:03 2018 =-=-=-=-=
=-=-=-=-= Iteration 400 Wed May  2 15:19:03 2018 =-=-=-=-=
=-=-=-=-= Iteration 500 Wed May  2 15:19:03 2018 =-=-=-=-=
=-=-=-=-= Iteration 600 Wed May  2 15:19:03 2018 =-=-=-=-=
=-=-=-=-= Iteration 700 Wed May  2 15:19:03 2018 =-=-=-=-=
=-=-=-=-= Iteration 800 Wed May  2 15:19:03 2018 =-=-=-=-=
=-=-=-=-= Iteration 900 Wed May  2 15:19:03 2018 =-=-=-=-=
Error in ans[negative] <- -(1 - quantile) * u[negative] : 
  NAs are not allowed in subscripted assignments
Calls: qreg.spike -> rowSums -> is.data.frame -> CheckFunction
Execution halted
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘tidyr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  29.7Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     3.3Mb
    doc   2.4Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'brms_overview.ltx' failed with diagnostics:
Running 'texi2dvi' on 'brms_overview.ltx' failed.
LaTeX errors:
! Undefined control sequence.
\UseRawInputEncoding ...tencodingname \@undefined 
                                                  \let \DeclareFontEncoding@...
l.59 \begin{document}
                     
! Missing \endcsname inserted.
<to be read again> 
                   \protect 
l.59 \begin{document}
                     
! Missing \endcsname inserted.
<to be read again> 
                   \cdp@elt 
l.59 \begin{document}
                     
! Missing \endcsname inserted.
<to be read again> 
                   \cdp@elt 
l.59 \begin{document}
                     
! Extra \else.
\@changed@cmd ... #1\expandafter \endcsname \else 
                                                  \noexpand #1\fi 
l.59 \begin{document}
                     
! Missing \endcsname inserted.
<to be read again> 
                   \def 
l.59 \begin{document}
           
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    bin    2.2Mb
    doc    1.1Mb
    libs   2.2Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  helpers.c:365:19: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of type 'float' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/BSquare.Rcheck/00install.out’ for details.
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    libs  31.2Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/bsts.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Running examples in ‘BTYDplus-Ex.R’ failed
The error most likely occurred in:

> ### Name: abe.GenerateData
> ### Title: Simulate data according to Pareto/NBD (Abe) model assumptions
> ### Aliases: abe.GenerateData
> 
> ### ** Examples
> 
> # generate artificial Pareto/NBD (Abe) with 2 covariates
> params <- list()
> params$beta  <- matrix(c(0.18, -2.5, 0.5, -0.3, -0.2, 0.8), byrow = TRUE, ncol = 2)
> params$gamma <- matrix(c(0.05, 0.1, 0.1, 0.2), ncol = 2)
> data <- abe.GenerateData(n = 2000, T.cal = 32, T.star = 32, params)
Error in `[.data.table`(elog_dt, , `:=`(first, min(date)), by = "cust") : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: abe.GenerateData -> elog2cbs -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 41-47 (BTYDplus-HowTo.Rmd) 
Error: processing vignette 'BTYDplus-HowTo.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.7Mb
    libs   1.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R        1.0Mb
    data     1.5Mb
    models   2.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Found the following significant warnings:
  slpcovis.cpp:381:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/catlearn.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Namespace in Imports field not imported from: ‘prettydoc’
  All declared Imports should be used.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘plot’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘plot’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Found the following significant warnings:
  ./MCMC_prob.h:2091:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/CCMnet.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘purrr’ ‘roxygen2’
  All declared Imports should be used.
Running examples in ‘CDECRetrieve-Ex.R’ failed
The error most likely occurred in:

> ### Name: cdec_available
> ### Title: Function returns a dataframe of the available data
> ### Aliases: cdec_available
> 
> ### ** Examples
> 
> # get a list of dataframes available for CCR
> cdec_datasets("ccr")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10000 milliseconds
Calls: cdec_datasets ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.1Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of 'int' to
  'interval'
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of 'label' to 'labels'
plot.cggd: no visible global function definition for ‘gen.beta’
plotCVcggd: no visible binding for global variable ‘cv’
plotCVcggd: no visible binding for global variable ‘cv.error’
predict.cggd: no visible binding for global variable ‘max.tk’
predict.cggd: no visible global function definition for ‘gen.beta’
Undefined global functions or variables:
  cv cv.error gen.beta max.tk
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/changepoint.np.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘foreach’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tools’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Files which contain pragma(s) suppressing diagnostics:
  ‘src/cld_3/protos/feature_extractor.pb.h’
  ‘src/cld_3/protos/sentence.pb.h’ ‘src/cld_3/protos/task_spec.pb.h’
Running examples in ‘cleanEHR-Ex.R’ failed
The error most likely occurred in:

> ### Name: ccRecord-class
> ### Title: The S4 class which holds all the CCHIC patient record - served
> ###   as a database.
> ### Aliases: ccRecord ccRecord-class
> 
> ### ** Examples
> 
> heart_rate <- data.frame(seq(10), rep(70, 10)) # NIHR_HIC_ICU_0108
> site_id <- "Q70" #  NIHR_HIC_ICU_0002
> episode_id <- "0000001" # NIHR_HIC_ICU_0005
> 
> # Create a new episode 
> ep <- new.episode(list(NIHR_HIC_ICU_0108=heart_rate, 
+                          NIHR_HIC_ICU_0002=site_id, 
+                          NIHR_HIC_ICU_0005=episode_id)) 
> 
> # modifying records 
> rec <- ccRecord() # a new record 
> rec <- rec + ep # adding a new episode to the record
> rec <- rec + NULL # adding nothing to the record
> rec <- rec + rec # adding a record to a record
Error in `[.data.table`(id, , `:=`("pid", .GRP), by = "id") : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: + -> + -> index.record -> [ -> [.data.table
Execution halted
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sp’
  All declared Imports should be used.
Running examples in ‘clickstream-Ex.R’ failed
The error most likely occurred in:

> ### Name: MarkovChain-class
> ### Title: Class 'MarkovChain'
> ### Aliases: MarkovChain-class
> ### Keywords: classes
> 
> ### ** Examples
> 
> 
> # show MarkovChain definition
> showClass("MarkovChain")
Class "MarkovChain" [package "clickstream"]

Slots:
                                                                           
Name:                  states                  order            transitions
Class:              character                numeric                   list
                                                                           
Name:                  lambda          logLikelihood           observations
Class:                numeric                numeric                numeric
                                                                           
Name:                   start                    end        transientStates
Class:                  table                  table              character
                                                    
Name:         absorbingStates absorbingProbabilities
Class:              character             data.frame
> 
> # fit a simple Markov chain from a list of click streams
> 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)
Error in `[.data.table`(dat, , eval(fun.call), by = c(varnames)) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: fitMarkovChain ... as.data.frame -> dcast.data.table -> [ -> [.data.table
Execution halted
Namespaces in Imports field not imported from:
  ‘R6’ ‘infuser’ ‘purrr’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data     3.5Mb
    exdata   5.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.1Mb
Error in re-building vignettes:
  ...
Quitting from lines 30-36 (coala-data-import.Rmd) 
Error: processing vignette 'coala-data-import.Rmd' failed with diagnostics:
there is no package called 'PopGenome'
Execution halted
Namespaces in Imports field not imported from:
  ‘graphics’ ‘pander’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 79-80 (codemeta-intro.Rmd) 
Error: processing vignette 'codemeta-intro.Rmd' failed with diagnostics:
GitHub API error (403): 403 Forbidden
  API rate limit exceeded for 163.1.211.17. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)
Execution halted
Namespaces in Imports field not imported from:
  ‘geometry’ ‘parallel’ ‘plot3D’ ‘reshape2’
  All declared Imports should be used.
Running examples in ‘CoDiNA-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.igraph
> ### Title: as.igraph
> ### Aliases: as.igraph
> 
> ### ** Examples
> 
> #' set.seed(123)
> Nodes = LETTERS[1:10]
> Net1 = data.frame(Node.1 = sample(Nodes) , Node.2 = sample(Nodes), wTO = runif(10,-1,1))
> Net2 = data.frame(Node.1 = sample(Nodes) , Node.2 = sample(Nodes), wTO = runif(10,-1,1))
> Net3 = data.frame(Node.1 = sample(Nodes) , Node.2 = sample(Nodes), wTO = runif(10,-1,1))
> DiffNet = makeDiffNet (x = list(Net1,Net2,Net3), Code = c('Net1', 'Net2', 'Net3') )
Starting now.
1
Edges: 10
2
Edges: 10
3
Edges: 10
Warning in CreateFullBase(x = x, Code = Code) :
  You have duplicated links. Results will be presented, but you should double check your input.
Total of nodes: 10
Total of edges: 23
Coding correlations.
Starting Phi categorization.
Coding the groups.
Recode is done!
Error in `[.data.table`(y, , `:=`(distance_Phi_tilda, normalize(dist_center)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: makeDiffNet -> [ -> [.data.table
Execution halted
Namespaces in Imports field not imported from:
  ‘flashClust’ ‘speedglm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rscala’
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/CompRandFld.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 36-42 (comtradr-vignette.Rmd) 
Error: processing vignette 'comtradr-vignette.Rmd' failed with diagnostics:
too few arguments
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Running examples in ‘constellation-Ex.R’ failed
The error most likely occurred in:

> ### Name: incidents
> ### Title: Identify incident events separated by a minimum time window
> ### Aliases: incidents
> 
> ### ** Examples
> 
> library(data.table)
> systolic_bp <- as.data.table(vitals[VARIABLE == "SYSTOLIC_BP"])
> systolic_bp[, RECORDED_TIME := as.POSIXct(RECORDED_TIME,
+   format = "%Y-%m-%dT%H:%M:%SZ", tz = "UTC")]
> 
> # Identify systolic blood pressure measurements for each patient that are
>  # separated by at least 24 hours
> incidents(systolic_bp, window_hours = 24, join_key = "PAT_ID",
+  time_var = "RECORDED_TIME")
Error in `[.data.table`(data, , `:=`(KEEP, get(time_var) >= (get(time_var)[1] +  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: incidents -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 70-76 (identify_sepsis.Rmd) 
Error: processing vignette 'identify_sepsis.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘MASS’ ‘geepack’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
Namespaces in Imports field not imported from:
  ‘Rtsne’ ‘scatterplot3d’
  All declared Imports should be used.
Running examples in ‘CorporaCoCo-Ex.R’ failed
The error most likely occurred in:

> ### Name: surface
> ### Title: Calculate Surface Co-occurrence Counts
> ### Aliases: surface
> 
> ### ** Examples
> 
>     # =====================
>     # surface co-occurrence
>     # =====================
> 
>     x <- c("a", "man", "a", "plan", "a", "canal", "panama")
>     surface(x, span = '2R')
Error in `[.data.table`(DT, !is.na(x) & !is.na(y), `:=`(M, sum(H) - H),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: surface -> [ -> [.data.table
Execution halted
Running examples in ‘corpustools-Ex.R’ failed
The error most likely occurred in:

> ### Name: summary.featureHits
> ### Title: S3 summary for featureHits class
> ### Aliases: summary.featureHits
> 
> ### ** Examples
> 
> text = c('A B C', 'D E F. G H I', 'A D', 'GGG')
> tc = create_tcorpus(text, doc_id = c('a','b','c','d'), split_sentences = TRUE)
> hits = tc$search_features(c('query label# A AND B', 'second query# (A AND Q) OR ("D E") OR I'))
created index for "token" column
> 
> summary(hits)
Error in `[.data.table`(data.table(object$hits), , list(hits = length(unique(hit_id)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: summary ... summary -> summary.featureHits -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 92-95 (corregp.Rnw) 
Error: processing vignette 'corregp.Rnw' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.5Mb
Namespace in Imports field not imported from: ‘xtable’
  All declared Imports should be used.
Package in Depends field not imported from: ‘calibrate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.2Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
Found the following significant warnings:
  ./bdsmatrix_stub.h:44:11: warning: incompatible pointer to integer conversion returning 'int *' from a function with result type 'int'; dereference with * [-Wint-conversion]
  ./bdsmatrix_stub.h:53:11: warning: incompatible pointer to integer conversion returning 'int *' from a function with result type 'int'; dereference with * [-Wint-conversion]
  ./bdsmatrix_stub.h:100:11: warning: incompatible pointer types returning 'double *' from a function with result type 'double **' [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-clang/coxme.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 38.8Mb
  sub-directories of 1Mb or more:
    libs  38.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/cplm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
QR.cd: no visible global function definition for ‘quantile’
QR.lasso.cd: no visible global function definition for ‘quantile’
cqr.cd: no visible global function definition for ‘quantile’
cqr.lasso.cd: no visible global function definition for ‘quantile’
cqr.lasso.mm: no visible global function definition for ‘quantile’
cqr.mm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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   4.7Mb
Note: found 4 marked Latin-1 strings
  Note: found 25 marked UTF-8 strings
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘AnnotationDbi’ ‘clusterProfiler’ ‘org.Hs.eg.db’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
Namespace in Imports field not imported from: ‘httpcode’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qte’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.9Mb
Note: found 59670 marked Latin-1 strings
  Note: found 16 marked UTF-8 strings
Found the following significant warnings:
  ./ctl.h:38:23: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
  ./ctl.h:36:25: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
See ‘/data/gannet/ripley/R/packages/tests-clang/ctl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/ctsem.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    extdata  31.9Mb
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   5.1Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
Running examples in ‘datadr-Ex.R’ failed
The error most likely occurred in:

> ### Name: addTransform
> ### Title: Add a Transformation Function to a Distributed Data Object
> ### Aliases: addTransform
> 
> ### ** Examples
> 
> # Create a distributed data frame using the iris data set, backed by the
> # kvMemory (in memory) connection
> bySpecies <- divide(iris, by = "Species")
OMP: Warning #96: Cannot form a team with 5 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).
Error in `[.data.table`(d, , ff(.SD), by = key(d), .SDcols = nms) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: divide -> getDivideDF -> [ -> [.data.table
Execution halted
Running examples in ‘DataExplorer-Ex.R’ failed
The error most likely occurred in:

> ### Name: group_category
> ### Title: Group categories for discrete features
> ### Aliases: group_category CollapseCategory
> ### Keywords: group_category
> 
> ### ** Examples
> 
> # load packages
> library(data.table)
> 
> # generate data
> data <- data.table("a" = as.factor(round(rnorm(500, 10, 5))), "b" = rexp(500, 1:500))
> 
> # view cumulative frequency without collpasing categories
> group_category(data, "a", 0.2)
     a cnt   pct cum_pct
 1:  8  50 0.100   0.100
 2: 10  42 0.084   0.184
 3: 13  39 0.078   0.262
 4:  9  39 0.078   0.340
 5: 12  38 0.076   0.416
 6:  7  36 0.072   0.488
 7: 11  27 0.054   0.542
 8: 15  26 0.052   0.594
 9: 14  25 0.050   0.644
10:  6  23 0.046   0.690
11:  5  19 0.038   0.728
12: 17  18 0.036   0.764
13:  4  18 0.036   0.800
> 
> # view cumulative frequency based on another measure
> group_category(data, "a", 0.2, measure = "b")
Error in `[.data.table`(data, , list(cnt = sum(get(measure))), by = feature) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: group_category -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Warning in cor(final_data, ...) : the standard deviation is zero
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).
Warning: Removed 464016 rows containing non-finite values (stat_boxplot).
Warning: Removed 76619 rows containing missing values (geom_point).
Warning: Removed 28290 rows containing missing values (geom_point).
Quitting from lines 187-188 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
.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.
Error in re-building vignettes:
  ...
Quitting from lines 50-72 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
cannot open the connection to 'https://raw.githubusercontent.com/JohnCoene/projects/gh-pages/htmlwidgets/echarts/data/sessions.csv'
Execution halted
Running examples in ‘dataPreparation-Ex.R’ failed
The error most likely occurred in:

> ### Name: aggregateByKey
> ### Title: Automatic dataSet aggregation by key
> ### Aliases: aggregateByKey
> 
> ### ** Examples
> 
> # Get generic dataset from R
> data("adult")
> 
> # Aggregate it using aggregateByKey, in order to extract characteristics for each country
> adult_aggregated <- aggregateByKey(adult, key = 'country')
[1] "aggregateByKey: I start to aggregate"
Error in `[.data.table`(dataSet, , .(mean.age = mean(get(col)), min.age = min(get(col)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Error in `[.data.table`(dat, , eval(fun.call), by = c(varnames)) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: aggregateByKey ... aggregateAcolumn -> dcast.data.table -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Loading required package: lubridate

Attaching package: 'lubridate'

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

    date

Loading required package: stringr
Loading required package: Matrix
Loading required package: progress
dataPreparation 0.3.5
Type dataPrepNews() to see new features/changes/bug fixes.

Attaching package: 'data.table'

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

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

Quitting from lines 253-254 (dataPreparation.Rmd) 
Error: processing vignette 'dataPreparation.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is 61.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  59.3Mb
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
Running examples in ‘data.table-Ex.R’ failed
The error most likely occurred in:

> ### Name: :=
> ### Title: Assignment by reference
> ### Aliases: := set
> ### Keywords: data
> 
> ### ** Examples
> 
> DT = data.table(a = LETTERS[c(3L,1:3)], b = 4:7)
> DT[, c := 8]                # add a numeric column, 8 for all rows
> DT[, d := 9L]               # add an integer column, 9L for all rows
> DT[, c := NULL]             # remove column c
> DT[2, d := -8L]             # subassign by reference to d; 2nd row is -8L now
> DT                          # DT changed by reference
   a b  d
1: C 4  9
2: A 5 -8
3: B 6  9
4: C 7  9
> DT[2, d := 10L][]           # shorthand for update and print
   a b  d
1: C 4  9
2: A 5 10
3: B 6  9
4: C 7  9
> 
> DT[b > 4, b := d * 2L]      # subassign to b with d*2L on those rows where b > 4 is TRUE
> DT[b > 4][, b := d * 2L]    # different from above. [, := ] is performed on the subset
>                             # which is an new (ephemeral) data.table. Result needs to be
>                             # assigned to a variable (using `<-`).
> 
> DT[, e := mean(d), by = a]  # add new column by group by reference
Error in `[.data.table`(DT, , `:=`(e, mean(d)), by = a) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$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 129-137 (datatable-faq.Rmd) 
Error: processing vignette 'datatable-faq.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Error in re-building vignettes:
  ...
OMP: Warning #96: Cannot form a team with 7 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).
Quitting from lines 57-64 (applications.Rmd) 
Error: processing vignette 'applications.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
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').
Running examples in ‘dblr-Ex.R’ failed
The error most likely occurred in:

> ### Name: dblr_train
> ### Title: Discrete Boosting Logistic Regression Training
> ### Aliases: dblr_train
> 
> ### ** Examples
> 
> # use iris data for example
> dat <- iris
> # create two categorical variables
> dat$Petal.Width <- as.factor((iris$Petal.Width<=0.2)*1+(iris$Petal.Width>1.0)*2)
> dat$Sepal.Length <- (iris$Sepal.Length<=3.0)*2+(iris$Sepal.Length>6.0)*1.25
> # create the response variable
> dat$Species <- as.numeric(dat$Species=='versicolor')
> set.seed(123)
> # random sampling
> index <- sample(1:150,100,replace = FALSE)
> # train the dblr model using the training data
> dblr_fit <- dblr_train(train_x=dat[index,c(1:4)],
+ train_y=dat[index,5],category_cols = c('Petal.Width','Sepal.Length'),
+ metric = 'logloss',subsample = 0.5,eta = 0.05,colsample = 1.0,
+ lambda = 1.0,cv_early_stops = 10,verbose=FALSE)
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).
Error in `[.data.table`(trees_nodes_0, , `:=`(vl = cumsum(l[.N:1])[.N:1],  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: dblr_train -> [ -> [.data.table
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   6.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘gridExtra’ ‘latticeExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘CDM’
  All declared Imports should be used.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
Namespace in Imports field not imported from: ‘oz’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘UScensus2010’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘JavaGD’ ‘OpenStreetMap’ ‘maptools’ ‘rgdal’ ‘scales’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Found the following significant warnings:
  DEploid/updateHap.cpp:670:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:678:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:681:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:682:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/DEploid.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Error in re-building vignettes:
  ...
Quitting from lines 133-140 (DescriptiveStatsObeu.Rmd) 
Error: processing vignette 'DescriptiveStatsObeu.Rmd' failed with diagnostics:
Required package curl not found. Please run: install.packages('curl')
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.4Mb
    libs   1.6Mb
Packages suggested but not available for checking: ‘gurobi’ ‘Rcplex’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    libs  45.9Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  17.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Running examples in ‘dgo-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgirt_fit-class
> ### Title: A class for fitted dynamic group IRT models
> ### Aliases: dgirt_fit-class dgirt_fit
> 
> ### ** Examples
> 
> data(toy_dgirtfit)
> # summarize the fitted results
> summary(toy_dgirtfit, pars = 'xi')
dgirt samples from 4 chains of 400 iterations, 200 warmup, thinned every 1 
  Drawn Fri Dec  1 11:54:14 2017 
  Package version 0.2.13 
  Model version 2017_01_04 
  43 parameters; 12 theta_bars (year state race3)
  2 periods 2009 to 2010 

n_eff
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  94.08  149.33  174.47  270.79  363.04  800.00 

Rhat
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.9971  1.0082  1.0225  1.0202  1.0291  1.0520 

Elapsed time
   chain warmup sample total
1:     1     5S     3S    8S
2:     2     5S     5S   10S
3:     3     5S     6S   11S
4:     4     5S     3S    8S
> 
> # get posterior means with a convenience function
> get_posterior_mean(toy_dgirtfit, pars = 'theta_bar')
OMP: Warning #96: Cannot form a team with 10 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).
Error in `[.data.table`(samples, , do_funs(list(value), funs), by = c(attr(samples,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: get_posterior_mean ... summarize -> summarize -> .local -> [ -> [.data.table
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dgo)
  Loading required package: dgodata
  Loading required package: rstan
  Loading required package: ggplot2
  Loading required package: StanHeaders
  rstan (Version 2.17.3, 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)
  > 
  > # https://stackoverflow.com/questions/12410694/rbundler-build-error-cannot-open-file-startup-rs-no-such-file-or-directory#27994299
  > Sys.setenv("R_TESTS" = "")
  > test_check("dgo")
  Error in `[.data.table`(item_data, , lapply(.SD, function(x) sum(!is.na(x)) >  : 
    SETLENGTH() cannot be applied to an ALTVEC object.
  Calls: test_check ... restrict_items -> drop_items_rare_in_time -> [ -> [.data.table
  Execution halted
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/dhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Sampling sensitivity with m=500 gamma=0.2 k=439
Sampling sensitivity with m=285 gamma=0.1 k=285
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).
Quitting from lines 296-310 (diffpriv.Rnw) 
Error: processing vignette 'diffpriv.Rnw' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    include  19.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   2.8Mb
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   5.8Mb
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 28.6Mb
  sub-directories of 1Mb or more:
    libs  26.5Mb
Namespaces in Imports field not imported from:
  ‘bit64’ ‘rstudioapi’ ‘tidyverse’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.5Mb
Found the following significant warnings:
  compnoreggilks.cpp:31:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compnoreggilks.cpp:90:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:32:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:88:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:150:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:207:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:380:8: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/DPWeibull.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shapefiles’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.1Mb
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  16.9Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘tools’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Running examples in ‘easycsv-Ex.R’ failed
The error most likely occurred in:

> ### Name: fread_folder
> ### Title: read multiple csv files into named data frames
> ### Aliases: fread_folder
> ### Keywords: ~utilities ~misc
> 
> ### ** Examples
> 
>   require(easycsv)
>   require("data.table")
>   directory = getwd()
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/table1.csv"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/table2.csv"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/table3.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/table4.txt"))
>   fread_folder(directory, extension = "BOTH")
Error in data.table::fread(input = tbl, sep = sep, nrows = nrows, header = header,  : 
  isTrueFalse(showProgress) is not TRUE
Calls: fread_folder -> <Anonymous> -> stopifnot
Execution halted
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’ ‘scales’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘base64enc’ ‘knitr’ ‘markdown’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘easySdcTable-Ex.R’ failed
The error most likely occurred in:

> ### Name: ProtectTable
> ### Title: Easy interface to sdcTable: Table suppression according to a
> ###   frequency rule.
> ### Aliases: ProtectTable
> 
> ### ** Examples
> 
>  # ==== Example 1 , 8 regions ====
>  z1 <- EasyData("z1")        
>  ProtectTable(z1,1:2,3)
...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).
.Error in `[.data.table`(subDat, , eval(expr), by = key(subDat)) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: ProtectTable ... c_quick_suppression -> c_quick_suppression -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-2>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-3>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-4>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-5>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-6>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

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).
Quitting from lines 67-68 (easySdcTableVignette.Rmd) 
Error: processing vignette 'easySdcTableVignette.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    hac    4.0Mb
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
Running examples in ‘edarf-Ex.R’ failed
The error most likely occurred in:

> ### Name: partial_dependence
> ### Title: Partial dependence using random forests
> ### Aliases: partial_dependence
> 
> ### ** Examples
> 
> library(randomForest)
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
> library(edarf)
> 
> data(iris)
> data(swiss)
> 
> ## classification
> fit = randomForest(Species ~ ., iris)
> pd = partial_dependence(fit, c("Sepal.Width", "Sepal.Length"),
+   data = iris[, -ncol(iris)])
OMP: Warning #96: Cannot form a team with 4 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).
Error in `[.data.table`(mp, , as.list(unlist(lapply(.SD, aggregate.fun))),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: partial_dependence ... renameColumns.randomForest -> do.call -> marginalPrediction -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
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.
OMP: Warning #96: Cannot form a team with 7 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).
Quitting from lines 35-38 (filters.Rmd) 
Error: processing vignette 'filters.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Running examples in ‘EdSurvey-Ex.R’ failed
The error most likely occurred in:

> ### Name: subset.edsurvey.data.frame
> ### Title: Subset the rows of an 'edsurvey.data.frame'.
> ### Aliases: subset.edsurvey.data.frame subset,edsurvey.data.frame-method
> ###   subset,light.edsurvey.data.frame-method
> 
> ### ** Examples
> 
> # read in the example data (generated, not real student data)
> sdf <- readNAEP(system.file("extdata/data", "M36NT2PM.dat", package = "NAEPprimer"))
> 
> # table to compare to subsequent tables with subsets:
> edsurveyTable(composite ~ dsex, data=sdf, returnMeans=FALSE, returnSepct=FALSE)
Error in `[.data.table`(setDT(copy(data)), , .(origwt = sumna(origwt)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: edsurveyTable ... fastAgg -> eval -> eval -> as.data.frame -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 162-164 (v1edsurvey.Rmd) 
Error: processing vignette 'v1edsurvey.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.2Mb
Running examples in ‘eechidna-Ex.R’ failed
The error most likely occurred in:

> ### Name: hexDat
> ### Title: Electorate hexagon data in a tidy form
> ### Aliases: hexDat
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(hexDat)
> library(plotly)
Loading required package: ggplot2

Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

    last_plot

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

    filter

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

    layout

> p <- ggplot(hexDat, aes(xcent, ycent, text = Electorate)) + 
+   geom_hex(stat = "identity") + 
+   lims(x=c(-80, 8), y=c(-40, 50))
> ggplotly(p, tooltip = "text")
We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/ggplot2')`
Error in `[.data.table`(dt, , c(.I, .I[1], NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: ggplotly ... geom2trace.GeomPolygon -> group2NA -> [ -> [.data.table
Execution halted
Running ‘test-all.R’ [17s/19s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  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).
  ── 1. Error: Zed (@test-calculators.R#169)  ────────────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: moves_calc(df) at testthat/test-calculators.R:169
  2: dt[, `:=`(moves, school_switch(.SD)), by = sid]
  3: `[.data.table`(dt, , `:=`(moves, school_switch(.SD)), by = sid)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 504 SKIPPED: 0 FAILED: 1
  1. Error: Zed (@test-calculators.R#169) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: ggplot2
OMP: Warning #96: Cannot form a team with 4 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).
Quitting from lines 72-87 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is 53.9Mb
  sub-directories of 1Mb or more:
    libs  53.2Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Namespaces in Imports field not imported from:
  ‘graphics’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  16.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    xsd   5.4Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Note: found 23639 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘BiocParallel’ ‘broom’ ‘reshape2’ ‘rmarkdown’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    3.3Mb
    help   3.4Mb
Found the following significant warnings:
  input2.c:767:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/epanet2toolkit.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘ROCR’ ‘c060’ ‘methods’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
OMP: Warning #96: Cannot form a team with 16 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).

Error: processing vignette 'flup.rnw' failed with diagnostics:
 chunk 11 
Error in `[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Namespaces in Imports field not imported from:
  ‘llogistic’ ‘logitnorm’
  All declared Imports should be used.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘searcher’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘modelr’
  All declared Imports should be used.
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(eurostat)
  > 
  > test_check("eurostat")
  trying URL 'http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ftsdtr210.tsv.gz'
  downloaded 17 KB
  
  ── 1. Error: (unknown) (@test-all.R#112)  ──────────────────────────────────────
  tsdtr210 does not exist or is not readable
  1: get_eurostat("tsdtr210", type = "label", keepFlags = T, cache = FALSE) at testthat/test-all.R:112
  2: get_eurostat_raw(id)
  3: stop(id, " does not exist or is not readable")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 14 FAILED: 1
  1. Error: (unknown) (@test-all.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/eVenn.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘openxlsx’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in ‘expss-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_rows
> ### Title: Add rows to data.frame/matrix/table
> ### Aliases: add_rows add_rows.data.frame %add_rows% .add_rows
> 
> ### ** Examples
> 
> a = data.frame(x = 1:5, y = 6:10)
> b = data.frame(y = 6:10, z = 11:15)
> 
> add_rows(a, b) # x, y, z
    x  y  z
1   1  6 NA
2   2  7 NA
3   3  8 NA
4   4  9 NA
5   5 10 NA
6  NA  6 11
7  NA  7 12
8  NA  8 13
9  NA  9 14
10 NA 10 15
> a %add_rows% b # the same result
    x  y  z
1   1  6 NA
2   2  7 NA
3   3  8 NA
4   4  9 NA
5   5 10 NA
6  NA  6 11
7  NA  7 12
8  NA  8 13
9  NA  9 14
10 NA 10 15
> 
> add_rows(a, b, nomatch_columns = "drop")  # y
    y
1   6
2   7
3   8
4   9
5  10
6   6
7   7
8   8
9   9
10 10
> 
> # simple tables
> data(mtcars)
> # apply labels
> mtcars = apply_labels(mtcars,
+                 mpg = "Miles/(US) gallon",
+                 cyl = "Number of cylinders",
+                 disp = "Displacement (cu.in.)",
+                 hp = "Gross horsepower",
+                 drat = "Rear axle ratio",
+                 wt = "Weight (lb/1000)",
+                 qsec = "1/4 mile time",
+                 vs = "V/S",
+                 vs = c("V-engine" = 0, "Straight engine" = 1),
+                 am = "Transmission (0 = automatic, 1 = manual)",
+                 am = c(automatic = 0, manual = 1),
+                 gear = "Number of forward gears",
+                 carb = "Number of carburetors"
+ )
> 
> tbl_mean = calculate(mtcars, cro_mean(cyl, am))
Error in `[.data.table`(raw_data, , lapply(.SD, fun), by = by_string) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: calculate ... lapply -> FUN -> elementary_cro_fun_df -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
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.

Use 'expss_output_rnotebook()' to display tables inside R Notebooks.
 To return to the console output, use 'expss_output_default()'.

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.
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).
Quitting from lines 79-138 (tables-with-labels.Rmd) 
Error: processing vignette 'tables-with-labels.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Namespace in Imports field not imported from: ‘refund’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forcats’ ‘formula.tools’
  All declared Imports should be used.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.1Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
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.
Namespace in Imports field not imported from: ‘whisker’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 53.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  50.6Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   7.1Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘cellranger’ ‘knitr’
  All declared Imports should be used.
Found the following significant warnings:
  ff.cpp:256:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ff.cpp:256:54: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/ff.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Namespace in Imports field not imported from: ‘desc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘rappdirs’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
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
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Namespaces in Imports field not imported from:
  ‘base’ ‘pbapply’ ‘stringr’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/frailtyHL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Running examples in ‘FREddyPro-Ex.R’ failed
The error most likely occurred in:

> ### Name: buildTimestamp
> ### Title: Build a timestamp
> ### Aliases: buildTimestamp
> 
> ### ** Examples
> 
> ## Load the data
> data(fluxes)
> 
> ## Clean fluxes
> fluxes=cleanFluxes(fluxes,sdCor=TRUE,sdTimes=3,timesList=3,distCor=TRUE,
+                    thresholdList=list(H=c(-100,1000),LE=c(-100,1000)))	
> 
> ## Remove some line as an example
> fluxes=fluxes[-c(832,833,834,835,840,953),]
> 
> ## Create timestamp from date and time
> fluxes=createTimestamp(fluxes)
> 
> ## Now fill the gap timestmaps with NA's
> fluxes=fillTimestamp(fluxes,flux=TRUE)
[1] Discontinuity in 3 instances
[1] 2014-06-14 03:30:00 UTC 2014-06-14 06:00:00 UTC 2014-06-16 14:30:00 UTC
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: fillTimestamp ... shift_time -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
Found the following significant warnings:
  psplines.c:975:16: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  psplines.c:1087:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/freeknotsplines.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
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  7.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.8Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘grDevices’ ‘graphics’ ‘matrixStats’ ‘stats’
  All declared Imports should be used.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Running examples in ‘funcy-Ex.R’ failed
The error most likely occurred in:

> ### Name: funcyOutList-class
> ### Title: Class '"funcyOutList"'
> ### Aliases: funcyOutList-class funcyOutList
> ### Keywords: classes
> 
> ### ** Examples
> 
> set.seed(2808)
> ds <- sampleFuncy(obsNr=30, k=4, timeNr=7)
> data <- Data(ds)
> clusters <- Cluster(ds)
> 
> res <- funcit(data=data, clusters=clusters, seed=2808,
+               methods=1:5, k=4, parallel=TRUE)
4 : * *Warning in funclustWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  It is not possible to set a seed for method funclust.
4 :Loading required namespace: funHDDC
 * * *Warning in funHDDCWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  Clustering with 4 classes is not possible. 3 clusters are used!
Warning in Funclustering::funclust(fd = fd, K = k, thd = thd, increaseDimension = increaseDimension,  :
  Convergence of the algorithm to a solution with at least one empty cluster.
            Restart or a choose a smaller value for K = 4
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 3 classes is not possible. 2 clusters are used!
 *Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 2 classes is not possible. 1 clusters are used!

Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 1 classes is not possible. 0 clusters are used!

Error in funcit(data = data, clusters = clusters, seed = 2808, methods = 1:5,  : 
  Method funHDDC : Clustering for this data not possible.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
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 11.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   8.6Mb
installed size is 63.1Mb
  sub-directories of 1Mb or more:
    libs  62.7Mb
installed size is 77.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     73.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  16.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Found the following significant warnings:
  cGetHCS.c:9:33: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  cIdentical.c:9:34: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/gdmp.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/GenABEL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   4.8Mb
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.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    exdata   5.1Mb
Running examples in ‘genomic.autocorr-Ex.R’ failed
The error most likely occurred in:

> ### Name: block.glm
> ### Title: block.glm
> ### Aliases: block.glm
> 
> ### ** Examples
> 
> 
> ## simulate data with 10 repeated observations in a row - ie there
> ## should be autocorrelation only within windows <= 10
> library(data.table)
> data <- genomic.autocorr:::.sim.data(beta=0.2) 
simulating 500 independent observations repeated in blocks of 10
> 
> ## suppose we ignored the autocorrelation and look at the
> ## confidence interval for the effect of x on y1
> r1<-summary(glm(y1 ~ x, data=data))$coefficients
> r1
               Estimate Std. Error  t value     Pr(>|t|)
(Intercept) -0.04496491 0.01493161 -3.01139 2.613551e-03
x            0.15692178 0.01476667 10.62675 4.241930e-26
> 
> ## if we know the block structure, as here, we can see the
> ## confidence interval is (inappropriately) much tighter than
> ## if we used just independent observations
> r2<-summary(glm(y1 ~ x, data=data[!duplicated(name),]))$coefficients
> r2
               Estimate Std. Error    t value     Pr(>|t|)
(Intercept) -0.04496491 0.04730315 -0.9505689 0.3422843644
x            0.15692178 0.04678064  3.3544173 0.0008559843
> 
> ## use block bootstrap - x should only have a significant effect
> ## on y1 and the confidence interval around its effect should be
> ## closer to r2, above
> r <- block.glm(f.lhs=c("y0","y1"), f.rhs="x",data=data,block.size=20,B=200)
Error in `[.data.table`(results, , .(beta.med = median(value), beta.025 = quantile(value,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: block.glm -> [ -> [.data.table
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(genomic.autocorr)
  > 
  > test_check("genomic.autocorr")
  ── 1. Error: /data/gannet/ripley/R/packages/tests-clang/genomic.autocorr/man/blo
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: block.glm(f.lhs = c("y0", "y1"), f.rhs = "x", data = data, block.size = 20, B = 200)
  2: results[, .(beta.med = median(value), beta.025 = quantile(value, 0.975), beta.975 = quantile(value, 
         0.025), se.beta = sd(value), nboot = .N), by = byvars]
  3: `[.data.table`(results, , .(beta.med = median(value), beta.025 = quantile(value, 
         0.975), beta.975 = quantile(value, 0.025), se.beta = sd(value), nboot = .N), 
         by = byvars)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: /data/gannet/ripley/R/packages/tests-clang/genomic.autocorr/man/block.glm.Rd 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs   3.7Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         3.5Mb
    extdata   1.4Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.8Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
Running examples in ‘geoSpectral-Ex.R’ failed
The error most likely occurred in:

> ### Name: spc.Read_ASD
> ### Title: Read the ASD Spectra from text file
> ### Aliases: spc.Read_ASD
> 
> ### ** Examples
> 
> filename = file.path(system.file(package = "geoSpectral"),"test_data", "106.064.txt")
> L = spc.Read_ASD(filename)
> class(L)
[1] "Spectra"
attr(,"package")
[1] "geoSpectral"
> spc.plot.plotly(L)
Error in `[.data.table`(dt, , c(.I, NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: <Anonymous> ... plotly_build.plotly -> lapply -> FUN -> group2NA -> [ -> [.data.table
Execution halted
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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
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  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Namespaces in Imports field not imported from:
  ‘GGEBiplotGUI’ ‘gge’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘lazyeval’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridGraphics’ ‘rvcheck’ ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘XML’ ‘mapproj’ ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHANES’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Running ‘test-add_pval.R’
Running the tests in ‘tests/test-add_pval.R’ failed.
Complete output:
  > library(ggpval)
  > library(ggplot2)
  > library(data.table)
  > A <- rnorm(200, 0, 3)
  > B <- rnorm(200, 2, 4)
  > G <- rep(c("G1", "G2"), each = 100)
  > dt <- data.table(A, B, G)
  > dt <- melt(dt, id.vars = "G")
  > dt[, G := factor(G, levels = c("G2", "G1"))]
  > 
  > plt <- ggplot(dt, aes(variable, value)) +
  +   geom_boxplot() +
  +   geom_jitter()
  > 
  > plt_facet <- ggplot(dt, aes(variable, value)) +
  +   geom_boxplot() +
  +   geom_jitter() +
  +   facet_wrap(~G)
  > 
  > add_pval(plt, pairs = list(c(1, 2)))
  > 
  > add_pval(plt_facet, pairs = list(c(1, 2)))
  OMP: Warning #96: Cannot form a team with 5 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).
  Error in `[.data.table`(data_2_test, , lapply(.SD, function(i) get(test)(response ~  : 
    SETLENGTH() cannot be applied to an ALTVEC object.
  Calls: add_pval -> [ -> [.data.table
  Execution halted
Error in re-building vignettes:
  ...
OMP: Warning #96: Cannot form a team with 5 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).
Quitting from lines 71-76 (ggpval.Rmd) 
Error: processing vignette 'ggpval.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘colourpicker’ ‘dplyr’ ‘ggrepel’ ‘grDevices’ ‘gridExtra’
  ‘lazyeval’ ‘markdown’ ‘plotly’ ‘quantreg’ ‘rlang’ ‘shinyjs’ ‘tidyr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.1Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘GGally’ ‘RColorBrewer’ ‘Rcpp’ ‘assertthat’ ‘backports’
  ‘colorspace’ ‘colourpicker’ ‘evaluate’ ‘futile.options’ ‘gdtools’
  ‘gtable’ ‘htmltools’ ‘htmlwidgets’ ‘httpuv’ ‘labeling’ ‘lambda.r’
  ‘lazyeval’ ‘magrittr’ ‘miniUI’ ‘munsell’ ‘plyr’ ‘reshape’ ‘rprojroot’
  ‘scales’ ‘stringi’ ‘stringr’ ‘svglite’ ‘tibble’ ‘xtable’ ‘yaml’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 332-362 (ggrepel.Rmd) 
Error: processing vignette 'ggrepel.Rmd' failed with diagnostics:
there is no package called 'gridExtra'
Execution halted
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    libs  50.2Mb
installed size is 47.4Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
Package suggested but not available for checking: ‘cplexAPI’
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.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘car’ ‘wordcloud’
  All declared Imports should be used.
Running examples in ‘gpg-Ex.R’ failed
The error most likely occurred in:

> ### Name: gpg_sign
> ### Title: PGP Signatures
> ### Aliases: gpg_sign gpg_verify gpg gpg_sign
> 
> ### ** Examples
> 
> # This requires you have the Debian master key in your keyring
> msg <- tempfile()
> sig <- tempfile()
> download.file("http://http.us.debian.org/debian/dists/jessie/Release", msg)
trying URL 'http://http.us.debian.org/debian/dists/jessie/Release'
Content type 'application/octet-stream' length 148406 bytes (144 KB)
==================================================
downloaded 144 KB

> download.file("http://http.us.debian.org/debian/dists/jessie/Release.gpg", sig)
trying URL 'http://http.us.debian.org/debian/dists/jessie/Release.gpg'
Content type 'application/octet-stream' length 2434 bytes
==================================================
downloaded 2434 bytes

> gpg_verify(sig, msg, error = FALSE)
Error: GnuPG detached verification error: General error
Execution halted
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    R  19.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Error in re-building vignettes:
  ...
trying URL 'https://raw.githubusercontent.com/hughparsonage/drat/gh-pages/src/contrib/taxstats_0.0.5.1415.tar.gz'
Content type 'application/octet-stream' length 60897655 bytes (58.1 MB)
==================================================
downloaded 58.1 MB

* installing *source* package ‘taxstats’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (taxstats)
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).
Quitting from lines 361-372 (grattan.Rmd) 
Error: processing vignette 'grattan.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘raster’ ‘rgeos’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘deldir’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Namespace in Imports field not imported from: ‘rrcov’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘methods’
  All declared Imports should be used.
installed size is 136.5Mb
  sub-directories of 1Mb or more:
    java  134.7Mb
Running examples in ‘hamlet-Ex.R’ failed
The error most likely occurred in:

> ### Name: mem.powersimu
> ### Title: Power simulations for the fixed effects of a mixed-effects model
> ###   through structured bootstrapping of the data and re-fitting of the
> ###   model
> ### Aliases: mem.powersimu
> ### Keywords: power design mem
> 
> ### ** Examples
> 
> # Use the VCaP ARN data as an example
> data(vcaplong)
> arn <- vcaplong[vcaplong[,"Group"] == "Vehicle" | vcaplong[,"Group"] == "ARN",]
> 
> # lme4 is required for mixed-effects models
> library(lme4)
Loading required package: Matrix
> # Fit an example fixed effects model
> fit <- lmer(PSA ~ 1 + DrugWeek + ARN:DrugWeek + (1|ID) + (0 + DrugWeek|ID), data = arn)
> 
> # For reproducibility, set a seed
> set.seed(123)
> # Run a brief power analysis with only a few selected N values and a limited number of bootstrapping
> # Balance strata over the ARN and non-ARN (=Vehicle) so that both contain equal count of individuals
> power <- mem.powersimu(fit, N=c(4, 7, 10), boot=20, strata="ARN", plot=TRUE)
Error: 'summary' is not an exported object from 'namespace:lmerTest'
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Found the following significant warnings:
  SNPHWEX.cpp:50:31: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  SNPHWEX.cpp:51:65: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/HardyWeinberg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./City.h:82:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:93:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:94:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:95:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:96:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:87:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:89:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:267:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:268:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ./Spooky.h:285:36: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/hashFunction.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ../inst/include/hashmap/sparsepp/spp.h:2342:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/hashmap/sparsepp/spp.h:2365:22: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/hashmap.Rcheck/00install.out’ for details.
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Error in re-building vignettes:
  ...
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 0.14.1

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

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

OMP: Warning #96: Cannot form a team with 12 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).
Quitting from lines 88-90 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Running examples in ‘hesim-Ex.R’ failed
The error most likely occurred in:

> ### Name: custom_table
> ### Title: Custom CEA summary table
> ### Aliases: custom_table
> 
> ### ** Examples
> 
> # simulation output
> nsims <- 100
> sim <- data.frame(sim = rep(seq(nsims), 4),
+              c = c(rlnorm(nsims, 5, .1), rlnorm(nsims, 5, .1),
+                     rlnorm(nsims, 11, .1), rlnorm(nsims, 11, .1)),
+              e = c(rnorm(nsims, 8, .2), rnorm(nsims, 8.5, .1),
+                    rnorm(nsims, 11, .6), rnorm(nsims, 11.5, .6)),
+              strategy = rep(paste0("Strategy ", seq(1, 2)),
+                            each = nsims * 2),
+              grp = rep(rep(c("Group 1", "Group 2"),
+                            each = nsims), 2)
+ )
> 
> # Custom summary table
> custom.fun <- function(x) list(mean = mean(x), median = median(x),
+                              quantile(x, c(.025, .975)))
> custom_table(sim, strategy = "strategy", grp = "grp",
+            custom_vars = "e", FUN = custom.fun)
Error in `[.data.table`(x, , as.list(unlist(lapply(.SD, FUN))), by = by,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: custom_table -> dt_agg -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
OMP: Warning #96: Cannot form a team with 6 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).
Quitting from lines 123-127 (cea-vignette.Rmd) 
Error: processing vignette 'cea-vignette.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Namespaces in Imports field not imported from:
  ‘memoise’ ‘ratelimitr’
  All declared Imports should be used.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    doc          13.7Mb
    htmlwidgets   1.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        7.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’
  All declared Imports should be used.
print.summary.hotspots: warning in sort(x$data, dec = TRUE): partial
  argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$positive, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$negative, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
Lchs: no visible global function definition for ‘plot’
Lchs: no visible global function definition for ‘points’
disprop: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘qnorm’
hotspots: no visible global function definition for ‘qt’
plot.hotspots: no visible global function definition for ‘par’
summary.hotspots: no visible global function definition for ‘median’
Undefined global functions or variables:
  median par plot points qnorm qt
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "median", "qnorm", "qt")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   2.5Mb
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  5.2Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    data  12.8Mb
    doc    1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   4.6Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(HURDAT)
  > 
  > test_check("HURDAT")
  ── 1. Error: (unknown) (@test-hurdat.R#4)  ─────────────────────────────────────
  HTTP error 404.
  1: get_hurdat(basin = "AL") at testthat/test-hurdat.R:4
  2: purrr::map_df(.x = basin, .f = parse_hurdat)
  3: map(.x, .f, ...)
  4: .f(.x[[i]], ...)
  5: readr::read_lines(file = url)
  6: datasource(file, skip = skip)
  7: datasource_connection(file, skip, comment)
  8: datasource_raw(read_connection(path), skip, comment = comment)
  9: new_datasource("raw", text, skip = skip, comment = comment)
  10: structure(list(x, skip = skip, comment = comment, ...), class = c(paste0("source_", 
         type), "source"))
  11: read_connection(path)
  12: open(con, "rb")
  13: open.connection(con, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-hurdat.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘hutils-Ex.R’ failed
The error most likely occurred in:

> ### Name: weight2rows
> ### Title: Expand a weighted data frame to an equivalent unweighted
> ### Aliases: weight2rows
> 
> ### ** Examples
> 
> 
> library(data.table)
> DT <- data.table(x = 1:5, y = c(1, 1, 1, 1, 2))
> weight2rows(DT, "y")
Error in `[.data.table`(., , lapply(.SD, rep_len, round(.BY[[1]] * .N)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: weight2rows ... freduce -> withVisible -> <Anonymous> -> [ -> [.data.table
Execution halted
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'lo' to 'locut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'hi' to 'hicut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘ggplot2’ ‘pander’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.2Mb
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.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.4Mb
    doc    3.3Mb
    libs  13.0Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.1Mb
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs  35.4Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  24.1Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.0Mb
installed size is 39.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     28.9Mb
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Quitting from lines 74-77 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
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’
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Namespace in Imports field not imported from: ‘prodlim’
  All declared Imports should be used.
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Running examples in ‘inTrees-Ex.R’ failed
The error most likely occurred in:

> ### Name: XGB2List
> ### Title: Transform an xgboost object to a list of trees
> ### Aliases: XGB2List
> ### Keywords: xgboost
> 
> ### ** Examples
> 
> 	library(data.table)
> 	library(xgboost)
> 	# test data set 1: iris
> 	X <- within(iris,rm("Species")); Y <- iris[,"Species"]
> 	X <- within(iris,rm("Species")); Y <- iris[,"Species"]
> 	model_mat <- model.matrix(~. -1, data=X)
> 	xgb <- xgboost(model_mat, label = as.numeric(Y) - 1, nrounds = 20, 
+ 		objective = "multi:softprob", num_class = 3 )
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]	train-merror:0.020000 
[2]	train-merror:0.026667 
[3]	train-merror:0.020000 
[4]	train-merror:0.020000 
[5]	train-merror:0.013333 
[6]	train-merror:0.013333 
[7]	train-merror:0.013333 
[8]	train-merror:0.013333 
[9]	train-merror:0.013333 
[10]	train-merror:0.013333 
[11]	train-merror:0.006667 
[12]	train-merror:0.006667 
[13]	train-merror:0.006667 
[14]	train-merror:0.006667 
[15]	train-merror:0.000000 
[16]	train-merror:0.000000 
[17]	train-merror:0.000000 
[18]	train-merror:0.000000 
[19]	train-merror:0.000000 
[20]	train-merror:0.000000 
> 	tree_list <- XGB2List(xgb,model_mat)
Error in `[.data.table`(x, j = list(.ll.tech.split = list(.SD)), by = "Tree",  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: XGB2List ... split.data.table -> eval -> eval -> [ -> [.data.table
Execution halted
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.4Mb
Namespace in Imports field not imported from: ‘irr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘animation’ ‘comtradr’ ‘ndtv’ ‘statnet’ ‘xergm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘lubridate’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fAssets’ ‘timeDate’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.6Mb
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.
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   3.7Mb
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      4.5Mb
Namespace in Imports field not imported from: ‘mclust’
  All declared Imports should be used.
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  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   8.2Mb
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
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  6.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R   7.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.7Mb
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
kztp: warning in rowMeans(kztp, dim = 2): partial argument match of
  'dim' to 'dims'
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
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.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs          13.9Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘scales’ ‘tibble’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘memoise’
  All declared Imports should be used.
Running examples in ‘lidR-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.raster.lasmetrics
> ### Title: Transform a 'lasmetrics' object into a spatial 'RasterLayer'
> ###   object
> ### Aliases: as.raster.lasmetrics
> 
> ### ** Examples
> 
> LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
> lidar = readLAS(LASfile)
> 
> meanHeight = grid_metrics(lidar, mean(Z))
OMP: Warning #96: Cannot form a team with 10 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).
Error in `[.data.table`(.las@data, , c(eval(call)), by = by) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: grid_metrics ... grid_metrics.LAS -> lasaggregate -> [ -> [.data.table
Execution halted
Running examples in ‘lime-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_superpixels
> ### Title: Test super pixel segmentation
> ### Aliases: plot_superpixels
> 
> ### ** Examples
> 
> image <- system.file('extdata', 'produce.png', package = 'lime')
> 
> # plot with default settings
> plot_superpixels(image)

 *** caught segfault ***
address 0x108, cause 'memory not mapped'

Traceback:
 1: magick_image_write_frame(image, format = format, i = i)
 2: image_write_frame(image, format = channels)
 3: image_data(x[i])
 4: `[[.magick-image`(image_channel(im_lab, "R"), 1)
 5: image_channel(im_lab, "R")[[1]]
 6: slic(image_channel(im_lab, "R")[[1]][1, , ], image_channel(im_lab,     "G")[[1]][1, , ], image_channel(im_lab, "B")[[1]][1, , ],     n_sp = n_superpixels, weight = weight, n_iter = n_iter)
 7: plot_superpixels(image)
An irrecoverable exception occurred. R is aborting now ...
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.1Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      21.9Mb
    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.
Running examples in ‘lmem.gwaser-Ex.R’ failed
The error most likely occurred in:

> ### Name: mq.g.diagnostics
> ### Title: Performs molecular markers quality diagnostics.
> ### Aliases: mq.g.diagnostics
> 
> ### ** Examples
> 
> data (QA_geno)
> data (QA_map)
> data (QA_pheno)
> 
> P.data <- QA_pheno
> G.data <- QA_geno
> map.data <- QA_map
> 
> cross.data  <- gwas.cross (P.data, G.data, map.data,
+ cross='gwas', heterozygotes=FALSE)
 --Read the following data:
	 179  individuals
	 811  markers
	 3  phenotypes
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1,2,3,4,5,6,7; use jittermap().
 --Cross type: bc 
> summary (cross.data)
Warning in summary.cross(cross.data) :
  Some markers at the same position on chr 1,2,3,4,5,6,7; use jittermap().
    Doubled haploids

    No. individuals:    179 

    No. phenotypes:     3 
    Percent phenotyped: 100 100 100 

    No. chromosomes:    7 
        Autosomes:      1 2 3 4 5 6 7 

    Total markers:      811 
    No. markers:        117 147 153 48 113 101 132 
    Percent genotyped:  99.9 
    Genotypes (%):      AA:41.7  BB:58.3 
> 
> #Marker Quality
> 
> mq.g.diagnostics (crossobj=cross.data,I.threshold=0.1,
+              p.val=0.01,na.cutoff=0.1)
Error in plot.missing(crossobj) : could not find function "plot.missing"
Calls: mq.g.diagnostics -> mq_missinggenotype_plot
Execution halted
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
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.
Running examples in ‘LogisticDx-Ex.R’ failed
The error most likely occurred in:

> ### Name: dx
> ### Title: Diagnostics for binomial regression
> ### Aliases: dx dx.glm
> 
> ### ** Examples
> 
> ## H&L 2nd ed. Table 5.8. Page 182.
> ## Pattern nos. 31, 477, 468
> data(uis)
> uis <- within(uis, {
+     NDRGFP1 <- 10 / (NDRGTX + 1)
+     NDRGFP2 <- NDRGFP1 * log((NDRGTX + 1) / 10)
+ })
> (d1 <- dx(g1 <- glm(DFREE ~ AGE + NDRGFP1 + NDRGFP2 + IVHX +
+                     RACE + TREAT + SITE +
+                     AGE:NDRGFP1 + RACE:SITE,
+                     family=binomial, data=uis)))
Error in `[.data.table`(res1, , `:=`("y", sum(y)), by = P) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: dx -> dx.glm -> [ -> [.data.table
Execution halted
Running examples in ‘LOGIT-Ex.R’ failed
The error most likely occurred in:

> ### Name: confusion_stat
> ### Title: Display confusion or classification matrix following logistic
> ###   regression using glm with binomial family.
> ### Aliases: confusion_stat
> ### Keywords: models
> 
> ### ** Examples
> 
> library(MASS)
> library(LOGIT)
> data(R84)
> R84$cage <- R84$age - mean(R84$age)
> R84$cdoc <- R84$docvis - mean(R84$docvis)
> mylogit <- glm(outwork ~ cdoc + female + kids + cage + factor(edlevel),
+ family=binomial, data=R84)
> mu <- predict(mylogit, type="response")
> cutpoint<-ROCtest(mylogit, fold=10, type="Sensitivity")$cut
> mu[mu>=cutpoint]<-1
> mu[mu<cutpoint]<-0
> confusion_stat(mu, R84$outwork)
Error: `data` and `reference` should be factors with the same levels.
Execution halted
Found the following significant warnings:
  lsdall.c:2078:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2200:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2209:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2219:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2225:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/logspline.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘NLRoot’ ‘ade4’ ‘glmnet’ ‘lars’ ‘lattice’ ‘logmult’ ‘pdist’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
installed size is 47.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  46.1Mb
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.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.3Mb
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  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 24.6Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
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 11.7Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   4.6Mb
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/ggplot2')`
Quitting from lines 105-106 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/ManifoldOptim.Rcheck/00install.out’ for details.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
Error in re-building vignettes:
  ...
Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/ggplot2')`
Quitting from lines 71-74 (mapfuser.Rmd) 
Error: processing vignette 'mapfuser.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.7Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
File ‘maxent/libs/maxent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_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:
    doc    2.1Mb
    libs  10.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/mdhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
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
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   8.0Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
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’ ‘formattable’ ‘ggplot2’
  ‘ggthemes’ ‘magrittr’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.4Mb
Running examples in ‘MendelianRandomization-Ex.R’ failed
The error most likely occurred in:

> ### Name: mr_plot
> ### Title: Draw a scatter plot of the genetic associations and/or causal
> ###   estimates
> ### Aliases: mr_plot mr_plot,MRInput-method mr_plot,MRAll-method
> 
> ### ** Examples
> 
> mr_plot(mr_input(bx = ldlc, bxse = ldlcse, by = chdlodds, byse = chdloddsse),
+   line="egger", orientate = TRUE)
We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/ggplot2')`
Error in `[.data.table`(dt, , c(.I, NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: mr_plot ... geom2trace.GeomPath -> group2NA -> [ -> [.data.table
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Namespace in Imports field not imported from: ‘rattle’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘reshape’
  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
Error in re-building vignettes:
  ...
Quitting from lines 133-137 (guide.Rnw) 
Error: processing vignette 'guide.Rnw' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-clang/MetaSubtract.Rcheck/MetaSubtract/extdata’, resetting
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 20.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  16.2Mb
    misc   1.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘mFilter/R/zzz.R’:
  .onLoad calls:
    writeLines(strwrap(txt, indent = 4, exdent = 4))

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

.onLoad: warning in packageDescription("mFilter", lib = mylib): partial
  argument match of 'lib' to 'lib.loc'
bkfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
cffilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘copula’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
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.
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  7.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   5.4Mb
Running examples in ‘miscset-Ex.R’ failed
The error most likely occurred in:

> ### Name: collapse
> ### Title: Collapse objects
> ### Aliases: collapse collapse.default collapse.data.frame
> 
> ### ** Examples
> 
> #
> 
> ### some data
> 
> set.seed(12)
> s <- s2 <- sample(LETTERS[1:4], 9, replace = TRUE)
> s2[1:2] <- rev(s2[1:2])
> d <- data.frame(group = rep(letters[c(3,1,2)], each = 3), 
+                 value = s,
+                 level = factor(s2),
+                 stringsAsFactors = FALSE)
> 
> ### collapse vectors
> 
> collapse(letters)
[1] "abcdefghijklmnopqrstuvwxyz"
> collapse(1:3)               # coerced to character
[1] "123"
> collapse(LETTERS[1:5], "-") # separated by '-'
[1] "A-B-C-D-E"
> 
> ### collapse data.frames
> 
> # by all columns (same as unique)
> collapse(d)
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).
  group value level
1     c     A     D
2     c     D     A
3     c     D     D
4     a     B     B
5     a     A     A
6     b     A     A
7     b     C     C
> # by a grouping column
> collapse(d, by = 1)
Error in `[.data.table`(x, , collapse_frame(.SD, sep, .unique, .sort,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: collapse -> collapse.data.frame -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
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).
Quitting from lines 326-327 (miscset.Rmd) 
Error: processing vignette 'miscset.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
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 39.2Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   4.0Mb
Namespace in Imports field not imported from: ‘rjags’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘deSolve’ ‘progress’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > suppressPackageStartupMessages({
  +   library(testthat)
  +   library(data.table)
  + })
  > 
  > test_check("mknapsack")
  Loading required package: mknapsack
  ── 1. Error: group_moq: combines data provided at unit level to MOQ level (@test
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: group_moq(units) at testthat/test-packing.R:17
  2: dt[, `:=`(cnt, 1:.N), by = sku]
  3: `[.data.table`(dt, , `:=`(cnt, 1:.N), by = sku)
  
  ── 2. Error: mknapsack: Generates vector of optimal containers for a given probl
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: group_moq(units) at testthat/test-packing.R:34
  2: dt[, `:=`(cnt, 1:.N), by = sku]
  3: `[.data.table`(dt, , `:=`(cnt, 1:.N), by = sku)
  
  ── 3. Error: mknapsack: with sold vector, sold items have highest priority (@tes
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: group_moq(units) at testthat/test-packing.R:74
  2: dt[, `:=`(cnt, 1:.N), by = sku]
  3: `[.data.table`(dt, , `:=`(cnt, 1:.N), by = sku)
  
  ── 4. Error: at contains MOQ line or after: combines data provided at unit level
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: group_moq(units) at testthat/test-packing.R:161
  2: dt[, `:=`(cnt, 1:.N), by = sku]
  3: `[.data.table`(dt, , `:=`(cnt, 1:.N), by = sku)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 4
  1. Error: group_moq: combines data provided at unit level to MOQ level (@test-packing.R#17) 
  2. Error: mknapsack: Generates vector of optimal containers for a given problem (@test-packing.R#34) 
  3. Error: mknapsack: with sold vector, sold items have highest priority (@test-packing.R#74) 
  4. Error: at contains MOQ line or after: combines data provided at unit level to MOQ level (@test-packing.R#161) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘iterators’ ‘parallel’
  All declared Imports should be used.
Running examples in ‘mlr-Ex.R’ failed
The error most likely occurred in:

> ### Name: benchmark
> ### Title: Benchmark experiment for multiple learners and tasks.
> ### Aliases: benchmark
> 
> ### ** Examples
> 
> lrns = list(makeLearner("classif.lda"), makeLearner("classif.rpart"))
> tasks = list(iris.task, sonar.task)
> rdesc = makeResampleDesc("CV", iters = 2L)
> meas = list(acc, ber)
> bmr = benchmark(lrns, tasks, rdesc, measures = meas)
Task: iris-example, Learner: classif.lda
Resampling: cross-validation
Measures:             acc       ber       
[Resample] iter 1:    0.9466667 0.0535714 
[Resample] iter 2:    0.9733333 0.0303030 


Aggregated Result: acc.test.mean=0.9600000,ber.test.mean=0.0419372


Task: Sonar-example, Learner: classif.lda
Resampling: cross-validation
Measures:             acc       ber       
[Resample] iter 1:    0.7884615 0.2140625 
[Resample] iter 2:    0.7211538 0.2749160 


Aggregated Result: acc.test.mean=0.7548077,ber.test.mean=0.2444893


Task: iris-example, Learner: classif.rpart
Resampling: cross-validation
Measures:             acc       ber       
[Resample] iter 1:    0.9333333 0.0654762 
[Resample] iter 2:    0.9466667 0.0582751 


Aggregated Result: acc.test.mean=0.9400000,ber.test.mean=0.0618756


Task: Sonar-example, Learner: classif.rpart
Resampling: cross-validation
Measures:             acc       ber       
[Resample] iter 1:    0.6153846 0.4109375 
[Resample] iter 2:    0.7115385 0.2892870 


Aggregated Result: acc.test.mean=0.6634615,ber.test.mean=0.3501123


> rmat = convertBMRToRankMatrix(bmr)
Error in `[.data.table`(df, , `:=`("alg.rank", rank(.SD$x, ties.method = ties.method)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: convertBMRToRankMatrix -> [ -> [.data.table
Execution halted
Running examples in ‘mltools-Ex.R’ failed
The error most likely occurred in:

> ### Name: auc_roc
> ### Title: Area Under the ROC Curve
> ### Aliases: auc_roc
> 
> ### ** Examples
> 
> library(data.table)
> preds <- c(.1, .3, .3, .9)
> actuals <- c(0, 0, 1, 1)
> auc_roc(preds, actuals)
Error in `[.data.table`(dt, , list(CountFalse = sum(Actual == 0), CountTrue = sum(Actual)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: auc_roc -> [ -> [.data.table
Execution halted
Namespace in Imports field not imported from: ‘sparsepp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
Running examples in ‘mmpf-Ex.R’ failed
The error most likely occurred in:

> ### Name: marginalPrediction
> ### Title: marginalizes prediction functions
> ### Aliases: marginalPrediction
> 
> ### ** Examples
> 
> X = replicate(3, rnorm(100))
> y = X %*% runif(3)
> data = data.frame(X, y)
> fit = lm(y ~ ., data)
> 
> marginalPrediction(data.frame(X), "X2", c(10, 25), fit,
+   aggregate.fun = function(x) c("mean" = mean(x), "variance" = var(x)))
Error in `[.data.table`(mp, , as.list(unlist(lapply(.SD, aggregate.fun))),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: marginalPrediction -> [ -> [.data.table
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mmpf)
  > 
  > test_check("mmpf")
  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).
  ── 1. Error: marginalPrediction works (@test_mp.R#6)  ──────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: marginalPrediction(data, c("X1", "X2"), c(10, 25), fit, FALSE, aggregate.fun = function(x) list(mean = mean(x), 
         var = var(x))) at testthat/test_mp.R:6
  2: mp[, as.list(unlist(lapply(.SD, aggregate.fun))), by = vars]
  3: `[.data.table`(mp, , as.list(unlist(lapply(.SD, aggregate.fun))), by = vars)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 40 SKIPPED: 0 FAILED: 1
  1. Error: marginalPrediction works (@test_mp.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
Running examples in ‘Modelcharts-Ex.R’ failed
The error most likely occurred in:

> ### Name: GAIN_CHART
> ### Title: Functions Gain Chart
> ### Aliases: GAIN_CHART
> 
> ### ** Examples
> 
> ## Not run: 
> ##D # Run it and see for yourself
> ## End(Not run)
> data.tmp<-read.csv(system.file("ext", "testdata.csv", package="Modelcharts"))
> GAIN_CHART(data.tmp,data.tmp$Probability,seq(0.95,0,-0.05),data.tmp$Outcome,"Y")
Error in `[.data.table`(dt, , c(.I, NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: <Anonymous> ... plotly_build.plotly -> lapply -> FUN -> group2NA -> [ -> [.data.table
Execution halted
'::' or ':::' import not declared from: ‘arrangements’
Namespaces in Imports field not imported from:
  ‘fields’ ‘iterpc’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   2.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
Namespace in Imports field not imported from: ‘ratelimitr’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.4Mb
Namespace in Imports field not imported from: ‘zoo’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.7Mb
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.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Running examples in ‘mschart-Ex.R’ failed
The error most likely occurred in:

> ### Name: chart_data_fill
> ### Title: Modify fill colour
> ### Aliases: chart_data_fill
> 
> ### ** Examples
> 
> my_scatter <- ms_scatterchart(data = iris, x = "Sepal.Length",
+   y = "Sepal.Width",  group = "Species")
Error in `[.data.table`(dat, , eval(fun.call), by = c(varnames)) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: ms_scatterchart ... shape_as_series -> dcast.data.table -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
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).
Quitting from lines 154-162 (details.Rmd) 
Error: processing vignette 'details.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    libs  44.6Mb
Running examples in ‘msmtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: augment
> ### Title: A fast and general method for building augmented data
> ### Aliases: augment
> 
> ### ** Examples
> 
> # loading data
> data( hosp )
> 
> # 1.
> # augmenting hosp
> hosp_augmented = augment( data = hosp, data_key = subj, n_events = adm_number,
+                           pattern = label_3, t_start = dateIN, t_end = dateOUT,
+                           t_cens = dateCENS )
Warning in augment(data = hosp, data_key = subj, n_events = adm_number,  :
  no t_death has been passed. Assuming that dateCENS contains both censoring and death times
-------------------------------------
# # # # setting everything up # # # #
-------------------------------------
checking monotonicity of adm_number
OMP: Warning #96: Cannot form a team with 11 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).
Error in `[.data.table`(data, , .(ev = all(get(cols[[2]]) == cummax(get(cols[[2]])))),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: augment -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
OMP: Warning #96: Cannot form a team with 11 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).
Quitting from lines 80-87 (msmtools.Rmd) 
Error: processing vignette 'msmtools.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 75.8Mb
  sub-directories of 1Mb or more:
    libs  75.6Mb
Namespaces in Imports field not imported from:
  ‘boot’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
Error in re-building vignettes:
  ...
Quitting from lines 82-83 (using_musica.Rmd) 
Error: processing vignette 'using_musica.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Error in re-building vignettes:
  ...
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).
Quitting from lines 250-252 (mvQuad_intro.Rmd) 
Error: processing vignette 'mvQuad_intro.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.8Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘knitr’
  All declared Imports should be used.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
Namespace in Imports field not imported from: ‘biomartr’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
Namespace in Imports field not imported from: ‘purrrlyr’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 49-50 (using-nauf.Rmd) 
Error: processing vignette 'using-nauf.Rmd' failed with diagnostics:
Unable to extract deviance function from model fit
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
Running examples in ‘neatmaps-Ex.R’ failed
The error most likely occurred in:

> ### Name: neatmap
> ### Title: Heatmap of Networks
> ### Aliases: neatmap
> 
> ### ** Examples
> 
> df <- netsDataFrame(net.attr.df = networkAttrDF,
+                     node.attr.df = nodeAttrDF,
+                     edge.df = edgeDF)
> heatmap <- neatmap(df, scale.df = "basic", mainTitle = "Heatmap", 
+                    xlabel = "Chararacteritics", ylabel = "Networks",
+                    link.method = "single", dist.method = "euclidean",
+                    nBootRep = 10)
Bootstrap (r = 0.5)... Done.
Bootstrap (r = 0.6)... Done.
Bootstrap (r = 0.7)... Done.
Bootstrap (r = 0.8)... Done.
Bootstrap (r = 0.9)... Done.
Bootstrap (r = 1.0)... Done.
Bootstrap (r = 1.1)... Done.
Bootstrap (r = 1.2)... Done.
Bootstrap (r = 1.3)... Done.
Bootstrap (r = 1.4)... Done.
We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/ggplot2')`
We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/ggplot2')`
OMP: Warning #96: Cannot form a team with 12 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).
Error in `[.data.table`(dt, , c(.I, NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: neatmap ... geom2trace.GeomPath -> group2NA -> [ -> [.data.table
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   6.3Mb
Running examples in ‘NetLogoR-Ex.R’ failed
The error most likely occurred in:

> ### Name: diffuse
> ### Title: Diffuse values in a world
> ### Aliases: diffuse diffuse,worldMatrix,missing,numeric,numeric-method
> ###   diffuse,worldArray,character,numeric,numeric-method
> 
> ### ** Examples
> 
> w1 <- createWorld(minPxcor = 0, maxPxcor = 4, minPycor = 0, maxPycor = 4,
+                           data = sample(1:3, size = 25, replace = TRUE))
> plot(w1)
> # Diffuse 50% of each patch value to its 8 neighbors
> w2 <- diffuse(world = w1, share = 0.5, nNeighbors = 8)
Error in `[.data.table`(dt, , `:=`(loose, sum(toGiveNeigh)), by = from) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: diffuse -> diffuse -> .local -> [ -> [.data.table
Execution halted
Running ‘test-all.R’ [41s/49s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(magrittr)
  > library(testthat)
  
  Attaching package: 'testthat'
  
  The following objects are masked from 'package:magrittr':
  
      equals, is_less_than, not
  
  > test_check("NetLogoR")
  Loading required package: NetLogoR
  Loading required package: raster
  Loading required package: sp
  
  Attaching package: 'raster'
  
  The following object is masked from 'package:magrittr':
  
      extract
  
  ── 1. Error: diffuse works with 4 neighbors (@test-patch-functions.R#5)  ───────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: diffuse(world = w1, share = 0.6, nNeighbors = 4) at testthat/test-patch-functions.R:5
  2: diffuse(world = w1, share = 0.6, nNeighbors = 4)
  3: .local(world, share, nNeighbors, torus)
  4: dt[, `:=`(loose, sum(toGiveNeigh)), by = from]
  5: `[.data.table`(dt, , `:=`(loose, sum(toGiveNeigh)), by = from)
  
  ── 2. Error: diffuse works with 8 neighbors (@test-patch-functions.R#52)  ──────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: diffuse(world = w1, share = 0.6, nNeighbors = 8) at testthat/test-patch-functions.R:52
  2: diffuse(world = w1, share = 0.6, nNeighbors = 8)
  3: .local(world, share, nNeighbors, torus)
  4: dt[, `:=`(loose, sum(toGiveNeigh)), by = from]
  5: `[.data.table`(dt, , `:=`(loose, sum(toGiveNeigh)), by = from)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1138 SKIPPED: 1 FAILED: 2
  1. Error: diffuse works with 4 neighbors (@test-patch-functions.R#5) 
  2. Error: diffuse works with 8 neighbors (@test-patch-functions.R#52) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   5.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
Running examples in ‘networkR-Ex.R’ failed
The error most likely occurred in:

> ### Name: mksib
> ### Title: Generate variables (or lists) of siblings from a file of ids of
> ###   persons and their father and mother.
> ### Aliases: mksib
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
> library( data.table )
> id <- 1:12
> pid <- c(NA,  1, 1, 1, NA, 23, 45, 5, 5, 7, 12, NA)
> mid <- c(NA, NA, 2, 2, 12, NA, 46, 6, 6, 6, NA, 12)
> indd <- data.table( id, mid, pid )
> indata <- copy( indd )
> indata
    id mid pid
 1:  1  NA  NA
 2:  2  NA   1
 3:  3   2   1
 4:  4   2   1
 5:  5  12  NA
 6:  6  NA  23
 7:  7  46  45
 8:  8   6   5
 9:  9   6   5
10: 10   6   7
11: 11  NA  12
12: 12  12  NA
> 
> str( xx <- mksib( indata ) )
Error in `[.data.table`(setDT(indata), , `:=`(msibs, list(list(id))),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: str -> mksib -> [ -> [.data.table
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘lme4’ ‘stringi’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(nima)
  nima: Nima Hejazi's R Toolbox
  Version: 0.4.5
  > 
  > test_check("nima")
  ── 1. Failure: attrnames finds the names of the attributes of a data frame (@tes
  attrnames(y) not equal to c("names", "row.names", "class").
  2/3 mismatches
  x[2]: "class"
  y[2]: "row.names"
  
  x[3]: "row.names"
  y[3]: "class"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 21 SKIPPED: 0 FAILED: 1
  1. Failure: attrnames finds the names of the attributes of a data frame (@test-attribute_names.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              5.8Mb
    classic-bugs   1.6Mb
    include        5.8Mb
    tests          1.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Namespaces in Imports field not imported from:
  ‘dparser’ ‘inline’
  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.
Namespaces in Imports field not imported from:
  ‘geosphere’ ‘lwgeom’
  All declared Imports should be used.
Running examples in ‘NNS-Ex.R’ failed
The error most likely occurred in:

> ### Name: NNS.caus
> ### Title: NNS Causation
> ### Aliases: NNS.caus
> ### Keywords: causation
> 
> ### ** Examples
> 
> ## x clearly causes y...
> set.seed(123)
> x <- rnorm(100) ; y <- x ^ 2
> NNS.caus(x, y, tau = "cs")
Error in `[.data.table`(data.table(x, y, quadrant = "q", prior.quadrant = "pq"),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: NNS.caus ... Uni.caus -> NNS.dep -> NNS.part -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 26-29 (NNSvignette_Clustering_and_Regression.Rmd) 
Error: processing vignette 'NNSvignette_Clustering_and_Regression.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘XML’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’
  ‘forcats’ ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc   8.6Mb
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/npcp.Rcheck/00install.out’ for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  14.2Mb
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
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
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
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.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 97.8Mb
  sub-directories of 1Mb or more:
    libs  97.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
Running examples in ‘openEBGM-Ex.R’ failed
The error most likely occurred in:

> ### Name: Qn
> ### Title: Calculate Qn
> ### Aliases: Qn
> ### Keywords: openEBGM
> 
> ### ** Examples
> 
> theta_init <- data.frame(
+   alpha1 = c(0.2, 0.1),
+   beta1  = c(0.1, 0.1),
+   alpha2 = c(2,   10),
+   beta2  = c(4,   10),
+   p      = c(1/3, 0.2)
+ )
> data(caers)
> proc <- processRaw(caers)
Error in `[.data.table`(data, , j = list(N = .countUnique(id)), by = .(var1,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: processRaw -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 45-46 (x2_rawDataProcessingVignette.Rmd) 
Error: processing vignette 'x2_rawDataProcessingVignette.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is 147.8Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    libs    137.9Mb
    models    4.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Running ‘testthat.R’ [21s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.2Mb
Running examples in ‘optiSel-Ex.R’ failed
The error most likely occurred in:

> ### Name: completeness
> ### Title: Calculates Pedigree Completeness
> ### Aliases: completeness
> 
> ### ** Examples
> 
> 
> #Computes the pedigree completeness of Hinterwald cattle 
> #born between 2006 and 2007 in each ancestral generation.
> 
> data(PedigWithErrors)
> Pedig <- prePed(PedigWithErrors)
Pedigree loops were detected. We recommend to correct them manually before
using prePed(). The parents of the following individuals are set to unknown
to remove the loops.
                           Sire             Dam
276000802875148 276000803622423 276000890878480
276000811476506 276000810087663 276000811476506

The sex of the following animals was not compatible with the pedigree, so
it was modified:
                           Sire             Dam
276000810087663 276000802940621 276000802925028

> compl <- completeness(Pedig, keep=Pedig$Born %in% (2006:2007), maxd=50, by="Indiv")
> head(compl)
              Indiv Generation Completeness
652 276000891875979          0          1.0
653 276000891875979          1          0.5
676 276000891967895          0          1.0
677 276000891967895          1          0.5
694 276000891955445          0          1.0
695 276000891955445          1          0.5
> 
> #Summary statistics can be computed directly from the pedigree:
> Summary <- summary(Pedig, keep=Pedig$Born %in% (2006:2007))
Error in `[.data.table`(compl, , list(maxGen = length(Completeness) -  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: summary -> summary.Pedig -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 464-468 (ocs-vignette.Rmd) 
Error: processing vignette 'ocs-vignette.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
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  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Running ‘testthat.R’ [34s/28s]
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. Error: (unknown) (@test-folds.R#96)  ─────────────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: validation_dt[, list(one_count = sum(strata_ids)), by = list(fold)] at testthat/test-folds.R:96
  2: `[.data.table`(validation_dt, , list(one_count = sum(strata_ids)), by = list(fold)) at testthat/test-folds.R:96
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 90 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-folds.R#96) 
  
  Error: testthat unit tests failed
  Execution halted
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.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Found the following significant warnings:
  ccaRevolution.c:31:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:44:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:97:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:98:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:110:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:111:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/osc.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   5.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Running examples in ‘osmplotr-Ex.R’ failed
The error most likely occurred in:

> ### Name: osm_structures
> ### Title: osm_structures
> ### Aliases: osm_structures
> 
> ### ** Examples
> 
> # Default structures:
> osm_structures ()
    structure      key value suffix      cols
1    building building           BU #646464FF
2     amenity  amenity            A #787878FF
3    waterway waterway            W #646478FF
4       grass  landuse grass      G #64A064FF
5     natural  natural            N #647864FF
6        park  leisure  park      P #647864FF
7     highway  highway            H #000000FF
8    boundary boundary           BO #C8C8C8FF
9        tree  natural  tree      T #64A064FF
10 background                          gray20
> # user-defined structures:
> structures <- c ('highway', 'park', 'grass')
> structs <- osm_structures (structures = structures, col_scheme = 'light')
> # make_osm_map returns potentially modified list of data
> dat <- make_osm_map (osm_data = london, structures = structs)
Downloading and extracting OSM data for 1 structures ...

  |                                                                            
  |                                                                      |   0%add_feature() is deprecated; please use add_osm_feature()
Error in check_for_error(doc) : General overpass server error; returned:
OSM3S ResponseThe data included in this document is from www.openstreetmap.org. The data is made available under ODbL.Error: line 8: parse error: ';' expected - ')' found. Error: line 11: parse error: Unexpected end of input. Error: line 8: static error: Element "print" cannot be subelement of element "union". 
Calls: make_osm_map ... extract_osm_objects -> <Anonymous> -> overpass_query -> check_for_error
Execution halted
Package suggested but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
Running examples in ‘otvPlots-Ex.R’ failed
The error most likely occurred in:

> ### Name: PlotNumVar
> ### Title: Create plots and summary statistics for a numerical variable
> ### Aliases: PlotNumVar
> 
> ### ** Examples
> 
> data(bankData)
> bankData <- PrepData(bankData, dateNm = "date", dateGp = "months", 
+                     dateGpBp = "years")
The following variables will be plotted:
Numerical: age balance duration campaign pdays previous
Categorical: job marital education default housing loan contact poutcome y

> plot(PlotNumVar("balance", bankData, NULL, "months", "years", 
+                  skewOpt = NULL, kSample = NULL)$p)
Error in `[.data.table`(dataFl, , { : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: plot -> PlotNumVar -> SummaryStats -> [ -> [.data.table
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.1Mb
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW: warning in return(x@u1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@u2): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@w1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW: warning in x@u1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@u2 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@w1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    extdata   9.5Mb
Running examples in ‘patternator-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract_features
> ### Title: Extract quantitative features from the continuous dorsal pattern
> ###   of a female brown anole lizard
> ### Aliases: extract_features
> 
> ### ** Examples
> 
> # load the sample dorsal pattern image
> data(anole)
> 
> # clean the dorsal pattern and extract quantitative features
> features <- extract_features(clean_patterns(anole))
Error in `[.data.table`(l, , list(x, x_max = x_mod * (abs(x_mod) == max(abs(x_mod)))),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: extract_features -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pbdMPI-guide.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte 146.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pbdRPC-guide.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 145.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte 146.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte 145.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte 146.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte 145.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    lib   9.5Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pbdZMQ-guide.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.1Mb
    libs   6.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
Running examples in ‘PCRedux-Ex.R’ failed
The error most likely occurred in:

> ### Name: visdat_pcrfit
> ### Title: Visualizing the content of data from an analysis with the
> ###   pcrfit_single function
> ### Aliases: visdat_pcrfit
> 
> ### ** Examples
> 
> 
> # Calculate curve features of an amplification curve data. Note that not all 
> # available CPU cores are used. If need set "all" to use all available cores.
> library(qpcR)
Loading required package: MASS
Loading required package: minpack.lm
Loading required package: rgl
Loading required package: robustbase
Loading required package: Matrix
> # take the samples F1.1 (positive) and F1.3 (negative) for this example.
> 
> test_data <- testdat[, c(1,2,4)]
> 
> # Plot the amplification curves
> 
> matplot(test_data[, 1], test_data[, -1], xlab="Cycle", ylab="RFU", 
+         main="testdat data set", type="l", lty=1, lwd=2, col=1:2)
> legend("topleft", paste(colnames(test_data)[-1], c("pos", "neg")), 
+        pch=19, col=1:2)
> 
> # Analyze the amplification curves with the pcrfit_single function
> res_1 <- cbind(runs="F1.1", pcrfit_single(test_data[, 2]))
Loading required package: bcp
Loading required package: grid
> res_2 <- cbind(runs="F1.3", pcrfit_single(test_data[, 3]))
> res <- rbind(F1.1=res_1, F1.3=res_2)
> 
> # Show all results in an interactive plot
> visdat_pcrfit(res)
Error in `[.data.table`(dt, , c(.I, .I[1], NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: visdat_pcrfit ... geom2trace.GeomPolygon -> group2NA -> [ -> [.data.table
Execution halted
Running examples in ‘pcrsim-Ex.R’ failed
The error most likely occurred in:

> ### Name: calibrateLb
> ### Title: Calibrate Inter-locus Balance
> ### Aliases: calibrateLb
> 
> ### ** Examples
> 
> # Experimental inter-locus balances for the STR kit to be simulated (sums to 1).
> target <- c(0.20, 0.10, 0.15, 0.25, 0.30)
>  
> # Find PCR efficiency values that upon simulation
> # satisfy the experimental data for 0.5 ng of input DNA.
> set.seed(10) # For reproducibility.
> calibrateLb(sim=10, target=target, amount=0.5, seed=0.85, progress=FALSE)
Error in `[.data.table`(simPh, , `:=`(TPH, sum(LPH, na.rm = TRUE)), by = list(Sample.Name)) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: calibrateLb -> [ -> [.data.table
Execution halted
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
Running examples in ‘PeakSegJoint-Ex.R’ failed
The error most likely occurred in:

> ### Name: multiClusterPeaks
> ### Title: multiClusterPeaks
> ### Aliases: multiClusterPeaks
> 
> ### ** Examples
> 
> 
> library(PeakSegJoint)
> data(chr7.peaks, envir=environment())
> library(ggplot2)
> ggplot()+
+   geom_segment(aes(
+     chromStart/1e3, sample.id,
+     xend=chromEnd/1e3, yend=sample.id),
+     data=chr7.peaks)
> 
> clustered <- multiClusterPeaks(chr7.peaks)
> library(data.table)
> clusters <- data.table(clustered)[, list(
+   clusterStart=as.integer(median(chromStart)),
+   clusterEnd=as.integer(median(chromEnd))
+   ), by=cluster]
Error in `[.data.table`(data.table(clustered), , list(clusterStart = as.integer(median(chromStart)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: [ -> [.data.table
Execution halted
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running examples in ‘penaltyLearning-Ex.R’ failed
The error most likely occurred in:

> ### Name: ROChange
> ### Title: ROC curve for changepoints
> ### Aliases: ROChange
> 
> ### ** Examples
> 
> 
> library(penaltyLearning)
> data(neuroblastomaProcessed, envir=environment())
> ## Get incorrect labels data for one profile.
> pid <- 11
> pro.errors <- neuroblastomaProcessed$errors[profile.id==pid,]
> ## Get the feature that corresponds to the BIC penalty = log(n),
> ## meaning log(penalty) = log(log(n)).
> chr.vec <- paste(c(1:4, 11, 17))
> pid.names <- paste0(pid, ".", chr.vec)
> BIC.feature <- neuroblastomaProcessed$feature.mat[pid.names, "log2.n"]
> pred <- data.table(pred.log.lambda=BIC.feature, chromosome=chr.vec)
> result <- ROChange(pro.errors, pred, "chromosome")
OMP: Warning #96: Cannot form a team with 13 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).
Error in `[.data.table`(err, pred, on = problem.vars, .SD[1, ], by = problem.vars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: ROChange -> [ -> [.data.table
Execution halted
Running ‘testthat.R’ [25s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("penaltyLearning")
  Loading required package: penaltyLearning
  Loading required package: data.table
  ── 1. Error: no error for finite limits (@test-errors.R#51)  ───────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: targetIntervalROC(ok3, 1:3) at testthat/test-errors.R:51
  2: target.errors[, `:=`(possible.fp, max(fp)), by = observation]
  3: `[.data.table`(target.errors, , `:=`(possible.fp, max(fp)), by = observation)
  
  ── 2. Error: no error for one col vector predictions (@test-errors.R#65)  ──────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: targetIntervalROC(ok3, cbind(foo = 1:3)) at testthat/test-errors.R:65
  2: target.errors[, `:=`(possible.fp, max(fp)), by = observation]
  3: `[.data.table`(target.errors, , `:=`(possible.fp, max(fp)), by = observation)
  
  ── 3. Error: (unknown) (@test-features.R#29)  ──────────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: featureMatrix(three, c("profile.id", "chromosome"), "logratio") at testthat/test-features.R:29
  2: data.table(data.sequences)[, list(features = list(featureVector(.SD[[data.var]]))), 
         by = problem.vars]
  3: `[.data.table`(data.table(data.sequences), , list(features = list(featureVector(.SD[[data.var]]))), 
         by = problem.vars)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 63 SKIPPED: 0 FAILED: 3
  1. Error: no error for finite limits (@test-errors.R#51) 
  2. Error: no error for one col vector predictions (@test-errors.R#65) 
  3. Error: (unknown) (@test-features.R#29) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Namespace in Imports field not imported from: ‘MASS’
  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’ ‘cluster’ ‘graph’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
ERROR: Duplicated records found in prim.key field
ERROR: NULL records found in prim.key field
OK: No duplicated records found in prim.key field
OK: No NULL records found in prim.key field
Quitting from lines 517-530 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
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.
Namespaces in Imports field not imported from:
  ‘DT’ ‘leaflet’ ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
Running examples in ‘PhenotypeSimulator-Ex.R’ failed
The error most likely occurred in:

> ### Name: readStandardGenotypes
> ### Title: Read genotypes from file.
> ### Aliases: readStandardGenotypes
> 
> ### ** Examples
> 
> # Genome format
> filename_genome  <- system.file("extdata/genotypes/genome/",
+ "genotypes_genome.txt",
+ package = "PhenotypeSimulator") 
> data_genome <- readStandardGenotypes(N=100, filename_genome, format ="genome")
Warning in data.table::fread(filename, skip = "Samples:", data.table = FALSE,  :
  Detected 1 column names but the data has 2 columns (i.e. invalid file). Added 1 extra default column name for the first column which is guessed to be row names or an index. Use setnames() afterwards if this guess is not correct, or fix the file write command that created the file to create a valid file.
Error in strsplit(data$V2, split = "") : non-character argument
Calls: readStandardGenotypes -> matrix -> unlist -> strsplit
Execution halted
Found the following significant warnings:
  phreeqcpp/cvode.cpp:3783:8: warning: explicitly assigning value of variable of type 'realtype' (aka 'double') to itself [-Wself-assign]
  phreeqcpp/model.cpp:3047:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/model.cpp:3048:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:142:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:155:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:167:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:179:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:193:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:205:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/transport.cpp:630:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/phreeqc.Rcheck/00install.out’ for details.
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.3Mb
Namespaces in Imports field not imported from:
  ‘gplots’ ‘phytools’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/picante.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘lubridate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘covr’ ‘knitr’
  All declared Imports should be used.
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Running examples in ‘Plasmidprofiler-Ex.R’ failed
The error most likely occurred in:

> ### Name: main
> ### Title: Main: Run everything
> ### Aliases: main
> 
> ### ** Examples
> 
> main(blastdata,
+ srst2data,
+ coverage.filter=NA,
+ sureness.filter=0.75,
+ length.filter=10000,
+ main.title="Example Results")
Selecting by pident
Saving 12 x 7 in image
Warning: Ignoring unknown aesthetics: label, text
We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/ggplot2')`
Error in `[.data.table`(dt, , c(.I, .I[1], NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: main ... geom2trace.GeomPolygon -> group2NA -> [ -> [.data.table
Execution halted
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:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
Running examples in ‘plotly-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_fun
> ### Title: Apply function to plot, without modifying data
> ### Aliases: add_fun
> 
> ### ** Examples
> 
> 
> txhousing %>% 
+   group_by(city) %>%
+   plot_ly(x = ~date, y = ~median) %>%
+   add_lines(alpha = 0.2, name = "Texan Cities") %>%
+   add_fun(function(plot) {
+     plot %>% filter(city == "Houston") %>% add_lines(name = "Houston")
+   }) %>%
+   add_fun(function(plot) {
+     plot %>% filter(city == "San Antonio") %>% add_lines(name = "San Antonio")
+   })
Error in `[.data.table`(dt, , c(.I, NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: <Anonymous> ... plotly_build.plotly -> lapply -> FUN -> group2NA -> [ -> [.data.table
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.0Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘PKNCA’ ‘grid’ ‘magrittr’ ‘plyr’ ‘xpose’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Running examples in ‘pointdensityP-Ex.R’ failed
The error most likely occurred in:

> ### Name: pointdensity
> ### Title: Point density function for geospatial data
> ### Aliases: pointdensity
> ### Keywords: density spatial
> 
> ### ** Examples
> 
> Arigon_test <- Arigon[1:1000,]
> Arigon_density <- pointdensity(df = Arigon_test, lat_col = "latitude", 
+ lon_col = "longitude", date_col = "date", grid_size = 1, radius = 2)

The radius was adjusted to  2.0016 km in order to accomodate the grid size


The grid size is  0.009  measured in degrees

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).
Error in `[.data.table`(o_DT, , list(lat_c = max(lat_c), lon_c = max(lon_c),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: pointdensity -> [ -> [.data.table
Execution halted
Found the following significant warnings:
  heftall.c:1389:2: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lsdall.c:2077:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:505:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:999:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:1078:18: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2199:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2208:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2218:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2224:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/polspline.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   2.5Mb
Running examples in ‘popEpi-Ex.R’ failed
The error most likely occurred in:

> ### Name: aggre
> ### Title: Aggregation of split 'Lexis' data
> ### Aliases: aggre
> 
> ### ** Examples
> 
> 
> ## form a Lexis object
> library(Epi)
> data(sibr)
> x <- sibr[1:10,]
> x[1:5,]$sex <- 0 ## pretend some are male
> x <- Lexis(data = x,
+            entry = list(AGE = dg_age, CAL = get.yrs(dg_date)),
+            exit = list(CAL = get.yrs(ex_date)),
+            entry.status=0, exit.status = status)
> x <- splitMulti(x, breaks = list(CAL = seq(1993, 2013, 5), 
+                                  AGE = seq(0, 100, 50)))
OMP: Warning #96: Cannot form a team with 14 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).
Error in `[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: splitMulti -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
OMP: Warning #96: Cannot form a team with 10 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).
Quitting from lines 70-80 (sir.Rmd) 
Error: processing vignette 'sir.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
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.
Found the following significant warnings:
  ppcctest_pearson3.c:19:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/ppcc.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
PP package calling ...
Follow this project on github: https://github.com/manuelreif/PP.git
Quitting from lines 47-68 (ppass_par_and_fit.Rmd) 
Error: processing vignette 'ppass_par_and_fit.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.6Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘methods’ ‘utils’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
Namespaces in Imports field not imported from:
  ‘DiagrammeRsvg’ ‘RColorBrewer’ ‘tidyr’
  All declared Imports should be used.
Running examples in ‘processanimateR-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_token_color
> ### Title: Adds a token color attribute
> ### Aliases: add_token_color
> 
> ### ** Examples
> 
> {
+   # Load example event log
+   library(eventdataR)
+ 
+   # Add token color based on a numeric attribute
+   add_token_color(patients, "time", "color")
+ 
+   # Add token color based on a factor attribute
+   add_token_color(patients, "employee", "color",
+                 color_mapping = scales::col_factor("Set3", patients$employee))
+ }
Event log consisting of:
5442 events
OMP: Warning #96: Cannot form a team with 8 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).
Error in `[.data.table`(eDT, , list(timestamp_classifier = min(get(timestamp(eventlog))),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: <Anonymous> ... trace_list -> trace_list.eventlog -> [ -> [.data.table
Execution halted
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      5.6Mb
Running examples in ‘ProFound-Ex.R’ failed
The error most likely occurred in:

> ### Name: FPtest
> ### Title: False Positive Reference Data
> ### Aliases: FPtest
> ### Keywords: datasets
> 
> ### ** Examples
> 
> image=readFITS(system.file("extdata", 'VIKING/mystery_VIKING_Z.fits', package="ProFound"))
> profound=profoundProFound(image, magzero=30, rotstats=TRUE)
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).
Error in `[.data.table`(tempDT, , .BY, by = segID) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: profoundProFound -> profoundSegimStats -> [ -> [.data.table
Execution halted
Package suggested but not available for checking: ‘qtbase’
Namespaces in Imports field not imported from:
  ‘distcrete’ ‘incidence’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Files which contain pragma(s) suppressing diagnostics:
  ‘src/geobuf.pb.h’ ‘src/rexp.pb.h’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
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.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘methods’ ‘pbkrtest’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: Rcpp
rstanarm (Version 2.17.4, packaged: 2018-04-13 01:51:52 UTC)
- Do not expect the default priors to remain the same in future rstanarm versions.
Thus, R scripts should specify priors explicitly, even if they are just the defaults.
- For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores())
- Plotting theme set to bayesplot::theme_default().

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: There were 1 divergent transitions after warmup. Increasing adapt_delta above 0.95 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems

Warning: There were 2 divergent transitions after warmup. Increasing adapt_delta above 0.95 may help. See
http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
Warning: Examine the pairs() plot to diagnose sampling problems


Attaching package: 'plotly'

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

    last_plot

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

    get_x, get_y

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

    filter

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

    layout

We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/ggplot2')`
Quitting from lines 503-531 (bayesian.Rmd) 
Error: processing vignette 'bayesian.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   2.4Mb
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    dict   5.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.3Mb
Error in re-building vignettes:
  ...
trying URL 'ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2015/11/PXD003133/txt_20min.zip'
Content type 'unknown' length 83554226 bytes (79.7 MB)
==================================================
OMP: Warning #96: Cannot form a team with 4 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).
Quitting from lines 33-62 (PTXQC-Basic_Guide_for_R_users.Rmd) 
Error: processing vignette 'PTXQC-Basic_Guide_for_R_users.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘descr’ ‘gee’ ‘lme4’ ‘nlme’ ‘nnet’ ‘ordinal’ ‘pander’
  ‘papeR’ ‘rmdformats’ ‘visreg’
  All declared Imports should be used.
Running examples in ‘Publish-Ex.R’ failed
The error most likely occurred in:

> ### Name: publish.Score
> ### Title: Publish predictive accuracy results
> ### Aliases: publish.Score
> 
> ### ** Examples
> 
> library(riskRegression)
Loading required package: data.table
Loading required package: ggplot2
> library(survival)
> learn = sampleData(100)
> val= sampleData(100)
> f1=CSC(Hist(time,event)~X1+X8,data=learn)
> f2=CSC(Hist(time,event)~X1+X5+X6+X8,learn)
> xs=Score(list(f1,f2),data=val,formula=Hist(time,event)~1)
OMP: Warning #96: Cannot form a team with 18 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).
Error in `[.data.table`(DT, , `:=`(IC0, residuals - mean(residuals)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: Score ... do.call -> Brier.competing.risks -> [ -> [.data.table
Execution halted
installed size is 39.7Mb
  sub-directories of 1Mb or more:
    libs  39.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Compilation used the following non-portable flag(s):
  ‘-Werror=format-security’ ‘-Wp,-D_FORTIFY_SOURCE=2’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
Found the following significant warnings:
  upwindorderedv4.c:542:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:542:72: 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.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
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       2.9Mb
    libs      1.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Running examples in ‘quantable-Ex.R’ failed
The error most likely occurred in:

> ### Name: determineCut
> ### Title: determine best Accuracy cuttoff
> ### Aliases: determineCut
> 
> ### ** Examples
> 
> library(pROC)
Type 'citation("pROC")' for a citation.

Attaching package: ‘pROC’

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

    cov, smooth, var

> cases <- rnorm(100,-1,1.1)
> controls <- rnorm(500,1,1.1)
> cut <- determineCut(cases,controls)
Error: `data` and `reference` should be factors with the same levels.
Execution halted
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  12.8Mb
Running examples in ‘quanteda-Ex.R’ failed
The error most likely occurred in:

> ### Name: bootstrap_dfm
> ### Title: Bootstrap a dfm
> ### Aliases: bootstrap_dfm
> ### Keywords: bootstrap dfm experimental
> 
> ### ** Examples
> 
> # bootstrapping from the original text
> txt <- c(textone = "This is a sentence.  Another sentence.  Yet another.", 
+          texttwo = "Premiere phrase.  Deuxieme phrase.")
> bootstrap_dfm(txt, n = 3)
Error in `[.data.table`(dt, , `:=`(temp, sample(1:.N, replace = TRUE)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: bootstrap_dfm ... bootstrap_dfm -> bootstrap_dfm.dfm -> [ -> [.data.table
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   4.9Mb
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
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
Namespaces in Imports field not imported from:
  ‘AlgDesign’ ‘psych’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   3.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dtplyr’
  All declared Imports should be used.
Running examples in ‘randomForestExplainer-Ex.R’ failed
The error most likely occurred in:

> ### Name: important_variables
> ### Title: Extract k most important variables in a random forest
> ### Aliases: important_variables
> 
> ### ** Examples
> 
> forest <- randomForest::randomForest(Species ~ ., data = iris, localImp = TRUE, ntree = 300)
> important_variables(measure_importance(forest), k = 2)
Error in `[.data.table`(data.table::as.data.table(min_depth_count_list[[1]]),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: important_variables ... get_min_depth_means -> %>% -> eval -> eval -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Quitting from lines 68-70 (randomForestExplainer.Rmd) 
Error: processing vignette 'randomForestExplainer.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Loading required package: plotrix
Warning: Computation failed in `stat_boxplot()`:
there is no package called 'quantreg'
Warning: Computation failed in `stat_boxplot()`:
there is no package called 'quantreg'
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 246.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘randomNames-Ex.R’ failed
The error most likely occurred in:

> ### Name: randomNames
> ### Title: Random Names Function
> ### Aliases: randomNames
> ### Keywords: misc models
> 
> ### ** Examples
> 
> randomNames()  ## Returns a single name in "last, first" format
[1] "Bradford, Quartus"
> 
> randomNames(5, which.names="first") ## Returns 5 first names
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).
Error in `[.data.table`(tmp.dt, , `:=`(first_name, first_names(gender,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: randomNames -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
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.
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).
Quitting from lines 43-44 (randomNames.Rmd) 
Error: processing vignette 'randomNames.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Error in re-building vignettes:
  ...
Loading required package: cluster
Loading required package: mclust
Package 'mclust' version 5.4
Type 'citation("mclust")' for citing this R package in publications.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RankAggreg.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 150.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.1Mb
Running examples in ‘RAtmosphere-Ex.R’ failed
The error most likely occurred in:

> ### Encoding: UTF-8
> 
> ### Name: suncalc
> ### Title: Sunrise and Sunset calculations
> ### Aliases: suncalc
> ### Keywords: sun sunset sunrise
> 
> ### ** Examples
> 
> t<-Sys.time()+seq(-3600*12,3600*12,,by=600)
> t0=as.POSIXlt(Sys.time(),tz='UTC')
> plot(t,90-SZA(t,Lat=0,Lon=0),main='SZA',xlab='Time',ylab='El [°deg]')
> sun=suncalc(t0[['yday']],UTC=TRUE)
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: suncalc -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
Namespace in Imports field not imported from: ‘lme4’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: RCurl
Loading required package: bitops
Loading required package: RJSONIO
Warning in postForm(url, .params = params, .opts = opts, binary = binary) :
  No inputs passed to form

Error: processing vignette 'rbiouml.Rnw' failed with diagnostics:
 chunk 8 
Error in queryJSON("/web/analysis", params = c(jobID = jobID, de = analysisName,  : 
  Internal server error: java.lang.NullPointerException
Execution halted
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   7.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Found the following significant warnings:
  Warning: replacing previous import ‘Rcmdr::Confint’ by ‘car::Confint’ when loading ‘RcmdrPlugin.BCA’
See ‘/data/gannet/ripley/R/packages/tests-clang/RcmdrPlugin.BCA.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ROpenOffice’
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_votacoes
> ### Title: Fetches all the votings which a proposition went through
> ### Aliases: fetch_votacoes
> 
> ### ** Examples
> 
> votacoes_pec241 <- fetch_votacoes(2088351)
Error in .congresso_api(.$path) : Not Found (HTTP 404).
Calls: fetch_votacoes ... overscope_eval_next -> .congresso_api -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 45-50 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
Column `id` must be a 1d atomic vector or a list
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
    libs      1.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Found the following warnings:
  ../inst/include/blaze/math/smp/openmp/Functions.h:98:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/data/gannet/ripley/R/packages/tests-clang/RcppBlaze.Rcheck/00install.out’ for details.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    include  25.5Mb
    libs      1.8Mb
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     23.5Mb
Running examples in ‘RcppGreedySetCover-Ex.R’ failed
The error most likely occurred in:

> ### Name: greedySetCover
> ### Title: Greedy Set Cover
> ### Aliases: greedySetCover
> ### Keywords: cover greedy set
> 
> ### ** Examples
> 
> # Create some data.
> set.seed(333)
> X <- data.table::rbindlist(
+   lapply(
+     seq_len(1e4L),
+     function(x) list(element=sample.int(n=1e3L,size=sample.int(50L,1L)))
+   ),
+   idcol="set"
+ )
> # Elements are integers 1,2,...,1000.
> 
> # Run set cover
> res <- greedySetCover(X,FALSE)
Error in `[.data.table`(X, , `:=`("i0", .GRP - 1L), by = n1) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: greedySetCover -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
You are recommended to install the tinytex package to build PDF.FALSE
Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55.
Loading required package: RcppGSL
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      39.2Mb
    libs     11.3Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     14.0Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.4Mb
    libs      4.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  cwb/cqp/corpmanag.c:1832:12: warning: comparison of function 'split_subcorpus_name' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/rcqp.Rcheck/00install.out’ for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘smcure’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rcompression’
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
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.
Error in re-building vignettes:
  ...
Quitting from lines 16-19 (rDVR-basics.Rmd) 
Error: processing vignette 'rDVR-basics.Rmd' failed with diagnostics:
there is no package called 'RSelenium'
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   8.6Mb
Found the following apparent object files/libraries:
  inst/obj/cube.obj inst/obj/cube_badmtl.obj
Object files/libraries should not be included in a source package.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
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
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
Running examples in ‘RecordLinkage-Ex.R’ failed
The error most likely occurred in:

> ### Name: classifySupv
> ### Title: Supervised Classification
> ### Aliases: classifySupv classifySupv-methods
> ###   classifySupv,RecLinkClassif,RecLinkData-method
> ###   classifySupv,RecLinkClassif,RLBigData-method
> ### Keywords: classif
> 
> ### ** Examples
> 
> # Split data into training and validation set, train and classify with rpart
> data(RLdata500)
> pairs=compare.dedup(RLdata500, identity=identity.RLdata500,
+                     blockfld=list(1,3,5,6,7))
Error in `[.data.table`(pair_ids, , 1, by = names(pair_ids)) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: compare.dedup -> as.matrix -> [ -> [.data.table
Execution halted
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   4.5Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  15.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/refund.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
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’
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
Running examples in ‘rENA-Ex.R’ failed
The error most likely occurred in:

> ### Name: ena.accumulate.data
> ### Title: Accumulate data from a data frame into a set of adjacency
> ###   (co-occurrence) vectors
> ### Aliases: ena.accumulate.data
> ### Keywords: accumulate data,
> 
> ### ** Examples
> 
> data(RS.data)
> 
> codeNames = c('Data','Technical.Constraints','Performance.Parameters',
+   'Client.and.Consultant.Requests','Design.Reasoning','Collaboration');
> 
> accum = ena.accumulate.data(
+   units = RS.data[,c("UserName","Condition")],
+   conversation = RS.data[,c("Condition","GroupName")],
+   metadata = RS.data[,c("CONFIDENCE.Change","CONFIDENCE.Pre","CONFIDENCE.Post")],
+   codes = RS.data[,codeNames],
+   window.size.back = 4
+ )
OMP: Warning #96: Cannot form a team with 8 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).
Error in `[.data.table`(dfDT_codes, , `:=`((codedTriNames), ref_window_df(.SD[,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: ena.accumulate.data ... <Anonymous> -> accumulate.data -> [ -> [.data.table
Execution halted
Namespaces in Imports field not imported from:
  ‘compiler’ ‘data.table’
  All declared Imports should be used.
Found the following significant warnings:
  gar.c:356:29: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  gar.c:356:80: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/repeated.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘methods’
  All declared Imports should be used.
Found the following significant warnings:
  system_files.cpp:284:8: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Rfast.Rcheck/00install.out’ for details.
installed size is 49.6Mb
  sub-directories of 1Mb or more:
    libs  48.5Mb
Error in re-building vignettes:
  ...
Warning: Ignoring unknown aesthetics: height
Warning in matrix(integer(nrnodes * nt), ncol = nt) :
  data length [25618] is not a sub-multiple or multiple of the number of rows [52]
Warning in matrix(integer(nrnodes * nt), ncol = nt) :
  data length [25618] is not a sub-multiple or multiple of the number of rows [52]
Warning in matrix(integer(nrnodes * nt), ncol = nt) :
  data length [25618] is not a sub-multiple or multiple of the number of rows [52]
Warning in matrix(double(nrnodes * nt), ncol = nt) :
  data length [25618] is not a sub-multiple or multiple of the number of rows [52]
Warning in matrix(integer(nrnodes * nt), ncol = nt) :
  data length [25618] is not a sub-multiple or multiple of the number of rows [52]
Warning in matrix(double(nrnodes * nt), ncol = nt) :
  data length [25618] is not a sub-multiple or multiple of the number of rows [52]
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.6Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.6Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
Rjava.init.warning: stack size reduced from unlimited to 7957504 bytes after JVM initialization.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    help  10.5Mb
    libs   8.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc   9.8Mb
Found the following significant warnings:
  filterhr.c:21:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:53: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:95: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RHRV.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘gWidgetsRGtk2’
  All declared Imports should be used.
Found the following significant warnings:
  computePvals.c:488:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ridge.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Running examples in ‘riskRegression-Ex.R’ failed
The error most likely occurred in:

> ### Name: Score.list
> ### Title: Score risk predictions
> ### Aliases: Score.list Score
> 
> ### ** Examples
> 
> # binary outcome
> library(lava)
lava version 1.6.1
> set.seed(18)
> learndat <- sampleData(48,outcome="binary")
> testdat <- sampleData(40,outcome="binary")
> 
> ## score logistic regression models
> lr1 = glm(Y~X1+X2+X7+X9,data=learndat,family=binomial)
> lr2 = glm(Y~X3+X5,data=learndat,family=binomial)
> Score(list("LR(X1+X2+X7+X9)"=lr1,"LR(X3+X5)"=lr2),formula=Y~1,data=testdat)
Error in `[.data.table`(DT, , data.table::data.table(Brier = sum(residuals)/N,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: Score ... computePerformance -> do.call -> Brier.binary -> [ -> [.data.table
Execution halted
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.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONGlobals.h:44:49: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONSharedString.h:180:47: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:182:66: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  JSONStream.cpp:8:130: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:8:157: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONStream.cpp:12:64: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:12:100: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONValidator.cpp:394:105: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  JSONValidator.cpp:397:104: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  internalJSONNode.cpp:78:117: warning: field '_name_encoded' will be initialized after field '_name' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/RJSONIO.Rcheck/00install.out’ for details.
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  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    rmd   6.1Mb
.onLoad: warning in dir(dll.path, pattern = this.ext, full = FALSE):
  partial argument match of 'full' to 'full.names'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[1], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[2], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: no visible global function definition for ‘quantile’
diagnos.envel: no visible global function definition for ‘qnorm’
diagnos.envel: no visible binding for global variable ‘quantile’
hrplot: no visible global function definition for ‘plot’
hrplot: no visible global function definition for ‘lines’
hrplot: no visible global function definition for ‘abline’
hrplot: no visible global function definition for ‘text’
sim.chain: no visible global function definition for ‘rnorm’
simRandWalk: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline lines plot qnorm quantile rnorm text
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
File ‘RMC/libs/RMC.so’:
  Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’
File ‘RMC/libs/RMC.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 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.4Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
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
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:172:13: warning: variable length arrays are a C99 feature [-Wvla-extension]
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:220:16: warning: variable length arrays are a C99 feature [-Wvla-extension]
See ‘/data/gannet/ripley/R/packages/tests-clang/rncl.Rcheck/00install.out’ for details.
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
Running examples in ‘RNewsflow-Ex.R’ failed
The error most likely occurred in:

> ### Name: directed.network.plot
> ### Title: A wrapper for plot.igraph for visualizing directed networks.
> ### Aliases: directed.network.plot
> 
> ### ** Examples
> 
> data(docnet)
> aggdocnet = network.aggregate(docnet, by='source')
OMP: Warning #96: Cannot form a team with 5 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).
Error in `[.data.table`(e, , list(edges = .N, edge.attribute = agg.FUN(get("var")),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: network.aggregate -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Loading required package: tm
Loading required package: NLP
Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: Matrix
Indexing articles by date/time
Comparing documents
Matching document meta
OMP: Warning #96: Cannot form a team with 5 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).
Quitting from lines 372-378 (RNewsflow.Rmd) 
Error: processing vignette 'RNewsflow.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is 97.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     95.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R   9.7Mb
Running examples in ‘robCompositions-Ex.R’ failed
The error most likely occurred in:

> ### Name: compareMahal
> ### Title: Compares Mahalanobis distances from two approaches
> ### Aliases: compareMahal getEstimates print.estimates plot.estimates
> ###   plot.mahal
> 
> ### ** Examples
> 
> 
> data(arcticLake)
> # generate some zeros
> arcticLake[1:10, 1] <- 0
> arcticLake[11:20, 2] <- 0
> m <- compareMahal(arcticLake)
Warning in (as.numeric(unlist(xilr)) - covs$center)/sqrt(covs$cov) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in (as.numeric(unlist(xilr)) - covs$center)/sqrt(covs$cov) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in `[.data.table`(df, , `:=`(obs, .N), by = list(group)) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: compareMahal -> [ -> [.data.table
Execution halted
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.
Running examples in ‘Robocoap-Ex.R’ failed
The error most likely occurred in:

> ### Name: novel.coap
> ### Title: novel.coap
> ### Aliases: novel.coap
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
> 
> ## Co-apperance vs Interaction Plots
> ## Co-apperance can be automatized, detect interactions is however a hard AI problem
> ## than can be approximated by the co-apperances when the story is long enough.
> 
> txt <- paste("A woman gets on a bus with her baby. The bus driver says:", "'Ugh,
+ that's the ugliest baby I've ever seen!' The woman walks", "to the rear of the
+ bus and sits down, fuming. She says to a man", "next to her: 'The driver just
+ insulted me!\n\nPun\n' The man says:", "'What? you just go back there and tell him
+ off. Go on, I'll hold", "your monkey for you.'")
> 
> res <- Robocoap::novel.coap(novel = txt, characters = c('woman','driver','baby|monkey','man'),
+                  split = 'Pun', language = 'english', plot = FALSE)
Error in `[.data.table`(dt, , .(section = paste("\"<", paste("[", section,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: <Anonymous> -> [ -> [.data.table
Execution halted
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
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.
Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.3Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘withr’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.3Mb
Namespace in Imports field not imported from: ‘vegan’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: robustbase
Scalable Robust Estimators with High Breakdown Point (version 1.4-3)

Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[[2L]], length = arrow.len) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[[2L]], length = arrow.len) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[[2L]], length = arrow.len) :
  zero-length arrow is of indeterminate angle and so skipped
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rrcov.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 252.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
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.
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Namespace in Imports field not imported from: ‘gdalUtils’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  49.6Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Namespace in Imports field not imported from: ‘pkgconfig’
  All declared Imports should be used.
installed size is 157.3Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    doc     2.9Mb
    libs  152.5Mb
installed size is 293.7Mb
  sub-directories of 1Mb or more:
    libs  291.1Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/rsunlight.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
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  5.5Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.5Mb
    projects   2.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.0Mb
Namespace in Imports field not imported from: ‘RGtk2’
  All declared Imports should be used.
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
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 24.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
    test  19.6Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
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.
Error in re-building vignettes:
  ...
OMP: Warning #96: Cannot form a team with 19 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).
Quitting from lines 39-51 (RWildbook_demo2_vignette.Rmd) 
Error: processing vignette 'RWildbook_demo2_vignette.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Found the following significant warnings:
  nchg.c:555:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RxCEcolInf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  call_dvode.c:746:18: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  sum.c:221:11: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:221:22: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:45: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  sum.c:227:53: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RxODE.Rcheck/00install.out’ for details.
Found the following significant warnings:
  yacas/src/obmalloc.cpp:584:23: warning: result of comparison of constant 384307168202282325 with expression of type 'unsigned int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Ryacas.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs    7.5Mb
    yacas   1.5Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
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.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Namespaces in Imports field not imported from:
  ‘purrr’ ‘tidyr’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
Running examples in ‘scorecard-Ex.R’ failed
The error most likely occurred in:

> ### Name: iv
> ### Title: Information Value
> ### Aliases: iv
> 
> ### ** Examples
> 
> # Load German credit data
> data(germancredit)
> 
> # information values
> dt_info_value = iv(germancredit, y = "creditability")
Warning in check_y(dt, y, positive) :
  The positive value in "creditability" was replaced by 1 and negative value by 0.
Error in `[.data.table`(data.table(x = x, y = y), , .(good = sum(y ==  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: iv ... eval -> sapply -> lapply -> FUN -> [ -> [.data.table
Execution halted
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘testthat’
  All declared Imports should be used.
Running examples in ‘sdcMicro-Ex.R’ failed
The error most likely occurred in:

> ### Name: freqCalc
> ### Title: Frequencies calculation for risk estimation
> ### Aliases: freqCalc
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
> data(francdat)
> f <- freqCalc(francdat, keyVars=c(2,4,5,6),w=8)
> f

 --------------------------
4 obs. violate 2-anonymity 
8 obs. violate 3-anonymity 
 --------------------------
> f$freqCalc
  Num1 Key1 Num2 Key2 Key3 Key4 Num3     w
1 0.30    1 0.40    2    5    1    4  18.0
2 0.12    1 0.22    2    1    1   22  45.5
3 0.18    1 0.80    2    1    1    8  39.0
4 1.90    3 9.00    3    1    5   91  17.0
5 1.00    4 1.30    3    1    4   13 541.0
6 1.00    4 1.40    3    1    1   14   8.0
7 0.10    6 0.01    2    1    5    1   5.0
8 0.15    1 0.50    2    5    1    5  92.0
> f$fk
[1] 2 2 2 1 1 1 1 2
> f$Fk
[1] 110.0  84.5  84.5  17.0 541.0   8.0   5.0 110.0
> ## with missings:
> x <- francdat
> x[3,5] <- NA
> x[4,2] <- x[4,4] <- NA
> x[5,6]  <- NA
> x[6,2]  <- NA
> f2 <- freqCalc(x, keyVars=c(2,4,5,6),w=8)
Error in `[.data.table`(dat_with_na, , `:=`(tmpid, .I)) : 
  Cannot use := to add columns to a null data.table (no columns), currently. You can use := to add (empty) columns to a 0-row data.table (1 or more empty columns), though.
Calls: freqCalc -> [ -> [.data.table
Execution halted
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.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.1Mb
    doc    1.2Mb
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.
Running examples in ‘segregation-Ex.R’ failed
The error most likely occurred in:

> ### Name: mutual_difference
> ### Title: Decomposes the difference between two M indices
> ### Aliases: mutual_difference
> 
> ### ** Examples
> 
> mutual_difference(schools00, schools05, unit="race", group="school",
+     weight="n", method="mrc")
Error in `[.data.table`(d1, , list(p_unit = sum(freq)/n_total1), by = unit) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: mutual_difference -> method -> [ -> [.data.table
Execution halted
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘XML’ ‘mgcv’
  All declared Imports should be used.
Running examples in ‘sentimentr-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract_sentiment_terms
> ### Title: Extract Sentiment Words
> ### Aliases: extract_sentiment_terms
> 
> ### ** Examples
> 
> library(data.table)
> set.seed(10)
> x <- get_sentences(sample(cannon_reviews[[2]], 1000, TRUE))
> sentiment(x)
Error in `[.data.table`(sent_dat, , `:=`(id2, seq_len(.N)), by = "id") : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: sentiment ... sentiment.get_sentences_character -> [ -> [.data.table
Execution halted
Running examples in ‘sentometrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: ctr_merge
> ### Title: Set up control for merging sentiment measures
> ### Aliases: ctr_merge
> 
> ### ** Examples
> 
> data("usnews", package = "sentometrics")
> data("lexicons", package = "sentometrics")
> data("valence", package = "sentometrics")
> 
> # construct a sentomeasures object to start with
> corpus <- sento_corpus(corpusdf = usnews)
> corpusSample <- quanteda::corpus_sample(corpus, size = 500)
> l <- setup_lexicons(lexicons[c("LM_eng", "HENRY_eng")], valence[["valence_eng"]])
> ctr <- ctr_agg(howTime = c("equal_weight", "linear"), by = "year", lag = 3)
> sentomeasures <- sento_measures(corpusSample, l, ctr)
Modify corpus to account for valence words... Done. 
Compute sentiment... Done. 
OMP: Warning #96: Cannot form a team with 9 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).
Error in `[.data.table`(s, , lapply(.SD, function(x) (x * 1)/x), by = date) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: sento_measures -> perform_agg -> agg_documents -> [ -> [.data.table
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > 
  > library(testthat)
  > library(sentometrics)
  Loading required package: data.table
  Loading required package: ggplot2
  Loading required package: foreach
  > 
  > test_check("sentometrics")
  Compute sentiment... Done. 
  OMP: Warning #96: Cannot form a team with 9 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. Error: (unknown) (@test_aggregation.R#15)  ───────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: sento_measures(corpus, lex, ctr) at testthat/test_aggregation.R:15
  2: perform_agg(toAgg, ctr)
  3: agg_documents(toAgg, by = by, how = howDocs, do.ignoreZeros = do.ignoreZeros)
  4: s[, lapply(.SD, function(x) (x * word_count)/x), by = date]
  5: `[.data.table`(s, , lapply(.SD, function(x) (x * word_count)/x), by = date)
  
  Compute sentiment... Done. 
  ── 2. Error: (unknown) (@test_attribution.R#15)  ───────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: sento_measures(corpus, lex, ctr) at testthat/test_attribution.R:15
  2: perform_agg(toAgg, ctr)
  3: agg_documents(toAgg, by = by, how = howDocs, do.ignoreZeros = do.ignoreZeros)
  4: s[, list(w = word_count/sum(word_count, na.rm = TRUE)), by = date]
  5: `[.data.table`(s, , list(w = word_count/sum(word_count, na.rm = TRUE)), by = date)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test_aggregation.R#15) 
  2. Error: (unknown) (@test_attribution.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘seoR-Ex.R’ failed
The error most likely occurred in:

> ### Name: lastCached
> ### Title: Function to get the last Google Cache Date for a URL
> ### Aliases: lastCached
> 
> ### ** Examples
> 
> lastCached("https://www.r-project.org/")
Error in if (is.na(res)) { : argument is of length zero
Calls: lastCached
Execution halted
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs  12.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Found the following significant warnings:
  vcf.c:253:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/00install.out’ for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
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  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    doc     10.8Mb
    libs     6.1Mb
    sqlite   1.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    www   9.7Mb
Namespace in Imports field not imported from: ‘shiny’
  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’ ‘gridExtra’ ‘knitr’ ‘latticeExtra’ ‘msm’ ‘plotly’
  ‘shinyBS’ ‘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  8.5Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    www   6.5Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘viridis’
  All declared Imports should be used.
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.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  10.9Mb
File ‘simpleboot/R/zzz.R’:
  .onLoad calls:
    require(boot)

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

lo.boot.resample: warning in sample(1:nrow(orig.data), rep = TRUE, prob
  = weights): partial argument match of 'rep' to 'replace'
lo.boot.resample: warning in sample(res, rep = TRUE, prob = weights):
  partial argument match of 'rep' to 'replace'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.9Mb
Running examples in ‘simPop-Ex.R’ failed
The error most likely occurred in:

> ### Name: ipu2
> ### Title: Iterative Proportional Updating
> ### Aliases: ipu2
> 
> ### ** Examples
> 
> data(eusilcS)
> setDT(eusilcS)
> eusilcS <- eusilcS[, list(db030,hsize,db040,age,rb090,netIncome,db090,rb050)]
> 
> ## rename columns
> setnames(eusilcS, "rb090", "gender")
> setnames(eusilcS, "db040", "state")
> setnames(eusilcS, "db030", "household")
> setnames(eusilcS, "rb050", "weight")
> 
> ## some recoding
> # generate age groups
> eusilcS[, agegroup := cut(age, c(-Inf, 10*1:9, Inf), right = FALSE)]
> # some recoding of netIncome for reasons of simplicity
> eusilcS[is.na(netIncome), netIncome := 0] 
> eusilcS[netIncome < 0, netIncome := 0] 
> # set hsize to 1,...,5+
> eusilcS[, hsize := cut(hsize, c(0:4, Inf), labels = c(1:4, "5+"))]
> # treat households as a factor variable
> eusilcS[, household := as.factor(household)]
> 
> ## example for base weights assuming a simple random sample of households stratified per region
> eusilcS[, regSamp := .N, by = state]
Error in `[.data.table`(eusilcS, , `:=`(regSamp, .N), by = state) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: [ -> [.data.table
Execution halted
Namespaces in Imports field not imported from:
  ‘BB’ ‘MASS’ ‘ggplot2’ ‘grid’ ‘triangle’
  All declared Imports should be used.
Running examples in ‘simstudy-Ex.R’ failed
The error most likely occurred in:

> ### Name: addPeriods
> ### Title: Create longitudinal/panel data
> ### Aliases: addPeriods
> 
> ### ** Examples
> 
> tdef <- defData(varname = "T", dist="binary", formula = 0.5)
> tdef <- defData(tdef, varname = "Y0", dist = "normal", formula = 10, variance = 1)
> tdef <- defData(tdef, varname = "Y1", dist = "normal", formula = "Y0 + 5 + 5 * T", variance = 1)
> tdef <- defData(tdef, varname = "Y2", dist = "normal", formula = "Y0 + 10 + 5 * T", variance = 1)
> 
> dtTrial <- genData( 5, tdef)
> dtTrial
   id T        Y0       Y1       Y2
1:  1 0 11.272429 16.26666 20.98297
2:  2 0 10.414641 17.81929 20.11543
3:  3 1  8.460050 19.22364 23.04854
4:  4 1  9.071433 18.27242 24.32366
5:  5 0  9.705280 13.55762 18.81336
> 
> dtTime <- addPeriods(dtTrial, nPeriods = 3, idvars = "id",
+                      timevars = c("Y0", "Y1", "Y2"), timevarName = "Y")
> dtTime
> 
> # Varying # of periods and intervals - need to have variables
> # called nCount and mInterval
> 
> def <- defData(varname = "xbase", dist = "normal", formula = 20, variance = 3)
> def <- defData(def,varname = "nCount", dist = "noZeroPoisson", formula = 6)
> def <- defData(def, varname = "mInterval", dist = "gamma", formula = 30, variance = .01)
> def <- defData(def, varname = "vInterval", dist = "nonrandom", formula = .07)
> 
> dt <- genData(200, def)
> dt[id %in% c(8,121)]
    id    xbase nCount mInterval vInterval
1:   8 20.87227      6  32.94064      0.07
2: 121 18.49349      5  27.77496      0.07
> 
> dtPeriod <- addPeriods(dt)
Error in `[.data.table`(dtTimes1, , `:=`(time, round(cumsum(timeElapsed))),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: addPeriods -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Loading required package: data.table
OMP: Warning #96: Cannot form a team with 4 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).
Quitting from lines 499-511 (simstudy.Rmd) 
Error: processing vignette 'simstudy.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
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.
Running examples in ‘SIRItoGTFS-Ex.R’ failed
The error most likely occurred in:

> ### Name: readGTFS
> ### Title: read GTFS files from a folder into R's environment
> ### Aliases: readGTFS
> ### Keywords: iteration utilities
> 
> ### ** Examples
> 
>   require(SIRItoGTFS)
>   directory = getwd()
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/agency.csv"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/calendar.csv"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/routes.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/shapes.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/stop_times.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/stops.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/translations.txt"))
>   write.csv(data.frame(matrix(1:9, nrow = 3)), file = file.path(directory,"/trips.txt"))
> 
>   # now we read just the minimal tables needed for `STG`,
>   # meaning everything besides shapes and translations
>   readGTFS(directory, minimal = TRUE, extension = "BOTH")
Error in data.table::fread(input = tbl, sep = sep, nrows = nrows, header = header,  : 
  isTrueFalse(showProgress) is not TRUE
Calls: readGTFS -> <Anonymous> -> stopifnot
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   4.8Mb
Running examples in ‘sitreeE-Ex.R’ failed
The error most likely occurred in:

> ### Name: biomass.M1988
> ### Title: Biomass functions of Marklund (1988) and Petterson and
> ###   Sth<c3><a5>l (2006)
> ### Aliases: biomass.M1988
> 
> ### ** Examples
> 
> 
> res <- sitree (tree.df   = tr,
+                 stand.df  = fl,
+                 functions = list(
+                     fn.growth     = 'grow.dbhinc.hgtinc',
+                     fn.dbh.inc = "dbhi.BN2009",
+                     fn.hgt.inc =  "height.korf", 
+                     fn.mort       = 'mort.B2007',
+                     fn.recr       = 'recr.BBG2008',
+                     fn.management = 'management.prob',
+                     fn.tree.removal = 'mng.tree.removal',
+                     fn.modif      = NULL,
+                     fn.prep.common.vars = 'prep.common.vars.fun'
+                 ),
+                 n.periods = 5,
+                 period.length = 5,
+                 mng.options = NA,
+                 print.comments = FALSE,
+                 species.spruce = c(1, 2, 3),
+                 species.pine = c(10, 11, 20, 21, 29),
+                 species.harw = c(30, 31),
+                 fun.final.felling = "harv.prob",
+                 fun.thinning      = "thin.prob",
+                 'BN2009',
+                 'BBG2008', 'SBA.m2.ha', 'spp','pr.spru.ba', 'QMD.cm',
+                 per.vol.harv = 0.83
+                 )
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).
Error in `[.data.table`(DT, , list(wret = mean(tree.age.years), w = (tree.BA.m2/sum(tree.BA.m2))),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: sitree ... do.call -> prep.common.vars.fun -> [ -> [.data.table
Execution halted
Running examples in ‘sitree-Ex.R’ failed
The error most likely occurred in:

> ### Name: management.prob
> ### Title: Final felling and thinning functions for Norwegian forest
> ### Aliases: harv.prob management.prob thin.prob
> 
> ### ** Examples
> 
> foo.matrix <-  matrix(0, nrow = length(tr$dbh), ncol = (5 +1))
> colnames(foo.matrix) <- paste("t", 0:5, sep = "")
> foo.dbh <- foo.height <- foo.matrix
> foo.dbh[,1] <- tr$dbh
> foo.height[,1] <- tr$height
> 
> trl <- list(
+   plot.id  = tr$plot.id,
+   treeid    = tr$treeid,
+   dbh.mm    = foo.dbh,
+   height.dm = foo.height,
+   yrs.sim   = rep(0, nrow(tr)),
+   tree.sp   = factor(tr$tree.sp)
+ )
> tr.i <- trList$new(data = trl, nperiods = as.integer(5))
> 
> common.vars <-  prep.common.vars.fun(
+   tr = tr.i,
+   fl = fl,
+   i.period       = 0,
+   this.period    = "t0",
+   common.vars    = "NULL",
+   vars.required  = c("spp", "SBA.m2.ha", "QMD.cm", "vuprha.m3.ha", "AgeTo5"),
+   period.length = 5,
+   species.spruce = c(1, 2, 3),
+   species.pine = c(10, 11, 20, 21, 29),
+   species.harw = c(30, 31)
+ )
OMP: Warning #96: Cannot form a team with 3 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
Error in `[.data.table`(DT, , list(wret = mean(tree.age.years), w = (tree.BA.m2/sum(tree.BA.m2))),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: prep.common.vars.fun -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
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).
Quitting from lines 98-180 (TestEquations.Rmd) 
Error: processing vignette 'TestEquations.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Namespace in Imports field not imported from: ‘mcmc’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.0Mb
Error in re-building vignettes:
  ...
Loading required package: magrittr
Loading required package: data.table
OMP: Warning #96: Cannot form a team with 7 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).
skm_mls: skm solver via skm_mls_cpp ...

Quitting from lines 266-276 (skm-vignettes.Rmd) 
Error: processing vignette 'skm-vignettes.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Error in re-building vignettes:
  ...
Quitting from lines 76-80 (slim.Rmd) 
Error: processing vignette 'slim.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
Namespace in Imports field not imported from: ‘ISLR’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.2Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘nlme’ ‘survival’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/sm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  /usr/include/python2.7/unicodeobject.h:534:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:553:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:575:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:593:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:173:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:174:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:175:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/data/gannet/ripley/R/packages/tests-clang/SnakeCharmR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./snappy-stubs-internal.h:95:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/snappier.Rcheck/00install.out’ for details.
Running examples in ‘socialmixr-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_survey
> ### Title: Get a survey, either from its Zenodo repository, a set of files,
> ###   or a survey variable
> ### Aliases: get_survey
> 
> ### ** Examples
> 
> list_surveys()
Error in `[.data.table`(multiple_records, , .I[datestamp == max(datestamp)],  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: list_surveys ... [ -> [.data.table -> eval -> eval -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 77-78 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
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
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
Running ‘test-all.R’ [194s/236s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  ── 1. Failure: simList object initializes correctly (@test-simList.R#17)  ──────────────────────────
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘fastdigest’ ‘httr’
  All declared Imports should be used.
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
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.
Namespaces in Imports field not imported from:
  ‘moments’ ‘poweRlaw’
  All declared Imports should be used.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    doc    4.7Mb
    help   5.0Mb
    libs   1.8Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
Error in re-building vignettes:
  ...
## ----- This is spikeSlabGAM 1.1-11 ----- ##
Please note that a recent update to gridExtra has made it necessary
  to change the interface for <plot.spikeSlabGAM> starting in version 1.1-9.
Instead of arguments 'rows', 'cols', 'widths', 'heights', 'maxPlotsPerPage',
  it now accepts only 'nrow' and 'ncol'.
Arguments 'widths' & 'heights' can still be defined and are handed over
  to <gridExtra:::marrangeGrob>.
Sorry for the inconvenience.
Loading required package: parallel
Loading required package: stabs
This is mboost 2.8-1. See 'package?mboost' and 'news(package  = "mboost")'
for a complete list of changes.


Attaching package: 'ggplot2'

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

    %+%

Warning in (function (xnew)  :
  predictions outside fitted range for lin(glucose).
Warning in (function (xnew)  :
  predictions outside fitted range for sm(glucose).
Warning in bsplines(mf[[i]], knots = args$knots[[i]]$knots, boundary.knots = args$knots[[i]]$boundary.knots,  :
  Some 'x' values are beyond 'boundary.knots'; Linear extrapolation used.
Warning in (function (xnew)  :
  predictions outside fitted range for lin(glucose).
Warning in (function (xnew)  :
  predictions outside fitted range for sm(glucose).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingSpikeSlabGAM.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 252.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘splitstackshape-Ex.R’ failed
The error most likely occurred in:

> ### Name: cSplit_f
> ### Title: Split Concatenated Cells in a data.frame or a data.table
> ### Aliases: cSplit_f
> 
> ### ** Examples
> 
> 
> ## Sample data. Change `n` to larger values to test on larger data
> set.seed(1)
> n <- 10
> mydf <- data.frame(id = sequence(n))
> mydf <- within(mydf, {
+   v3 <- do.call(paste, c(data.frame(matrix(sample(
+   letters, n*4, TRUE), ncol = 4)), sep = "_"))
+   v2 <- do.call(paste, c(data.frame(matrix(sample(
+   LETTERS, n*3, TRUE), ncol = 3)), sep = "."))
+   v1 <- do.call(paste, c(data.frame(matrix(sample(
+   10, n*2, TRUE), ncol = 2)), sep = "-"))
+ })
> mydf
   id   v1    v2      v3
1   1  4-5 V.M.X g_f_y_m
2   2  9-8 Q.W.H j_e_f_p
3   3  4-4 U.L.L o_r_q_m
4   4  4-4 O.G.I x_j_d_e
5   5  5-8 N.B.Q f_u_g_v
6   6  9-3 U.C.G x_m_k_r
7   7  9-8 A.I.M y_s_a_u
8   8  4-2 M.N.T r_z_j_c
9   9  8-3 T.R.C q_j_w_s
10 10 10-2 S.K.W b_u_i_k
> 
> cSplit_f(mydf, splitCols = c("v1", "v2", "v3"), sep = c("-", ".", "_"))
Error in fread(x, sep[i], header = FALSE) : 
  You can provide 'input=' or 'file=', not both.
Calls: cSplit_f -> fread
Execution halted
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   7.7Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  12.0Mb
Namespaces in Imports field not imported from:
  ‘BayesX’ ‘BayesXsrc’ ‘automap’ ‘plyr’ ‘rgdal’ ‘splines’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘viridisLite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
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.
OMP: Warning #96: Cannot form a team with 4 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).
Quitting from lines 694-697 (packageAPI.Rmd) 
Error: processing vignette 'packageAPI.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
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 10.6Mb
  sub-directories of 1Mb or more:
    include   9.1Mb
    lib       1.5Mb
Namespaces in Imports field not imported from:
  ‘readr’ ‘tools’
  All declared Imports should be used.
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.
Running examples in ‘statar-Ex.R’ failed
The error most likely occurred in:

> ### Name: fill_gap
> ### Title: Add rows corresponding to gaps in some variable
> ### Aliases: fill_gap
> 
> ### ** 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(lubridate)

Attaching package: ‘lubridate’

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

    date

> df <- data_frame(
+     id    = c(1, 1, 1, 2),
+     datem  = as.monthly(mdy(c("04/03/1992", "01/04/1992", "03/15/1992", "05/11/1992"))),
+     value = c(4.1, 4.5, 3.3, 3.2)
+ )
> df %>% group_by(id) %>% fill_gap(datem)
Error in `[.data.table`(ans, , list(seq(min(datem), max(datem), by = 1L)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: %>% ... fill_gap -> lazy_eval -> eval -> eval -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'StatCharrms.tex' failed.
LaTeX errors:
! FancyVerb Error:
  Extraneous input `	\end{}' between \end{RBox} and line end
.
\FV@Error ... {FancyVerb Error:
\space \space #1
! FancyVerb Error:
  Extraneous input `	\end{}' between \end{RBox} and line end
.
\FV@Error ... {FancyVerb Error:
\space \space #1
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringr’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘lattice’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: rbenchmark
Loading required package: quantmod
Loading required package: xts
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: TTR
Version 0.4-0 included new data defaults. See ?getSymbols.
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.


WARNING: There have been significant changes to Yahoo Finance data.
Please see the Warning section of '?getSymbols.yahoo' for details.

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
Results are for 2002-07-30 to 2018-03-02
Results are for 2002-07-30 to 2018-03-02
Results are for 2015-03-02 to 2018-03-02
Results are for 2013-03-04 to 2018-03-02
Quitting from lines 155-158 (stocks.Rmd) 
Error: processing vignette 'stocks.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Running examples in ‘stranger-Ex.R’ failed
The error most likely occurred in:

> ### Name: crazyfy
> ### Title: Data preparation before detection of strangers
> ### Aliases: crazyfy
> 
> ### ** Examples
> 
> library(stranger)
> data(iris)
> crazy <- crazyfy(iris[,1:4])
Error in `[.data.table`(dup, , `:=`(g, .GRP), by = cols) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: crazyfy -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
OMP: Warning #96: Cannot form a team with 6 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).
Warning: Using size for a discrete variable is not advised.
Quitting from lines 85-95 (stranger_for_the_impatient.Rmd) 
Error: processing vignette 'stranger_for_the_impatient.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Running examples in ‘strataG-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.data.frame.gtypes
> ### Title: Convert 'gtypes' To 'data.frame'
> ### Aliases: as.data.frame.gtypes as.data.frame,gtypes-method as.data.frame
> 
> ### ** Examples
> 
> data(msats.g)
> 
> # with defaults (alleles in multiple columns, with ids and stratification)
> df <- as.data.frame(msats.g)
OMP: Warning #96: Cannot form a team with 5 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).
Error in `[.data.table`(x@data, , unlist(.SD), by = ids, .SDcols = !c("ids",  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: as.data.frame ... as.matrix -> as.matrix -> .local -> [ -> [.data.table
Execution halted
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/streamR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stringr)
  > 
  > test_check("stringr")
  ── 1. Failure: special case are correct (@test-match.r#13)  ────────────────────
  str_match(NA, "(a)") not equal to matrix(NA_character_).
  Lengths differ: 2 is not 1
  
  ── 2. Failure: special case are correct (@test-match.r#14)  ────────────────────
  str_match(character(), "(a)") not equal to matrix(character(), 0, 1).
  Attributes: < Component "dim": Mean relative difference: 0.5 >
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 217 SKIPPED: 0 FAILED: 2
  1. Failure: special case are correct (@test-match.r#13) 
  2. Failure: special case are correct (@test-match.r#14) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
Running examples in ‘strvalidator-Ex.R’ failed
The error most likely occurred in:

> ### Name: calculateHb
> ### Title: Calculate Heterozygote Balance
> ### Aliases: calculateHb
> 
> ### ** Examples
> 
> data(ref2)
> data(set2)
> # Calculate average balances.
> calculateHb(data=set2, ref=ref2)
'kit' not provided. Attempting auto detection.
Detected kit(s): SGMPlus
Extracting known alleles from dataset...
Using 'fast' allele filtering method.
This method discards NA alleles/loci/samples.
1 "NA" in 'Allele' converted to NA
Removed 1 rows where Allele=<NA>
Audit trail created for res in function filterProfile.
Audit trail updated by function filterProfile.
Estimating size of alleles...
Audit trail updated by function addSize.
Error in `[.data.table`(DT, !is.na(Height), `:=`(Peaks, .N), list(Sample.Name,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: calculateHb -> [ -> [.data.table
Execution halted
Running ‘testthat.R’ [8s/13s]
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")
  ── 1. Error: child process is terminated in Linux (@test-termination.R#85)  ────
  is_process_handle(handle) is not TRUE
  1: expect_true(wait_until_appears(child_id)) at testthat/test-termination.R:85
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: wait_until_appears(child_id)
  5: process_wait(handle, TIMEOUT_IMMEDIATE) at /data/gannet/ripley/R/packages/tests-clang/subprocess.Rcheck/tests/testthat/helper-processes.R:58
  6: stopifnot(is_process_handle(handle))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 71 SKIPPED: 2 FAILED: 1
  1. Error: child process is terminated in Linux (@test-termination.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘classInt’ ‘grDevices’ ‘graphics’ ‘pixmap’ ‘rgeos’
  ‘sp’
  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/SuppDists.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘matrixStats’ ‘nloptr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.5Mb
Running examples in ‘surveyplanning-Ex.R’ failed
The error most likely occurred in:

> ### Name: optsize
> ### Title: Optimal sample size allocation
> ### Aliases: optsize
> ### Keywords: surveyplanning
> 
> ### ** Examples
> 
> 
> data <- data.table(H = 1 : 3,
+                    s2h=10 * runif(3),
+                    s2h2 = 10 * runif(3),
+                    poph = 8 * 1 : 3,
+                    Rh = rep(1, 3),
+                    dd = c(1, 1, 1))
> 
> vars <- optsize(H = "H",
+                 s2h=c("s2h", "s2h2"),
+                 n = 10, poph = "poph",
+                 Rh = "Rh",
+                 fullsampleh = NULL, 
+                 dataset = data)
Error in `[.data.table`(resulth, fullsampleh == 0, `:=`(nh, nh_cor * pnh/sum(pnh)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: optsize -> [ -> [.data.table
Execution halted
installed size is 69.6Mb
  sub-directories of 1Mb or more:
    libs  68.7Mb
Namespace in Imports field not imported from: ‘cowplot’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
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
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: ggplot2
Loading required package: ggpubr
Loading required package: magrittr
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
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.
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).
Quitting from lines 119-122 (Specifiying_weights_in_log-rank_comparisons.Rmd) 
Error: processing vignette 'Specifiying_weights_in_log-rank_comparisons.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Running examples in ‘survMisc-Ex.R’ failed
The error most likely occurred in:

> ### Name: ci
> ### Title: *c*onfidence *i*ntervals for survival curves.
> ### Aliases: ci ci.stratTen ci.ten
> ### Keywords: survival
> 
> ### ** Examples
> 
> ## K&M 2nd ed. Section 4.3. Example 4.2, pg 105.
> data("bmt", package="KMsurv")
> b1 <- bmt[bmt$group==1, ] # ALL patients
> ## K&M 2nd ed. Section 4.4. Example 4.2 (cont.), pg 111.
> ## patients with ALL
> t1 <- ten(Surv(t2, d3) ~ 1, data=bmt[bmt$group==1, ])
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).
Error in `[.data.table`(x, , `:=`("ncg", rev(seq.int(length(n)))), by = cg) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: ten ... ten.data.frame -> ten -> ten.data.table -> [ -> [.data.table
Execution halted
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.
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: ‘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-clang/SWATmodel.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rgeos’ ‘stringr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: sn
Loading required package: stats4

Attaching package: 'sn'

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

    sd

Loading required package: mclust
Package 'mclust' version 5.4
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: cluster
Warning in .tkmeans.warn(O, ret) :
  Clusters with size < n * 0.02 found - try reducing k.
Warning in .tclust.warn(O, O$ret) :
  The result is artificially constrained due to restr.fact = 12.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'tclust.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    sql   8.7Mb
Running examples in ‘tcpl-Ex.R’ failed
The error most likely occurred in:

> ### Name: tcplCytoPt
> ### Title: Calculate the cytotoxicity point based on the "burst" endpoints
> ### Aliases: tcplCytoPt
> 
> ### ** Examples
> 
> ## Store the current config settings, so they can be reloaded at the end 
> ## of the examples
> conf_store <- tcplConfList()
> tcplConfDefault()
> 
> ## Load the "burst" endpoints -- none are defined in the example dataset
> tcplLoadAeid(fld = "burst_assay", val = 1)
Empty data.table (0 rows) of 3 cols: burst_assay,aeid,aenm
> 
> ## Calculate the cytotoxicity distributions using both example endpoints
> tcplCytoPt(aeid = 1:2)
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).
Error in `[.data.table`(dat, , `:=`(chit, mean(hitc[hitc %in% 0:1]) >=  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: tcplCytoPt -> tcplSubsetChid -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package ‘RSQLite’ for request: ‘dbGetQuery’ when loading ‘tcpl’
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /data/gannet/ripley/R/packages/tests-clang/tcpl.Rcheck/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.
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).

Error: processing vignette 'tcpl_Overview.Rnw' failed with diagnostics:
 chunk 18 
Error in `[.data.table`(ms, , lapply(.SD, list), by = list(mthd, ordr)) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
installed size is 36.8Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    apps   2.6Mb
    libs   1.5Mb
Namespaces in Imports field not imported from:
  ‘data.table’ ‘datasets’ ‘stats’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
Namespaces in Imports field not imported from:
  ‘nlme’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
Running examples in ‘TeXCheckR-Ex.R’ failed
The error most likely occurred in:

> ### Name: parse_tex
> ### Title: Parse LaTeX lines
> ### Aliases: parse_tex
> 
> ### ** Examples
> 
> parse_tex(c("A{}", "B[a]{b{c}{d}}z"))
Error in `[.data.table`(out, tex_group == j, `:=`((GROUP_IDj), .GRP),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: parse_tex -> [ -> [.data.table
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   5.3Mb
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"
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
Running examples in ‘textrank-Ex.R’ failed
The error most likely occurred in:

> ### Name: textrank_candidates_lsh
> ### Title: Use locality-sensitive hashing to get combinations of sentences
> ###   which contain words which are in the same minhash bucket
> ### Aliases: textrank_candidates_lsh
> 
> ### ** Examples
> 
> library(textreuse)
> lsh_probability(h = 1000, b = 500, s = 0.1) # A 10 percent Jaccard overlap will be detected well
[1] 0.9934295
> 
> minhash <- minhash_generator(n = 1000, seed = 123456789)
> 
> data(joboffer)
> terminology <- subset(joboffer, upos %in% c("NOUN", "ADJ"), select = c("sentence_id", "lemma"))
> candidates <- textrank_candidates_lsh(x = terminology$lemma, sentence_id = terminology$sentence_id,
+                                       minhashFUN = minhash, bands = 500)
Error in `[.data.table`(buckets, , list(bucket = digest::digest(object = list(hashes = hash,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: textrank_candidates_lsh -> mapply -> <Anonymous> -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
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 140-149 (textrank.Rmd) 
Error: processing vignette 'textrank.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Running examples in ‘textshape-Ex.R’ failed
The error most likely occurred in:

> ### Name: combine
> ### Title: Combine Elements
> ### Aliases: combine combine.default combine.data.frame
> 
> ### ** Examples
> 
> (x <- split_token(DATA[["state"]][1], FALSE))
[[1]]
[1] "Computer" "is"       "fun"      "."        "Not"      "too"      "fun"     
[8] "."       

> combine(x)
[1] "Computer is fun. Not too fun."
> 
> (x2 <- split_token(DATA[["state"]], FALSE))
[[1]]
[1] "Computer" "is"       "fun"      "."        "Not"      "too"      "fun"     
[8] "."       

[[2]]
[1] "No"   "it's" "not"  ","    "it's" "dumb" "."   

[[3]]
[1] "What"   "should" "we"     "do"     "?"     

[[4]]
[1] "You"    "liar"   ","      "it"     "stinks" "!"     

[[5]]
[1] "I"       "am"      "telling" "the"     "truth"   "!"      

[[6]]
[1] "How"     "can"     "we"      "be"      "certain" "?"      

[[7]]
[1] "There" "is"    "no"    "way"   "."    

[[8]]
[1] "I"        "distrust" "you"      "."       

[[9]]
[1] "What"    "are"     "you"     "talking" "about"   "?"      

[[10]]
[1] "Shall" "we"    "move"  "on"    "?"     "Good"  "then"  "."    

[[11]]
[1] "I'm"     "hungry"  "."       "Let's"   "eat"     "."       "You"    
[8] "already" "?"      

> combine(x2)
 [1] "Computer is fun. Not too fun."       "No it's not, it's dumb."            
 [3] "What should we do?"                  "You liar, it stinks!"               
 [5] "I am telling the truth!"             "How can we be certain?"             
 [7] "There is no way."                    "I distrust you."                    
 [9] "What are you talking about?"         "Shall we move on? Good then."       
[11] "I'm hungry. Let's eat. You already?"
> 
> (x3 <- split_sentence(DATA))
Error in `[.data.table`(z, , `:=`("sentence_id", 1:.N), by = list(element_id)) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: split_sentence -> split_sentence.data.frame -> [ -> [.data.table
Execution halted
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    3.8Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘splancs’ ‘tidyverse’
  All declared Imports should be used.
Running examples in ‘TideTables-Ex.R’ failed
The error most likely occurred in:

> ### Name: TideTable
> ### Title: Compute tide tables
> ### Aliases: TideTable
> 
> ### ** Examples
> 
> TideTable(dataInput=observation, asdate=observation$observation_date[1], 
+ astime=observation$observation_time[1], 
+ aedate="1991/05/01", aetime="21:00:00", ssdate="1995/01/01", 
+ sstime="00:00:00", sedate="1995/01/31", setime="21:00:00")
Error in `[.data.table`(input, , `:=`(n_mhist, .N), by = mhist) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: TideTable -> EstimateTmhwi -> [ -> [.data.table
Execution halted
Namespaces in Imports field not imported from:
  ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyinftheo)
  > 
  > test_check("tidyinftheo")
  ── 1. Error: right number of columns given (@test-errors.R#10)  ────────────────
  argument "expr" is missing, with no default
  1: expect_length(tab %>% select(vs) %>% shannon_entropy(), 1) at testthat/test-errors.R:10
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tab %>% select(vs) %>% shannon_entropy()
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: withVisible(function_list[[k]](value))
  11: function_list[[k]](value)
  12: shannon_entropy(.)
  13: reduce_data(.data, !!enquo(X), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !!!quos(...))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘broom’ ‘curl’ ‘devtools’ ‘rvest’ ‘timeSeries’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dbplyr’ ‘reprex’ ‘rlang’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/TimeMachine.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘forecast’
  All declared Imports should be used.
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.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.3Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    examples  14.9Mb
    include    3.0Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
Note: found 42 marked Latin-1 strings
  Note: found 360 marked UTF-8 strings
Error in re-building vignettes:
  ...
Loading required package: data.table
No methods found in package 'RSQLite' for request: 'dbGetQuery' when loading 'tcpl'
tcpl (v1.2.2) loaded with the following settings:
  TCPL_DB:    /data/gannet/ripley/R/test-clang/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in TCPL.conf. See ?tcplConf for more information.
toxboot 0.1.1
MongoDB settings (?toxbootConf):
  TOXBOOT_HOST: NA
  TOXBOOT_DBNS: NA
  TOXBOOT_USER: NA
  TOXBOOT_DB: NA
MySQL settings:
  Host: localhost
  Database: 
  User: 
Loading required package: DBI
Quitting from lines 197-204 (toxboot.Rmd) 
Error: processing vignette 'toxboot.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
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  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.7Mb
Namespace in Imports field not imported from: ‘neuralnet’
  All declared Imports should be used.
Running examples in ‘translateSPSS2R-Ex.R’ failed
The error most likely occurred in:

> ### Name: xpssMeans
> ### Title: Simple descriptive statistics
> ### Aliases: xpssMeans
> 
> ### ** Examples
> 
> # mean of variable V3
> xpssMeans(x=fromXPSS,variables="V3")
$V3
$V3$summary
     valid_obs. percent missing obs. percent overall percent
[1,] "20"       "100%"  "0"          "0%"    "20"    "100%" 

$V3$cells
   mean        sd  n
1:  2.2 0.7677719 20


> 
> # mean of variable V3 and V4
> xpssMeans(x=fromXPSS,variables=c("V3","V4"))
$V3
$V3$summary
     valid_obs. percent missing obs. percent overall percent
[1,] "20"       "100%"  "0"          "0%"    "20"    "100%" 

$V3$cells
   mean        sd  n
1:  2.2 0.7677719 20


$V4
$V4$summary
     valid_obs. percent missing obs. percent overall percent
[1,] "20"       "100%"  "0"          "0%"    "20"    "100%" 

$V4$cells
   mean        sd  n
1:  1.4 0.5026247 20


> 
> # mean of variable V3 and V6 by V4
> xpssMeans(x=fromXPSS,variables=c("V3","V6"),by="V4")
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).
Error in `[.data.table`(tinput, , eval(parse(text = express)), by = byarg) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: xpssMeans -> [ -> [.data.table
Execution halted
Namespaces in Imports field not imported from:
  ‘lme4’ ‘nlme’
  All declared Imports should be used.
Running examples in ‘treemap-Ex.R’ failed
The error most likely occurred in:

> ### Name: random.hierarchical.data
> ### Title: Create random hierarchical data
> ### Aliases: random.hierarchical.data
> 
> ### ** Examples
> 
> d <- random.hierarchical.data(200)
> treemap(d, index=names(d)[1:(ncol(d)-1)], vSize="x")
OMP: Warning #96: Cannot form a team with 8 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).
Error in `[.data.table`(dtfDT, , list(s = fn(s), c = do.call("fun", c(list(c),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: treemap ... tmAggregate -> tmAggregateStep -> [ -> [.data.table
Execution halted
Running examples in ‘trelliscope-Ex.R’ failed
The error most likely occurred in:

> ### Name: applyCogFn
> ### Title: Apply Cognostics Function to a Key-Value Pair
> ### Aliases: applyCogFn
> 
> ### ** Examples
> 
> # create a division with a between-subset variable
> d <- divide(iris, by = "Species",
+   bsvFn = function(x) list(msl = mean(x$Sepal.Length)))
OMP: Warning #96: Cannot form a team with 5 threads, using 2 instead.
OMP: Hint Consider unsetting KMP_DEVICE_THREAD_LIMIT (KMP_ALL_THREADS), KMP_TEAMS_THREAD_LIMIT, and OMP_THREAD_LIMIT (if any are set).
Error in `[.data.table`(d, , ff(.SD), by = key(d), .SDcols = nms) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: divide -> getDivideDF -> [ -> [.data.table
Execution halted
installed size is 37.5Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespace in Imports field not imported from: ‘gsDesign’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘forecast’
  All declared Imports should be used.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$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.
Running examples in ‘TSstudio-Ex.R’ failed
The error most likely occurred in:

> ### Name: EURO_Brent
> ### Title: Crude Oil Prices: Brent - Europe
> ### Aliases: EURO_Brent
> ### Keywords: datasets
> 
> ### ** Examples
> 
> ts.plot_ly(EURO_Brent)
[1] "The ts.plot_ly function will be deprecated on the next release, please use ts_plot instead"
Error in `[.data.table`(dt, , c(.I, NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: <Anonymous> ... plotly_build.plotly -> lapply -> FUN -> group2NA -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: TTR
Version 0.4-0 included new data defaults. See ?getSymbols.
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.


WARNING: There have been significant changes to Yahoo Finance data.
Please see the Warning section of '?getSymbols.yahoo' for details.

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
Quitting from lines 37-64 (TSstudio_Intro.Rmd) 
Error: processing vignette 'TSstudio_Intro.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs       22.3Mb
Running examples in ‘udpipe-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.data.frame.udpipe_connlu
> ### Title: Convert the result of udpipe_annotate to a tidy data frame
> ### Aliases: as.data.frame.udpipe_connlu
> 
> ### ** Examples
> 
> x <- udpipe_download_model(language = "dutch-lassysmall")
Downloading udpipe model from https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.0/master/inst/udpipe-ud-2.0-170801/dutch-lassysmall-ud-2.0-170801.udpipe to /data/gannet/ripley/R/packages/tests-clang/udpipe.Rcheck/dutch-lassysmall-ud-2.0-170801.udpipe
trying URL 'https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.0/master/inst/udpipe-ud-2.0-170801/dutch-lassysmall-ud-2.0-170801.udpipe'
Content type 'application/octet-stream' length 9208258 bytes (8.8 MB)
==================================================
downloaded 8.8 MB

> ud_dutch <- udpipe_load_model(x$file_model)
> txt <- c("Ik ben de weg kwijt, kunt u me zeggen waar de Lange Wapper ligt? Jazeker meneer", 
+          "Het gaat vooruit, het gaat verbazend goed vooruit")
> x <- udpipe_annotate(ud_dutch, x = txt)
> x <- as.data.frame(x)
Error in `[.data.table`(out, , `:=`(paragraph_id, cumsum(is_newparagraph)),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: as.data.frame ... as.data.frame.udpipe_connlu -> read_connlu -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Downloading udpipe model from https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.0/master/inst/udpipe-ud-2.0-170801/dutch-ud-2.0-170801.udpipe to /data/gannet/ripley/R/packages/tests-clang/udpipe.Rcheck/vign_test/udpipe/vignettes/dutch-ud-2.0-170801.udpipe
trying URL 'https://raw.githubusercontent.com/jwijffels/udpipe.models.ud.2.0/master/inst/udpipe-ud-2.0-170801/dutch-ud-2.0-170801.udpipe'
Content type 'application/octet-stream' length 19992491 bytes (19.1 MB)
==================================================
downloaded 19.1 MB

Quitting from lines 93-99 (udpipe-annotation.Rmd) 
Error: processing vignette 'udpipe-annotation.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.6Mb
    libs   2.6Mb
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
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.
Error in re-building vignettes:
  ...
Quitting from lines 92-93 (regress_intro.Rmd) 
Error: processing vignette 'regress_intro.Rmd' failed with diagnostics:
object 'ttodth' not found
Execution halted
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Running examples in ‘vardpoor-Ex.R’ failed
The error most likely occurred in:

> ### Name: vardannual
> ### Title: Variance estimation for measures of annual net change or annual
> ###   for single and multistage stage cluster sampling designs
> ### Aliases: vardannual
> ### Keywords: vardchangannual
> 
> ### ** Examples
> 
> 
> ### Example 
> data("eusilc")
> set.seed(1)
> eusilc1 <- eusilc[1 : 100,]
> set.seed(1)
> data <- data.table(rbind(eusilc1, eusilc1),
+                    year = c(rep(2010, nrow(eusilc1)),
+                             rep(2011, nrow(eusilc1))))
> data[, country := "AT"]
> data[, quarter:= .I - 4 * trunc((.I - 1) / 4)]
> data[age < 0, age:= 0]
> PSU <- data[, .N, keyby = "db030"][, N:= NULL]
> PSU[, PSU:= trunc(runif(nrow(PSU), 0, 5))]
> data <- merge(data, PSU, all = TRUE, by = "db030")
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).
> PSU <- eusilc <- NULL
> data[, strata := c("XXXX")]
> 
> data[, employed := trunc(runif(nrow(data), 0, 2))]
> data[, unemployed := trunc(runif(nrow(data), 0, 2))]
> data[, labour_force := employed + unemployed]
> data[, id_lv2 := paste0("V", .I)]
> 
> result <- vardannual(Y = "employed", H = "strata",
+                      PSU = "PSU", w_final = "rb050",
+                      ID_level1 = "db030", ID_level2 = "id_lv2",
+                      Dom = NULL, Z = NULL, country = "country",
+                      years = "year", subperiods = "quarter",
+                      dataset = data, percentratio = 100,
+                      confidence = 0.95, method = "cros")
Error in `[.data.table`(DT1, , `:=`(nh, .N), by = c(namesperc2, names_H)) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: vardannual -> vardcros -> [ -> [.data.table
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of 'arg' to
  'args'
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.2Mb
    help   2.7Mb
Running examples in ‘VIM-Ex.R’ failed
The error most likely occurred in:

> ### Name: hotdeck
> ### Title: Hot-Deck Imputation
> ### Aliases: hotdeck
> ### Keywords: manip
> 
> ### ** Examples
> 
> 
> data(sleep)
> sleepI <- hotdeck(sleep)
OMP: Warning #96: Cannot form a team with 22 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).
> sleepI2 <- hotdeck(sleep,ord_var="BodyWgt",domain_var="Pred")
Error in `[.data.table`(x, , imputeHD(.SD, variableX = variable, varTypeX = varType,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: hotdeck ... hotdeck.data.frame -> hotdeck_work -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 157-163 (using_visdat.Rmd) 
Error: processing vignette 'using_visdat.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc           4.8Mb
    htmlwidgets   3.7Mb
Running examples in ‘vistime-Ex.R’ failed
The error most likely occurred in:

> ### Name: vistime
> ### Title: vistime
> ### Aliases: vistime vistime-package vistime
> ### Keywords: gantt plotly timeline vistime
> 
> ### ** Examples
> 
> # presidents and vice presidents
> pres <- data.frame(Position=c(rep("President", 3), rep("Vice", 3)),
+                   Name = c("Washington", "Adams", "Jefferson", "Adams", "Jefferson", "Burr"),
+                   start = rep(c("1789-03-29", "1797-02-03", "1801-02-03"), 2),
+                   end = rep(c("1797-02-03", "1801-02-03", "1809-02-03"), 2),
+                   color = c('#cbb69d', '#603913', '#c69c6e'),
+                   rep(c("black", "white", "black"), 2))
> 
> vistime(pres, events="Position", groups="Name", title="Presidents of the USA",
+               lineInterval = 60*60*24*365*5)
Error in `[.data.table`(dt, , c(.I, NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: vistime ... plotly_build.plotly -> lapply -> FUN -> group2NA -> [ -> [.data.table
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    extdata  10.8Mb
Running examples in ‘vortexR-Ex.R’ failed
The error most likely occurred in:

> ### Name: Nadults
> ### Title: Calculate the harmonic mean of the total number of adults
> ### Aliases: Nadults
> 
> ### ** Examples
> 
> # Using Pacioni et al. example data. See ?pac.yr for more details.
> data(pac.yr)
> NadultAll <- Nadults(data=pac.yr[[2]], scenarios='all', gen=2.54, yr0=50,
+                      yrt=120, save2disk=FALSE)
Calculating the harmonic means of total number of individuals and number of adults from year 50 to year 117
NOTE: The last year used in the calculations is adjusted using the generation time provided (yrt - gen). See documentation for more information.
Error in `[.data.table`(slcensusMeans, , lapply(.SD, HarmMean), .SDcols = c("Nad",  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: Nadults -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 187-190 (vortexRguide.Rmd) 
Error: processing vignette 'vortexRguide.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
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.
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  50.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘shinyjs’ ‘shinythemes’ ‘spThin’
  ‘spocc’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘pbmcapply’ ‘proxy’ ‘signal’
  All declared Imports should be used.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
Namespace in Imports field not imported from: ‘fauxpas’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘minqa’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: Matrix
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'wgsea.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 252.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Namespaces in Imports field not imported from:
  ‘drc’ ‘imputeTestbench’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RandomFields’ ‘data.table’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
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 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Running examples in ‘WVPlots-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotlyROC
> ### Title: Use 'plotly' to produce a ROC plot.
> ### Aliases: plotlyROC
> 
> ### ** Examples
> 
> 
> 
> d <- data.frame(x= 1:5, y= c(TRUE, FALSE , TRUE, TRUE, TRUE))
> plotlyROC(d, 'x', 'y', TRUE, 'example plot')
Error in `[.data.table`(dt, , c(.I, NA), by = keyVars) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: <Anonymous> ... plotly_build.plotly -> lapply -> FUN -> group2NA -> [ -> [.data.table
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.4Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
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 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
Running examples in ‘yCrypticRNAs-Ex.R’ failed
The error most likely occurred in:

> ### Name: bam_to_reads
> ### Title: Convert BAM files into BED files containing the reads overlaping
> ###   the specified annotations.
> ### Aliases: bam_to_reads
> 
> ### ** Examples
> 
> bamfile <- system.file("extdata", "wt_rep1.bam", package = "yCrypticRNAs")
> data(annotations)
> bam_to_reads(bamfile, annotations)
Warning: The RangesList() constructor is deprecated. Please coerce to
  IRangesList instead e.g. do 'as(list(x1, x2), "IRangesList")' instead
  of 'RangesList(x1, x2)'. Alternatively, you can use the IRangesList()
  constructor e.g. 'IRangesList(x1, x2, compress=FALSE)'. See
  '?IRangesList' for more information.
Error in new(Class) : 
  trying to generate an object from a virtual class ("SimpleIntegerRangesList")
Calls: bam_to_reads ... .bam_to_reads_by_gene -> <Anonymous> -> <Anonymous> -> new
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-60 (yCrypticRNAs.Rmd) 
Error: processing vignette 'yCrypticRNAs.Rmd' failed with diagnostics:
trying to generate an object from a virtual class ("SimpleIntegerRangesList")
Execution halted
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘MatchIt’ ‘WhatIf’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.7Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
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.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
Running examples in ‘AdhereR-Ex.R’ failed
The error most likely occurred in:

> ### Name: CMA1
> ### Title: CMA1 and CMA3 constructors.
> ### Aliases: CMA1 CMA3
> 
> ### ** Examples
> 
> cma1 <- CMA1(data=med.events,
+              ID.colname="PATIENT_ID",
+              event.date.colname="DATE",
+              event.duration.colname="DURATION",
+              followup.window.start=30,
+              observation.window.start=30,
+              observation.window.duration=365,
+              date.format="%m/%d/%Y"
+             );
Error in `[.data.table`(data, , `:=`(c(".FU.START.DATE", ".FU.END.DATE",  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: CMA1 ... compute.event.int.gaps -> .compute.function -> fnc -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 188-208 (AdhereR-overview.Rmd) 
Error: processing vignette 'AdhereR-overview.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Found the following significant warnings:
  ADM3.c:37:12: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:37:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:54:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/ADM3.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Running examples in ‘aLFQ-Ex.R’ failed
The error most likely occurred in:

> ### Name: AbsoluteQuantification
> ### Title: Absolute label-free quantification of mass spectrometry
> ###   proteomics experiments
> ### Aliases: AbsoluteQuantification AbsoluteQuantification.default
> ###   predict.AbsoluteQuantification cval cval.default
> ###   cval.AbsoluteQuantification print.AbsoluteQuantification
> ###   plot.AbsoluteQuantification hist.AbsoluteQuantification pivot
> ###   pivot.default pivot.AbsoluteQuantification export export.default
> ###   export.AbsoluteQuantification
> ### Keywords: AbsoluteQuantification absolute label-free quantification
> 
> ### ** Examples
> 
> data(UPS2MS)
> 
> UPS2_SRM<-head(UPS2_SRM,100) # Remove this line for real applications
> data_PI <- ProteinInference(UPS2_SRM)
Error in `[.data.table`(data.dt, , list(min_mean_transition_intensity = min(strictnessfilter.ProteinInference(sort(mean_transition_intensity,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: ProteinInference ... [ -> [.data.table -> eval -> eval -> [ -> [.data.table
Execution halted
Found the following significant warnings:
  em.cpp:208:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/Amelia.Rcheck/00install.out’ for details.
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > #Copyright © 2016 RTE Réseau de transport d’électricité
  > 
  > require(testthat)
  Loading required package: testthat
  > require(antaresRead)
  Loading required package: antaresRead
  > require(plyr)
  Loading required package: plyr
  > 
  > 
  > #Maybe include this in some test-file.R 
  > #is.solaris<-function(){
  > #  grepl('SunOS',Sys.info()['sysname'])
  > #}
  > 
  > #if(!is.solaris()){
  > 
  > test_check("antaresRead")
  Error in `[.data.table`(x, , mapply(function(x, f) { : 
    SETLENGTH() cannot be applied to an ALTVEC object.
  Calls: test_check ... eval -> eval -> suppressMessages -> withCallingHandlers
  Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See ‘/data/gannet/ripley/R/packages/tests-devel/audio.Rcheck/00install.out’ for details.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   3.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 156.7Mb
  sub-directories of 1Mb or more:
    libs  155.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.3Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Running examples in ‘batchtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: Tags
> ### Title: Add or Remove Job Tags
> ### Aliases: Tags addJobTags removeJobTags getUsedJobTags
> 
> ### ** Examples
> 
> tmp = makeRegistry(file.dir = NA, make.default = FALSE)
No configuration file found
Created registry in '/tmp/RtmpgnTVhG/registry3115731b08a7' using cluster functions 'Interactive'
> ids = batchMap(sqrt, x = -3:3, reg = tmp)
Adding 7 jobs ...
> 
> # Add new tag to all ids
> addJobTags(ids, "needs.computation", reg = tmp)
> getJobTags(reg = tmp)
   job.id              tags
1:      1 needs.computation
2:      2 needs.computation
3:      3 needs.computation
4:      4 needs.computation
5:      5 needs.computation
6:      6 needs.computation
7:      7 needs.computation
> 
> # Add more tags
> addJobTags(findJobs(x < 0, reg = tmp), "x.neg", reg = tmp)
> addJobTags(findJobs(x > 0, reg = tmp), "x.pos", reg = tmp)
> getJobTags(reg = tmp)
Error in `[.data.table`(reg$tags[ids, on = "job.id"], , list(tags = stri_flatten(sort(tag,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: getJobTags -> [ -> [.data.table
Execution halted
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  17.5Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 53.5Mb
  sub-directories of 1Mb or more:
    libs  52.8Mb
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  29.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 98.1Mb
  sub-directories of 1Mb or more:
    libs  98.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 93.3Mb
  sub-directories of 1Mb or more:
    libs  91.9Mb
Running examples in ‘behavr-Ex.R’ failed
The error most likely occurred in:

> ### Name: bin_apply
> ### Title: Bin a variable (typically time) and compute an aggregate for
> ###   each bin
> ### Aliases: bin_apply bin_apply_all
> 
> ### ** Examples
> 
> metadata <- data.frame(id = paste0("toy_experiment|",1:5))
> dt <- toy_activity_data(metadata, duration = days(2))
> 
> # average by 30min time bins, default
> dt_binned <- bin_apply_all(dt, moving)
Error in `[.data.table`(data, , bin_apply(data = .SD, ...), by = eval(data.table::key(data))) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: bin_apply_all -> [ -> [.behavr -> NextMethod -> [.data.table
Execution halted
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/biclust.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.3Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.8Mb
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  30.2Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
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  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
blighty: no visible global function definition for ‘par’
blighty: no visible global function definition for ‘polygon’
blighty: no visible global function definition for ‘points’
blighty: no visible global function definition for ‘box’
blighty: no visible global function definition for ‘axis’
blighty: no visible global function definition for ‘abline’
map.scale: no visible global function definition for ‘locator’
map.scale: no visible global function definition for ‘segments’
map.scale: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘locator’
north.pointer: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘arrows’
north.pointer: no visible global function definition for ‘segments’
sqlimits: no visible global function definition for ‘frame’
sqlimits: no visible global function definition for ‘par’
Undefined global functions or variables:
  abline arrows axis box frame locator par points polygon segments text
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "locator", "par", "points", "polygon", "segments", "text")
to your NAMESPACE file.
installed size is 52.6Mb
  sub-directories of 1Mb or more:
    libs  51.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
installed size is 594.6Mb
  sub-directories of 1Mb or more:
    include    3.2Mb
    lib      591.0Mb
installed size is 134.6Mb
  sub-directories of 1Mb or more:
    libs  134.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  30.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    bin    2.5Mb
    doc    1.1Mb
    libs   2.4Mb
installed size is 36.8Mb
  sub-directories of 1Mb or more:
    libs  35.6Mb
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-devel/bsts.Rcheck/00install.out’ for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    5.7Mb
    libs   1.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.8Mb
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   9.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
Found the following significant warnings:
  exact.cpp:10:9: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  exact.cpp:125:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  exact.cpp:174:10: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  exact.cpp:204:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/clusrank.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   5.9Mb
Found the following significant warnings:
  sbp.cpp:627:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  sbp.cpp:627:50: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  sbp.cpp:649:22: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  principal_balances.cpp:114:32: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/coda.base.Rcheck/00install.out’ for details.
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Found the following significant warnings:
  bdsmatrix_stub.h:41:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:44:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:50:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:53:12: warning: return makes integer from pointer without a cast [-Wint-conversion]
  bdsmatrix_stub.h:97:5: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  bdsmatrix_stub.h:100:12: warning: return from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/data/gannet/ripley/R/packages/tests-devel/coxme.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/cplm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
Found the following significant warnings:
  instabCorrection.cpp:34:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/cstab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/ctsem.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   6.1Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/DatABEL.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Running examples in ‘datadr-Ex.R’ failed
The error most likely occurred in:

> ### Name: addTransform
> ### Title: Add a Transformation Function to a Distributed Data Object
> ### Aliases: addTransform
> 
> ### ** Examples
> 
> # Create a distributed data frame using the iris data set, backed by the
> # kvMemory (in memory) connection
> bySpecies <- divide(iris, by = "Species")
Error in `[.data.table`(d, , ff(.SD), by = key(d), .SDcols = nms) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: divide -> getDivideDF -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Warning in cor(final_data, ...) : the standard deviation is zero
Warning: Removed 464016 rows containing non-finite values (stat_boxplot).
Warning: Removed 76619 rows containing missing values (geom_point).
Warning: Removed 28290 rows containing missing values (geom_point).
Quitting from lines 187-188 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is 41.7Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  39.6Mb
Error in re-building vignettes:
  ...
Quitting from lines 57-64 (applications.Rmd) 
Error: processing vignette 'applications.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Running examples in ‘dblr-Ex.R’ failed
The error most likely occurred in:

> ### Name: dblr_train
> ### Title: Discrete Boosting Logistic Regression Training
> ### Aliases: dblr_train
> 
> ### ** Examples
> 
> # use iris data for example
> dat <- iris
> # create two categorical variables
> dat$Petal.Width <- as.factor((iris$Petal.Width<=0.2)*1+(iris$Petal.Width>1.0)*2)
> dat$Sepal.Length <- (iris$Sepal.Length<=3.0)*2+(iris$Sepal.Length>6.0)*1.25
> # create the response variable
> dat$Species <- as.numeric(dat$Species=='versicolor')
> set.seed(123)
> # random sampling
> index <- sample(1:150,100,replace = FALSE)
> # train the dblr model using the training data
> dblr_fit <- dblr_train(train_x=dat[index,c(1:4)],
+ train_y=dat[index,5],category_cols = c('Petal.Width','Sepal.Length'),
+ metric = 'logloss',subsample = 0.5,eta = 0.05,colsample = 1.0,
+ lambda = 1.0,cv_early_stops = 10,verbose=FALSE)
Error in `[.data.table`(trees_nodes_0, , `:=`(vl = cumsum(l[.N:1])[.N:1],  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: dblr_train -> [ -> [.data.table
Execution halted
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   7.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.4Mb
    libs   2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 43.5Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  25.0Mb
Running examples in ‘dgo-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgirt_fit-class
> ### Title: A class for fitted dynamic group IRT models
> ### Aliases: dgirt_fit-class dgirt_fit
> 
> ### ** Examples
> 
> data(toy_dgirtfit)
> # summarize the fitted results
> summary(toy_dgirtfit, pars = 'xi')
dgirt samples from 4 chains of 400 iterations, 200 warmup, thinned every 1 
  Drawn Fri Dec  1 11:54:14 2017 
  Package version 0.2.13 
  Model version 2017_01_04 
  43 parameters; 12 theta_bars (year state race3)
  2 periods 2009 to 2010 

n_eff
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  94.08  149.33  174.47  270.79  363.04  800.00 

Rhat
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
 0.9971  1.0082  1.0225  1.0202  1.0291  1.0520 

Elapsed time
   chain warmup sample total
1:     1     5S     3S    8S
2:     2     5S     5S   10S
3:     3     5S     6S   11S
4:     4     5S     3S    8S
> 
> # get posterior means with a convenience function
> get_posterior_mean(toy_dgirtfit, pars = 'theta_bar')
Error in `[.data.table`(samples, , do_funs(list(value), funs), by = c(attr(samples,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: get_posterior_mean ... summarize -> summarize -> .local -> [ -> [.data.table
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/dhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Sampling sensitivity with m=500 gamma=0.2 k=439
Sampling sensitivity with m=285 gamma=0.1 k=285
Quitting from lines 296-310 (diffpriv.Rnw) 
Error: processing vignette 'diffpriv.Rnw' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    include  19.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.7Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   6.0Mb
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.0Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  19.0Mb
Running examples in ‘easySdcTable-Ex.R’ failed
The error most likely occurred in:

> ### Name: ProtectTable
> ### Title: Easy interface to sdcTable: Table suppression according to a
> ###   frequency rule.
> ### Aliases: ProtectTable
> 
> ### ** Examples
> 
>  # ==== Example 1 , 8 regions ====
>  z1 <- EasyData("z1")        
>  ProtectTable(z1,1:2,3)
....Error in `[.data.table`(subDat, , eval(expr), by = key(subDat)) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: ProtectTable ... c_quick_suppression -> c_quick_suppression -> [ -> [.data.table
Execution halted
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-2>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-3>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-4>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-5>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-6>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 67-68 (easySdcTableVignette.Rmd) 
Error: processing vignette 'easySdcTableVignette.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Running examples in ‘edarf-Ex.R’ failed
The error most likely occurred in:

> ### Name: partial_dependence
> ### Title: Partial dependence using random forests
> ### Aliases: partial_dependence
> 
> ### ** Examples
> 
> library(randomForest)
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
> library(edarf)
> 
> data(iris)
> data(swiss)
> 
> ## classification
> fit = randomForest(Species ~ ., iris)
> pd = partial_dependence(fit, c("Sepal.Width", "Sepal.Length"),
+   data = iris[, -ncol(iris)])
Error in `[.data.table`(mp, , as.list(unlist(lapply(.SD, aggregate.fun))),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: partial_dependence ... renameColumns.randomForest -> do.call -> marginalPrediction -> [ -> [.data.table
Execution halted
Found the following significant warnings:
  oregMclust.cc:227:25: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  oregMclust.cc:531:31: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
  oregMclust.cc:532:22: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/edci.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
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 35-38 (filters.Rmd) 
Error: processing vignette 'filters.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Running ‘test-all.R’ [17s/48s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(eeptools)
  Loading required package: ggplot2
  > 
  > test_check("eeptools")
  ── 1. Error: Zed (@test-calculators.R#169)  ────────────────────────────────────
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: moves_calc(df) at testthat/test-calculators.R:169
  2: dt[, `:=`(moves, school_switch(.SD)), by = sid]
  3: `[.data.table`(dt, , `:=`(moves, school_switch(.SD)), by = sid)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 504 SKIPPED: 0 FAILED: 1
  1. Error: Zed (@test-calculators.R#169) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Quitting from lines 72-87 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    libs  48.7Mb
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  27.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...

Error: processing vignette 'flup.rnw' failed with diagnostics:
 chunk 11 
Error in `[.data.table`(l, , `:=`((tmp_ie), shift(.SD, n = 1, type = "lead")),  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/eVenn.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$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 79-138 (tables-with-labels.Rmd) 
Error: processing vignette 'tables-with-labels.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Found the following significant warnings:
  optile.c:3122:26: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3127:26: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3189:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3192:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3340:28: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3353:28: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3408:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3411:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/extracat.Rcheck/00install.out’ for details.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.7Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.6Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Found the following significant warnings:
  FastRCS.cpp:152:9: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/FastRCS.Rcheck/00install.out’ for details.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
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.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.8Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  47.6Mb
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs  11.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/frailtyHL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.8Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
Running examples in ‘funcy-Ex.R’ failed
The error most likely occurred in:

> ### Name: funcyOutList-class
> ### Title: Class '"funcyOutList"'
> ### Aliases: funcyOutList-class funcyOutList
> ### Keywords: classes
> 
> ### ** Examples
> 
> set.seed(2808)
> ds <- sampleFuncy(obsNr=30, k=4, timeNr=7)
> data <- Data(ds)
> clusters <- Cluster(ds)
> 
> res <- funcit(data=data, clusters=clusters, seed=2808,
+               methods=1:5, k=4, parallel=TRUE)
4 : *4 : * *Warning in funclustWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  It is not possible to set a seed for method funclust.
Loading required namespace: funHDDC
 * * *

Warning in Funclustering::funclust(fd = fd, K = k, thd = thd, increaseDimension = increaseDimension,  :
  Convergence of the algorithm to a solution with at least one empty cluster.
            Restart or a choose a smaller value for K = 4
Warning in funHDDCWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  Clustering with 4 classes is not possible. 3 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 3 classes is not possible. 2 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 2 classes is not possible. 1 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 1 classes is not possible. 0 clusters are used!
Error in funcit(data = data, clusters = clusters, seed = 2808, methods = 1:5,  : 
  Method funHDDC : Clustering for this data not possible.
Execution halted
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  12.9Mb
installed size is 59.3Mb
  sub-directories of 1Mb or more:
    libs  58.9Mb
installed size is 80.8Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     77.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  17.6Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/GenABEL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   5.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Running ‘testthat.R’ [9s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(genomic.autocorr)
  > 
  > test_check("genomic.autocorr")
  ── 1. Error: /data/gannet/ripley/R/packages/tests-devel/genomic.autocorr/man/blo
  SETLENGTH() cannot be applied to an ALTVEC object.
  1: block.glm(f.lhs = c("y0", "y1"), f.rhs = "x", data = data, block.size = 20, B = 200)
  2: results[, .(beta.med = median(value), beta.025 = quantile(value, 0.975), beta.975 = quantile(value, 
         0.025), se.beta = sd(value), nboot = .N), by = byvars]
  3: `[.data.table`(results, , .(beta.med = median(value), beta.025 = quantile(value, 
         0.975), beta.975 = quantile(value, 0.025), se.beta = sd(value), nboot = .N), 
         by = byvars)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: /data/gannet/ripley/R/packages/tests-devel/genomic.autocorr/man/block.glm.Rd 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs   5.0Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  13.8Mb
.ldots.set: no visible global function definition for ‘getS3method’
grf: no visible global function definition for ‘chull’
image.grf: no visible global function definition for ‘heat.colors’
image.krige.bayes: no visible global function definition for
  ‘heat.colors’
legend.krige: no visible global function definition for ‘heat.colors’
points.geodata: no visible global function definition for
  ‘terrain.colors’
points.geodata: no visible global function definition for ‘gray’
read.geodata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  chull getS3method gray heat.colors read.table terrain.colors
Consider adding
  importFrom("grDevices", "chull", "gray", "heat.colors",
             "terrain.colors")
  importFrom("utils", "getS3method", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  Extended_Metropolis_Hastings_Sampler.cpp:1426:33: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Extended_Metropolis_Hastings_Sampler.cpp:1471:33: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Extended_Metropolis_Hastings_Sampler.cpp:1969:27: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Extended_Metropolis_Hastings_Sampler.cpp:2007:27: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:523:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:527:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:531:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:535:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:539:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:543:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:772:33: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  Metropolis_Hastings_Sampler.cpp:823:33: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/GERGM.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Running ‘test-add_pval.R’ [3s/11s]
Running the tests in ‘tests/test-add_pval.R’ failed.
Complete output:
  > library(ggpval)
  > library(ggplot2)
  > library(data.table)
  > A <- rnorm(200, 0, 3)
  > B <- rnorm(200, 2, 4)
  > G <- rep(c("G1", "G2"), each = 100)
  > dt <- data.table(A, B, G)
  > dt <- melt(dt, id.vars = "G")
  > dt[, G := factor(G, levels = c("G2", "G1"))]
  > 
  > plt <- ggplot(dt, aes(variable, value)) +
  +   geom_boxplot() +
  +   geom_jitter()
  > 
  > plt_facet <- ggplot(dt, aes(variable, value)) +
  +   geom_boxplot() +
  +   geom_jitter() +
  +   facet_wrap(~G)
  > 
  > add_pval(plt, pairs = list(c(1, 2)))
  > 
  > add_pval(plt_facet, pairs = list(c(1, 2)))
  Error in `[.data.table`(data_2_test, , lapply(.SD, function(i) get(test)(response ~  : 
    SETLENGTH() cannot be applied to an ALTVEC object.
  Calls: add_pval -> [ -> [.data.table
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 71-76 (ggpval.Rmd) 
Error: processing vignette 'ggpval.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 51.9Mb
  sub-directories of 1Mb or more:
    libs  51.0Mb
installed size is 46.3Mb
  sub-directories of 1Mb or more:
    libs  45.1Mb
Found the following significant warnings:
  calculategphmm.cpp:217:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/gphmm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rothmana.cpp:123:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/graphicalVAR.Rcheck/00install.out’ for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Error in re-building vignettes:
  ...
trying URL 'https://raw.githubusercontent.com/hughparsonage/drat/gh-pages/src/contrib/taxstats_0.0.5.1415.tar.gz'
Content type 'application/octet-stream' length 60897655 bytes (58.1 MB)
==================================================
downloaded 58.1 MB

* installing *source* package ‘taxstats’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (taxstats)
Quitting from lines 361-372 (grattan.Rmd) 
Error: processing vignette 'grattan.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Found the following significant warnings:
  _t_array_properties.cpp:10:13: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/gRbase.Rcheck/00install.out’ for details.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
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 136.5Mb
  sub-directories of 1Mb or more:
    java  134.8Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
Error in re-building vignettes:
  ...
Loading required package: plotly
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 0.14.1

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

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

Quitting from lines 88-90 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 123-127 (cea-vignette.Rmd) 
Error: processing vignette 'cea-vignette.Rmd' failed with diagnostics:
SETLENGTH() cannot be applied to an ALTVEC object.
Execution halted
print.tsum: warning in print.default(x$resid, digits = digits, na = "",
  print.gap = 2): partial argument match of 'na' to 'na.print'
print.tsum: no visible global function definition for ‘quantile’
print.tsum: no visible global function definition for ‘printCoefmat’
print.tsum: no visible global function definition for ‘symnum’
tlm: no visible global function definition for ‘formula’
tlm: no visible binding for global variable ‘na.fail’
tlm: no visible global function definition for ‘model.matrix’
tlm: no visible global function definition for ‘model.extract’
tlm: no visible binding for global variable ‘response’
tlm: no visible global function definition for ‘lm.fit’
tlm: no visible global function definition for ‘coef’
tlm: no visible global function definition for ‘resid’
tlm: no visible global function definition for ‘Gamma’
tlm: no visible binding for global variable ‘dofse’
tlm: no visible binding for global variable ‘logLik’
tscore: no visible global function definition for ‘model.extract’
tscore: no visible binding for global variable ‘response’
tscore : <anonymous>: no visible global function definition for
  ‘model.matrix’
tscore: no visible global function definition for ‘resid’
tscore: no visible global function definition for ‘pchisq’
tscore: no visible global function definition for ‘printCoefmat’
tsum: no visible global function definition for ‘pnorm’
tsum: no visible global function definition for ‘pt’
tsum: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  Gamma coef dofse formula lm.fit logLik model.extract model.matrix
  na.fail pchisq pnorm printCoefmat pt quantile resid residuals
  response symnum
Consider adding
  importFrom("stats", "Gamma", "coef", "formula", "lm.fit", "logLik",
             "model.extract", "model.matrix", "na.fail", "pchisq",
             "pnorm", "printCoefmat", "pt", "quantile", "resid",
             "residuals", "symnum")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        6.8Mb
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  6.1Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   5.3Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   8.2Mb
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.4Mb
    doc    3.3Mb
    libs  15.3Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.3Mb
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs  37.0Mb
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  25.7Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.4Mb
Found the following significant warnings:
  regTree.c:317:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  regTree.c:336:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/iJRF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  transformations.cpp:274:15: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/imager.Rcheck/00install.out’ for details.
installed size is 43.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     32.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
Running examples in ‘inTrees-Ex.R’ failed
The error most likely occurred in:

> ### Name: XGB2List
> ### Title: Transform an xgboost object to a list of trees
> ### Aliases: XGB2List
> ### Keywords: xgboost
> 
> ### ** Examples
> 
> 	library(data.table)
> 	library(xgboost)
> 	# test data set 1: iris
> 	X <- within(iris,rm("Species")); Y <- iris[,"Species"]
> 	X <- within(iris,rm("Species")); Y <- iris[,"Species"]
> 	model_mat <- model.matrix(~. -1, data=X)
> 	xgb <- xgboost(model_mat, label = as.numeric(Y) - 1, nrounds = 20, 
+ 		objective = "multi:softprob", num_class = 3 )
[1]	train-merror:0.020000 
[2]	train-merror:0.026667 
[3]	train-merror:0.020000 
[4]	train-merror:0.020000 
[5]	train-merror:0.013333 
[6]	train-merror:0.013333 
[7]	train-merror:0.013333 
[8]	train-merror:0.013333 
[9]	train-merror:0.013333 
[10]	train-merror:0.013333 
[11]	train-merror:0.006667 
[12]	train-merror:0.006667 
[13]	train-merror:0.006667 
[14]	train-merror:0.006667 
[15]	train-merror:0.000000 
[16]	train-merror:0.000000 
[17]	train-merror:0.000000 
[18]	train-merror:0.000000 
[19]	train-merror:0.000000 
[20]	train-merror:0.000000 
> 	tree_list <- XGB2List(xgb,model_mat)
Error in `[.data.table`(x, j = list(.ll.tech.split = list(.SD)), by = "Tree",  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: XGB2List ... split.data.table -> eval -> eval -> [ -> [.data.table
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.9Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   8.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.9Mb
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      4.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   9.7Mb
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  7.2Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   4.2Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs          15.0Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs     24.0Mb
Found the following significant warnings:
  LBLasso.c:98:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  LBlogistic.c:100:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  LBmultilogistic.c:110:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ggm.c:69:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ising.c:83:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  potts.c:99:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/Libra.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Running examples in ‘lidR-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.raster.lasmetrics
> ### Title: Transform a 'lasmetrics' object into a spatial 'RasterLayer'
> ###   object
> ### Aliases: as.raster.lasmetrics
> 
> ### ** Examples
> 
> LASfile <- system.file("extdata", "Megaplot.laz", package="lidR")
> lidar = readLAS(LASfile)
> 
> meanHeight = grid_metrics(lidar, mean(Z))
Error in `[.data.table`(.las@data, , c(eval(call)), by = by) : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: grid_metrics ... grid_metrics.LAS -> lasaggregate -> [ -> [.data.table
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
    libs      1.3Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 45.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  43.7Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   4.0Mb
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  25.9Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   6.1Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   8.5Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   9.0Mb
plot.mathgraph: no visible global function definition for ‘plot’
plot.mathgraph: no visible global function definition for ‘box’
plot.mathgraph: no visible global function definition for ‘segments’
plot.mathgraph: no visible global function definition for ‘arrows’
plot.mathgraph: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows box plot segments text
Consider adding
  importFrom("graphics", "arrows", "box", "plot", "segments", "text")
to your NAMESPACE file.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  17.1Mb
Found the following significant warnings:
  mue_nelmC.cpp:147:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nelmC.cpp:185:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nelmC.cpp:230:22: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:135:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:173:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:218:22: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/mcIRT.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Found the following significant warnings:
  cHDPHMMpoisson.cc:441:18: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  cHDPHMMpoisson.cc:445:18: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  cHDPHMMpoisson.cc:449:18: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/MCMCpack.Rcheck/00install.out’ for details.
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  25.8Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/mdhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
    libs      1.4Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   9.2Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   5.9Mb
Found the following significant warnings:
  Warning: working directory was changed to ‘/data/gannet/ripley/R/packages/tests-devel/MetaSubtract.Rcheck/MetaSubtract/extdata’, resetting
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  17.5Mb
    misc   1.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   6.8Mb
Running examples in ‘miscset-Ex.R’ failed
The error most likely occurred in:

> ### Name: collapse
> ### Title: Collapse objects
> ### Aliases: collapse collapse.default collapse.data.frame
> 
> ### ** Examples
> 
> #
> 
> ### some data
> 
> set.seed(12)
> s <- s2 <- sample(LETTERS[1:4], 9, replace = TRUE)
> s2[1:2] <- rev(s2[1:2])
> d <- data.frame(group = rep(letters[c(3,1,2)], each = 3), 
+                 value = s,
+                 level = factor(s2),
+                 stringsAsFactors = FALSE)
> 
> ### collapse vectors
> 
> collapse(letters)
[1] "abcdefghijklmnopqrstuvwxyz"
> collapse(1:3)               # coerced to character
[1] "123"
> collapse(LETTERS[1:5], "-") # separated by '-'
[1] "A-B-C-D-E"
> 
> ### collapse data.frames
> 
> # by all columns (same as unique)
> collapse(d)
  group value level
1     c     A     D
2     c     D     A
3     c     D     D
4     a     B     B
5     a     A     A
6     b     A     A
7     b     C     C
> # by a grouping column
> collapse(d, by = 1)
Error in `[.data.table`(x, , collapse_frame(.SD, sep, .unique, .sort,  : 
  SETLENGTH() cannot be applied to an ALTVEC object.
Calls: collapse -> collapse.data.frame -> [ -> [.data.table
Execution halted