* using log directory ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/hgm.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 ‘hgm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘hgm’ version ‘1.23’
* 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 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 ‘hgm’ can be installed ... OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-gcc/hgm-00install.html' for details.
* used C compiler: ‘gcc-14 (Debian 14.2.0-16) 14.2.0’
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [4s/4s] OK
* checking Rd files ... [0s/0s] NOTE
checkRd: (-1) hgm.Rhgm.Rd:32: Lost braces; missing escapes or markup?
    32 |          If time = NULL, the set {0,1} is used, and only the final value is returned.
       |                                  ^
checkRd: (-1) hgm.Rhgm.Rd:48: Lost braces; missing escapes or markup?
    48 |     d G_j / d th_i = (dG.fun(th, G))_{i,j}
       |                                      ^
checkRd: (-1) hgm.se.hgm.Bingham.Rd:32: Lost braces; missing escapes or markup?
    32 |      If time = NULL, the set {0,1} is used, and only the final value is returned.
       |                              ^
checkRd: (-1) hgm.so3nc.Rd:22: Lost braces; missing escapes or markup?
    22 |      Theta=diag(theta_{ii}) of the Fisher distribution on SO(3).
       |                       ^
checkRd: (-1) hgm.so3nc.Rd:24: Lost braces; missing escapes or markup?
    24 |      theta_{11}, theta_{22}, theta_{33} respectively.
       |            ^
checkRd: (-1) hgm.so3nc.Rd:24: Lost braces; missing escapes or markup?
    24 |      theta_{11}, theta_{22}, theta_{33} respectively.
       |                        ^
checkRd: (-1) hgm.so3nc.Rd:24: Lost braces; missing escapes or markup?
    24 |      theta_{11}, theta_{22}, theta_{33} respectively.
       |                                    ^
checkRd: (-1) hgm.so3nc.Rd:54: Lost braces; missing escapes or markup?
    54 | The output is an array of c(Theta) and its derivatives with respect to Theta_{11},Theta_{22},Theta_{33}. It is the vector C of the reference below. When log=1, the output is an array of log of them.
       |                                                                              ^
checkRd: (-1) hgm.so3nc.Rd:54: Lost braces; missing escapes or markup?
    54 | The output is an array of c(Theta) and its derivatives with respect to Theta_{11},Theta_{22},Theta_{33}. It is the vector C of the reference below. When log=1, the output is an array of log of them.
       |                                                                                         ^
checkRd: (-1) hgm.so3nc.Rd:54: Lost braces; missing escapes or markup?
    54 | The output is an array of c(Theta) and its derivatives with respect to Theta_{11},Theta_{22},Theta_{33}. It is the vector C of the reference below. When log=1, the output is an array of log of them.
       |                                                                                                    ^
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* 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 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 use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking examples ... [1s/1s] OK
* checking PDF version of manual ... [4s/5s] OK
* checking HTML version of manual ... [0s/0s] OK
* checking for non-standard things in the check directory ... OK
* DONE
Status: 1 NOTE