- using R version 4.3.0 beta (2023-04-08 r84203)
- using platform: x86_64-apple-darwin20 (64-bit)
- R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
- running under: macOS Ventura 13.3
- using session charset: UTF-8
- checking for file ‘mboost/DESCRIPTION’ ... OK
- this is package ‘mboost’ version ‘2.9-7’
- checking package namespace information ... OK
- checking package dependencies ... NOTE
Package suggested but not available for checking: ‘kangar00’
- checking if this is a source package ... OK
- checking if there is a namespace ... OK
- checking for executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘mboost’ can be installed ... [11s/14s] OK
- used C compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
- used SDK: ‘MacOSX11.3.sdk’
- checking installed package size ... OK
- checking package directory ... 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 ... [1s/2s] OK
- checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
- checking whether the package can be unloaded cleanly ... [1s/2s] OK
- checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
- checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
- checking loading without being on the library search path ... [1s/2s] OK
- checking startup messages can be suppressed ... [1s/2s] OK
- checking dependencies in R code ... OK
- checking S3 generic/method consistency ... OK
- checking replacement functions ... OK
- checking foreign function calls ... OK
- checking R code for possible problems ... [11s/15s] OK
- checking Rd files ... [1s/1s] OK
- checking Rd metadata ... OK
- checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘kangar00’
- checking for missing documentation entries ... OK
- checking for code/documentation mismatches ... OK
- checking Rd \usage sections ... OK
- checking Rd contents ... OK
- checking for unstated dependencies in examples ... OK
- checking line endings in shell scripts ... OK
- checking line endings in C/C++/Fortran sources/headers ... OK
- checking line endings in Makefiles ... OK
- checking compilation flags in Makevars ... OK
- checking for GNU extensions in Makefiles ... OK
- checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
- checking use of PKG_*FLAGS in Makefiles ... OK
- checking compiled code ... OK
- checking sizes of PDF files under ‘inst/doc’ ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [21s/29s] OK
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes in ‘inst/doc’ ... OK
- checking running R code from vignettes ... [39s/53s] OK
‘SurvivalEnsembles.Rnw’... [13s/17s] OK
‘mboost.Rnw’... [8s/11s] OK
‘mboost_illustrations.Rnw’... [9s/14s] OK
‘mboost_tutorial.Rnw’ using ‘UTF-8’... [8s/9s] OK
- checking re-building of vignette outputs ... [52s/67s] NOTE
Error(s) in re-building vignettes:
--- re-building ‘SurvivalEnsembles.Rnw’ using Sweave
Loading required package: parallel
Loading required package: stabs
Loading required package: TH.data
Loading required package: survival
Loading required package: MASS
Attaching package: ‘TH.data’
The following object is masked from ‘package:MASS’:
geyser
Loading required package: rpart
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Attaching package: ‘partykit’
The following object is masked from ‘package:mboost’:
varimp
Error: processing vignette 'SurvivalEnsembles.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'SurvivalEnsembles.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.31 ^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘SurvivalEnsembles.Rnw’
--- re-building ‘mboost.Rnw’ using Sweave
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
Loading required package: partykit
Loading required package: grid
Loading required package: libcoin
Loading required package: mvtnorm
Attaching package: ‘partykit’
The following object is masked from ‘package:mboost’:
varimp
--- finished re-building ‘mboost.Rnw’
--- re-building ‘mboost_illustrations.Rnw’ using Sweave
Loading required package: parallel
Loading required package: stabs
Warning in gamboost(DEXfat ~ ., data = bodyfat, baselearner = "bss") :
bss and bns are deprecated, bbs is used instead
Warning in glmboost.matrix(x, yfit, family = L2fm, center = TRUE, control = boost_control(mstop = 200)) :
model with centered covariates does not contain intercept
Warning in hatvalues.gamboost(model) :
AIC might not be reasonable for family user-specified
NOTE: Coefficients from a Binomial model are half the size of coefficients
from a model fitted via glm(... , family = 'binomial').
See Warning section in ?coef.mboost
NOTE: Coefficients from a Binomial model are half the size of coefficients
from a model fitted via glm(... , family = 'binomial').
See Warning section in ?coef.mboost
Warning in gamboost(status ~ ., data = wpbc2, family = Binomial(), baselearner = "bss") :
bss and bns are deprecated, bbs is used instead
Error: processing vignette 'mboost_illustrations.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'mboost_illustrations.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.32 ^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘mboost_illustrations.Rnw’
--- re-building ‘mboost_tutorial.Rnw’ using Sweave
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
Warning in bsplines(mf[[i]], knots = args$knots[[i]]$knots, boundary.knots = args$knots[[i]]$boundary.knots, :
Some ‘x’ values are beyond ‘boundary.knots’; Linear extrapolation used.
Warning in bsplines(mf[[i]], knots = args$knots[[i]]$knots, boundary.knots = args$knots[[i]]$boundary.knots, :
Some ‘x’ values are beyond ‘boundary.knots’; Linear extrapolation used.
Warning in bsplines(mf[[i]], knots = args$knots[[i]]$knots, boundary.knots = args$knots[[i]]$boundary.knots, :
Some ‘x’ values are beyond ‘boundary.knots’; Linear extrapolation used.
Warning in bsplines(mf[[i]], knots = args$knots[[i]]$knots, boundary.knots = args$knots[[i]]$boundary.knots, :
Some ‘x’ values are beyond ‘boundary.knots’; Linear extrapolation used.
Warning in bsplines(mf[[i]], knots = args$knots[[i]]$knots, boundary.knots = args$knots[[i]]$boundary.knots, :
Some ‘x’ values are beyond ‘boundary.knots’; Linear extrapolation used.
Warning in bsplines(mf[[i]], knots = args$knots[[i]]$knots, boundary.knots = args$knots[[i]]$boundary.knots, :
Some ‘x’ values are beyond ‘boundary.knots’; Linear extrapolation used.
Error: processing vignette 'mboost_tutorial.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'mboost_tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
! Emergency stop.
<read *>
l.16 \usepackage
{subfigure}^^M
! ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘mboost_tutorial.Rnw’
SUMMARY: processing the following files failed:
‘SurvivalEnsembles.Rnw’ ‘mboost_illustrations.Rnw’
‘mboost_tutorial.Rnw’
Error: Vignette re-building failed.
Execution halted
- checking PDF version of manual ... [5s/7s] OK
- DONE
Status: 3 NOTEs
- using check arguments '--no-clean-on-error '