* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/kpcalg.Rcheck’
* using R Under development (unstable) (2025-02-25 r87824)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-14 (Debian 14.2.0-16) 14.2.0
    GNU Fortran (Debian 14.2.0-16) 14.2.0
* running under: Debian GNU/Linux trixie/sid
* using session charset: UTF-8
* checking for file ‘kpcalg/DESCRIPTION’ ... OK
* this is package ‘kpcalg’ version ‘1.0.1’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Package suggested but not available for checking: ‘Rgraphviz’
* 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 serialization versions ... OK
* checking whether package ‘kpcalg’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/kpcalg-00install.html' for details.
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [3s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/4s] OK
* checking whether the package can be unloaded cleanly ... [3s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] OK
* checking use of S3 registration ... 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 ... [16s/21s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) hsic.perm.Rd:36: Lost braces; missing escapes or markup?
    36 | Let x and y be two samples of length n. Gram matrices K and L are defined as: \eqn{K_{i,j} = \exp\frac{(x_i-x_j)^2}{\sigma^2}}{K_{i,j} =exp((x_i-x_j)^2/sig^2)} and \eqn{L_{i,j} = \exp\frac{(y_i-y_j)^2}{\sigma^2}}{L_{i,j} =exp((y_i-y_j)^2/sig^2)}. \eqn{H_{i,j} = \delta_{i,j} - \frac{1}{n}}{H_{i,j} = \delta_{i,j} - 1/n}. Let \eqn{A=HKH} and \eqn{B=HLH}, then \eqn{HSIC(x,y)=\frac{1}{n^2}Tr(AB)}{HSIC(x,y)=Tr(AB)/n^2}. Permutation test permutes y p times to get \eqn{y_{(p)}} and calculates HSIC(x,y_{(p)}). \eqn{pval = \frac{1(HSIC(x,y)>HSIC(x,y_{(p)}))}{p}}{(HSIC(x,y)>HSIC(x,y_{(p)}))/p}.
       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    ^
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... NOTE
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  dcov.gamma.Rd: dcov.test
  frml.additive.smooth.Rd: gam
  frml.full.smooth.Rd: gam
  kernelCItest.Rd: skeleton, pc
  kpc.Rd: pc, dcov.test, udag2pdag, pcAlgo
  regrVonPS.Rd: gam
  regrXonS.Rd: gam
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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 LazyData ... INFO
  'LazyData' is specified without a 'data' directory
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/12s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [5s/5s] ERROR
Error(s) in re-building vignettes:
  ...
--- re-building ‘kpcalg_tutorial.Rnw’ using knitr

Quitting from lines 61-65 [unnamed-chunk-2] (kpcalg_tutorial.Rnw)
Error: processing vignette 'kpcalg_tutorial.Rnw' failed with diagnostics:
package required but not installed: 'Rgraphviz'
--- failed re-building ‘kpcalg_tutorial.Rnw’

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

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [4s/5s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 ERROR, 2 NOTEs