* 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