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partykitx log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2021-05-11-11-27/RF_PKG_CHECK/PKGS/partykitx.Rcheck'
* using R version 4.0.5 Patched (2021-03-31 r80182)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'partykitx/DESCRIPTION' ... OK
* this is package 'partykitx' version '1.9-0'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Torsten Hothorn '

New submission

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'partykitx' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  '.rfweights'
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call(partykit:::R_rfweights, ...)
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
prepare_Rd: extree_variable.Rd:30-32: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'splitselect_loop' 'varselect_loop'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'extree_control':
extree_control
  Code: function(criterion = "p.value", critvalue = 0.05, padjust =
                 TRUE, minsplit = 20L, minbucket = 7L, minprob = 0.01,
                 stump = FALSE, maxsurrogate = 0L, numsurrogate =
                 FALSE, mtry = Inf, maxdepth = Inf, splittry = 2L,
                 majority = FALSE, caseweights = TRUE, update = NULL,
                 nmax = Inf, lookahead = FALSE, multiway = FALSE, save
                 = NULL, varselect = NULL, splitselect = NULL,
                 svarselect = NULL, ssplitselect = NULL, applyfun =
                 NULL, cores = NULL, ..., bonferroni = NULL, saveinfo =
                 TRUE, selectfun = NULL, splitfun = NULL, svselectfun =
                 NULL, svsplitfun = NULL, unweighted = TRUE)
  Docs: function(criterion, logmincriterion, minsplit = 20L, minbucket
                 = 7L, minprob = 0.01, nmax = Inf, stump = FALSE,
                 lookahead = FALSE, maxsurrogate = 0L, numsurrogate =
                 FALSE, mtry = Inf, maxdepth = Inf, multiway = FALSE,
                 splittry = 2L, majority = FALSE, caseweights = TRUE,
                 applyfun = NULL, cores = NULL, saveinfo = TRUE,
                 bonferroni = FALSE, update = NULL, selectfun,
                 splitfun, svselectfun, svsplitfun)
  Argument names in code not in docs:
    critvalue padjust save varselect splitselect svarselect
    ssplitselect ... unweighted
  Argument names in docs not in code:
    logmincriterion
  Mismatches in argument names (first 3):
    Position: 2 Code: critvalue Docs: logmincriterion
    Position: 3 Code: padjust Docs: minsplit
    Position: 4 Code: minsplit Docs: minbucket
  Mismatches in argument default values (first 3):
    Name: 'criterion' Code: "p.value" Docs: 
    Name: 'bonferroni' Code: NULL Docs: FALSE
    Name: 'selectfun' Code: NULL Docs: 

Codoc mismatches from documentation object 'extree_data':
extree_data
  Code: function(formula, data, subset, na.action = na.pass, weights,
                 offset, cluster, strata, yx = c("none", "matrix"),
                 ytype = c("vector", "data.frame", "matrix"), nmax =
                 c(yx = Inf, z = Inf), ...)
  Docs: function(formula, data, subset, na.action = na.pass, weights,
                 offset, cluster, strata, scores = NULL, yx = c("none",
                 "matrix"), ytype = c("vector", "data.frame",
                 "matrix"), nmax = c(yx = Inf, z = Inf), ...)
  Argument names in docs not in code:
    scores
  Mismatches in argument names (first 3):
    Position: 9 Code: yx Docs: scores
    Position: 10 Code: ytype Docs: yx
    Position: 11 Code: nmax Docs: ytype

Codoc mismatches from documentation object 'extree_fit':
extree_fit
  Code: function(data, trafo, converged, varselect = ctrl$varselect,
                 splitselect = ctrl$splitselect, svarselect =
                 ctrl$svarselect, ssplitselect = ctrl$ssplitselect,
                 partyvars, subset, weights, ctrl, doFit = TRUE)
  Docs: function(data, trafo, converged, selectfun = ctrl$selectfun,
                 splitfun = ctrl$splitfun, svselectfun =
                 ctrl$svselectfun, svsplitfun = ctrl$svsplitfun,
                 partyvars, subset, weights, ctrl, doFit = TRUE)
  Argument names in code not in docs:
    varselect splitselect svarselect ssplitselect
  Argument names in docs not in code:
    selectfun splitfun svselectfun svsplitfun
  Mismatches in argument names (first 3):
    Position: 4 Code: varselect Docs: selectfun
    Position: 5 Code: splitselect Docs: splitfun
    Position: 6 Code: svarselect Docs: svselectfun

Codoc mismatches from documentation object 'mob':
mob
  Code: function(formula, data, subset, na.action = na.omit, weights =
                 NULL, offset, cluster, fit, control =
                 mob_control(...), converged = NULL, doFit = TRUE, ...)
  Docs: function(formula, data, subset, na.action, weights, offset,
                 cluster, fit, control = mob_control(), ...)
  Argument names in code not in docs:
    converged doFit
  Mismatches in argument names:
    Position: 10 Code: converged Docs: ...
  Mismatches in argument default values:
    Name: 'na.action' Code: na.omit Docs: 
    Name: 'weights' Code: NULL Docs: 
    Name: 'control' Code: mob_control(...) Docs: mob_control()

Codoc mismatches from documentation object 'mob_control':
mob_control
  Code: function(alpha = 0.05, mincriterion = 1 - alpha, parm = NULL,
                 bonferroni = TRUE, breakties = FALSE, nrep = 10000L,
                 ordinal = c("chisq", "max", "L2"), trim = 0.1,
                 splittry = 1L, vcov = c("opg", "info", "sandwich"),
                 catsplit = "binary", numsplit = "left", majority =
                 FALSE, maxsurrogate = 0, numsurrogate = FALSE,
                 lookahead = FALSE, maxdepth = Inf, minbucket =
                 minsize, minprob = 0.01, minsplit = minsize, minsize =
                 NULL, stump = FALSE, caseweights = TRUE, dfsplit =
                 TRUE, applyfun = NULL, cores = NULL, restart = TRUE,
                 inner = "object", model = TRUE, terminal = "object",
                 mtry = Inf, nmax = Inf, ytype = c("vector",
                 "data.frame", "matrix"), verbose, xtype, prune)
  Docs: function(alpha = 0.05, bonferroni = TRUE, minsize = NULL,
                 maxdepth = Inf, mtry = Inf, trim = 0.1, breakties =
                 FALSE, parm = NULL, dfsplit = TRUE, prune = NULL,
                 restart = TRUE, verbose = FALSE, caseweights = TRUE,
                 ytype = "vector", xtype = "matrix", terminal =
                 "object", inner = terminal, model = TRUE, numsplit =
                 "left", catsplit = "binary", vcov = "opg", ordinal =
                 "chisq", nrep = 10000, minsplit = minsize, minbucket =
                 minsize, applyfun = NULL, cores = NULL)
  Argument names in code not in docs:
    mincriterion splittry majority maxsurrogate numsurrogate lookahead
    minprob stump nmax
  Mismatches in argument names (first 3):
    Position: 2 Code: mincriterion Docs: bonferroni
    Position: 3 Code: parm Docs: minsize
    Position: 4 Code: bonferroni Docs: maxdepth
  Mismatches in argument default values (first 3):
    Name: 'ordinal' Code: c("chisq", "max", "L2") Docs: "chisq"
    Name: 'vcov' Code: c("opg", "info", "sandwich") Docs: "opg"
    Name: 'inner' Code: "object" Docs: terminal

* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'extree'
  'doFit'

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... WARNING
Argument items with no description in Rd object 'extree_control':
  'nmax'

* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... WARNING
  'gs+qpdf' made some significant size reductions:
     compacted 'constparty.pdf' from 394Kb to 138Kb
     compacted 'ctree.pdf' from 511Kb to 218Kb
     compacted 'mob.pdf' from 680Kb to 380Kb
     compacted 'partykit.pdf' from 407Kb to 135Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'partykitx-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: glmtree
> ### Title: Generalized Linear Model Trees
> ### Aliases: glmtree plot.glmtree predict.glmtree print.glmtree
> ### Keywords: tree
> 
> ### ** Examples
> 
> if(require("mlbench")) {
+ 
+ ## Pima Indians diabetes data
+ data("PimaIndiansDiabetes", package = "mlbench")
+ 
+ ## recursive partitioning of a logistic regression model
+ pid_tree2 <- glmtree(diabetes ~ glucose | pregnant +
+   pressure + triceps + insulin + mass + pedigree + age,
+   data = PimaIndiansDiabetes, family = binomial)
+ 
+ ## printing whole tree or individual nodes
+ print(pid_tree2)
+ print(pid_tree2, node = 1)
+ 
+ ## visualization
+ plot(pid_tree2)
+ plot(pid_tree2, tp_args = list(cdplot = TRUE))
+ plot(pid_tree2, terminal_panel = NULL)
+ 
+ ## estimated parameters
+ coef(pid_tree2)
+ coef(pid_tree2, node = 5)
+ summary(pid_tree2, node = 5)
+ 
+ ## deviance, log-likelihood and information criteria
+ deviance(pid_tree2)
+ logLik(pid_tree2)
+ AIC(pid_tree2)
+ BIC(pid_tree2)
+ 
+ ## different types of predictions
+ pid <- head(PimaIndiansDiabetes)
+ predict(pid_tree2, newdata = pid, type = "node")
+ predict(pid_tree2, newdata = pid, type = "response")
+ predict(pid_tree2, newdata = pid, type = "link")
+ 
+ }
Loading required package: mlbench
Error in switch(control$xtype, matrix = model.matrix(mtY, mf), data.frame = Formula::model.part(formula,  : 
  EXPR must be a length 1 vector
Calls: glmtree -> eval -> eval -> 
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'bugfixes.R'
  Comparing 'bugfixes.Rout' to 'bugfixes.Rout.save' ... OK
  Running 'regtest-MIA.R'
  Comparing 'regtest-MIA.Rout' to 'regtest-MIA.Rout.save' ... OK
  Running 'regtest-cforest.R'
  Comparing 'regtest-cforest.Rout' to 'regtest-cforest.Rout.save' ... OK
  Running 'regtest-ctree.R'
  Comparing 'regtest-ctree.Rout' to 'regtest-ctree.Rout.save' ... OK
  Running 'regtest-glmtree.R' [20s]
  Comparing 'regtest-glmtree.Rout' to 'regtest-glmtree.Rout.save' ...236c236
<   ..$ object:List of 24
---
>   ..$ object:List of 23
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<   ..$ object:List of 24
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>   ..$ object:List of 23
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<   ..$ object:List of 24
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>   ..$ object:List of 23
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<   ..$ object:List of 24
---
>   ..$ object:List of 23
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<   ..$ object:List of 24
---
>   ..$ object:List of 23
264c264
<   ..$ object:List of 24
---
>   ..$ object:List of 23
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<   ..$ object:List of 24
---
>   ..$ object:List of 23
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<   ..$ object:List of 24
---
>   ..$ object:List of 23
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<   ..$ object:List of 24
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>   ..$ object:List of 23
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<   ..$ object:List of 24
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>   ..$ object:List of 23
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<   ..$ object:List of 24
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>   ..$ object:List of 23
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<   ..$ object:List of 24
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>   ..$ object:List of 23
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<   ..$ object:List of 24
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>   ..$ object:List of 23
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<   ..$ object:List of 24
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>   ..$ object:List of 23
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<   ..$ object:List of 24
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>   ..$ object:List of 23
344c344
<   ..$ object:List of 24
---
>   ..$ object:List of 23
  Running 'regtest-lmtree.R'
  Running 'regtest-nmax.R'
  Comparing 'regtest-nmax.Rout' to 'regtest-nmax.Rout.save' ... OK
  Running 'regtest-node.R'
  Comparing 'regtest-node.Rout' to 'regtest-node.Rout.save' ... OK
  Running 'regtest-party-random.R'
  Running 'regtest-party.R'
  Comparing 'regtest-party.Rout' to 'regtest-party.Rout.save' ... OK
  Running 'regtest-split.R'
  Comparing 'regtest-split.Rout' to 'regtest-split.Rout.save' ... OK
  Running 'regtest-weights.R'
  Comparing 'regtest-weights.Rout' to 'regtest-weights.Rout.save' ... OK
  Running 'tinytest.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ...
  'constparty.Rnw'... OK
  'ctree.Rnw' using 'UTF-8'... NOTE
differences from 'ctree.Rout.save'
46,48d45
< $maxvar
< [1] Inf
< 
191,193d187
< $maxvar
< [1] Inf
< 
336,338d329
< $maxvar
< [1] Inf
< 
481,483d471
< $maxvar
< [1] Inf
< 
626,628d613
< $maxvar
< [1] Inf
< 
1472c1457
< [1] 371.5366
---
> [1] 446.0366
  'mob.Rnw'... NOTE
differences from 'mob.Rout.save'
127c127
< xglucose      0.03787    0.00325    11.6   <2e-16 ***
---
> xglucose      0.03787    0.00325    11.7   <2e-16 ***
  'partykit.Rnw'... OK
 NOTE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 5 WARNINGs, 5 NOTEs
See
  'R:/run/building/build_2021-05-11-11-27/RF_PKG_CHECK/PKGS/partykitx.Rcheck/00check.log'
for details.

Run time: 209.07 seconds.