Merge pull request #115 from furrer-lab/114-provide-guidance-on-prere…

…quisite-for-installing-abn

114 provide guidance on prerequisite for installing abn

README.md

@@ -40,6 +40,21 @@ We have implemented a rigorous testing framework similar to CRAN's to validate t
 Our aim is to maximize the reliability of the `abn` package under various conditions, and we are dedicated to providing a robust and reliable package. 
 We appreciate your understanding as we work towards making `abn` available on CRAN soon.
 
+## Required System libraries
+
+The following system libraries are required to install the [abn](https://cran.r-project.org/package=abn) package:
+
+- [GSL](https://www.gnu.org/software/gsl/): The GNU Scientific Library is a numerical library for C/C++. It is required for the [abn](https://cran.r-project.org/package=abn) package to compile the C/C++ code.
+    - On Ubuntu, install the library with `sudo apt-get install libgsl-dev`.
+    - On Fedora, install the library with `sudo dnf install gsl-devel`.
+    - On macOS, install the library with `brew install gsl`.
+    - On Windows, download the binaries from the [GSL website](https://www.gnu.org/software/gsl/).
+- [JAGS](https://mcmc-jags.sourceforge.io/): Just Another Gibbs Sampler is a program for analyzing Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation. It is required for the [abn](https://cran.r-project.org/package=abn) package to run simulations.
+    - On Ubuntu, install the library with `sudo apt-get install jags`.
+    - On Fedora, install the library with `sudo dnf install jags`.
+    - On macOS, install the library with `brew install jags`.
+    - On Windows, download the installer from the [JAGS website](https://mcmc-jags.sourceforge.io/).
+
 ## Additional libraries
 
 The following additional libraries are recommended to best profit from the [abn](https://cran.r-project.org/package=abn) features.

configure

@@ -1,6 +1,6 @@
 #! /bin/sh
 # Guess values for system-dependent variables and create Makefiles.
-# Generated by GNU Autoconf 2.71 for abn 3.0.7.
+# Generated by GNU Autoconf 2.71 for abn 3.1.1.
 #
 #
 # Copyright (C) 1992-1996, 1998-2017, 2020-2021 Free Software Foundation,
@@ -607,13 +607,14 @@ MAKEFLAGS=
 # Identity of this package.
 PACKAGE_NAME='abn'
 PACKAGE_TARNAME='abn'
-PACKAGE_VERSION='3.0.7'
-PACKAGE_STRING='abn 3.0.7'
+PACKAGE_VERSION='3.1.1'
+PACKAGE_STRING='abn 3.1.1'
 PACKAGE_BUGREPORT=''
 PACKAGE_URL=''
 
 ac_subst_vars='LTLIBOBJS
 LIBOBJS
+JAGS
 GSL_LIBS
 GSL_CFLAGS
 GSL_CONFIG
@@ -1211,7 +1212,7 @@ if test "$ac_init_help" = "long"; then
   # Omit some internal or obsolete options to make the list less imposing.
   # This message is too long to be a string in the A/UX 3.1 sh.
   cat <<_ACEOF
-\`configure' configures abn 3.0.7 to adapt to many kinds of systems.
+\`configure' configures abn 3.1.1 to adapt to many kinds of systems.
 
 Usage: $0 [OPTION]... [VAR=VALUE]...
 
@@ -1273,7 +1274,7 @@ fi
 
 if test -n "$ac_init_help"; then
   case $ac_init_help in
-     short | recursive ) echo "Configuration of abn 3.0.7:";;
+     short | recursive ) echo "Configuration of abn 3.1.1:";;
    esac
   cat <<\_ACEOF
 
@@ -1341,7 +1342,7 @@ fi
 test -n "$ac_init_help" && exit $ac_status
 if $ac_init_version; then
   cat <<\_ACEOF
-abn configure 3.0.7
+abn configure 3.1.1
 generated by GNU Autoconf 2.71
 
 Copyright (C) 2021 Free Software Foundation, Inc.
@@ -1378,7 +1379,7 @@ cat >config.log <<_ACEOF
 This file contains any messages produced by compilers while
 running configure, to aid debugging if configure makes a mistake.
 
-It was created by abn $as_me 3.0.7, which was
+It was created by abn $as_me 3.1.1, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   $ $0$ac_configure_args_raw
@@ -1780,6 +1781,56 @@ fi
 
 
 
+## Check for non-standard programs: JAGS
+# Extract the first word of "jags", so it can be a program name with args.
+set dummy jags; ac_word=$2
+{ printf "%s\n" "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5
+printf %s "checking for $ac_word... " >&6; }
+if test ${ac_cv_path_JAGS+y}
+then :
+  printf %s "(cached) " >&6
+else $as_nop
+  case $JAGS in
+  [\\/]* | ?:[\\/]*)
+  ac_cv_path_JAGS="$JAGS" # Let the user override the test with a path.
+  ;;
+  *)
+  as_save_IFS=$IFS; IFS=$PATH_SEPARATOR
+for as_dir in $PATH
+do
+  IFS=$as_save_IFS
+  case $as_dir in #(((
+    '') as_dir=./ ;;
+    */) ;;
+    *) as_dir=$as_dir/ ;;
+  esac
+    for ac_exec_ext in '' $ac_executable_extensions; do
+  if as_fn_executable_p "$as_dir$ac_word$ac_exec_ext"; then
+    ac_cv_path_JAGS="$as_dir$ac_word$ac_exec_ext"
+    printf "%s\n" "$as_me:${as_lineno-$LINENO}: found $as_dir$ac_word$ac_exec_ext" >&5
+    break 2
+  fi
+done
+  done
+IFS=$as_save_IFS
+
+  ;;
+esac
+fi
+JAGS=$ac_cv_path_JAGS
+if test -n "$JAGS"; then
+  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: $JAGS" >&5
+printf "%s\n" "$JAGS" >&6; }
+else
+  { printf "%s\n" "$as_me:${as_lineno-$LINENO}: result: no" >&5
+printf "%s\n" "no" >&6; }
+fi
+
+
+if test "${JAGS}" = ""; then
+    as_fn_error $? "jags not found, is JAGS installed?" "$LINENO" 5
+fi
+
 ac_config_files="$ac_config_files src/Makevars"
 
 cat >confcache <<\_ACEOF
@@ -2317,7 +2368,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
 # report actual input values of CONFIG_FILES etc. instead of their
 # values after options handling.
 ac_log="
-This file was extended by abn $as_me 3.0.7, which was
+This file was extended by abn $as_me 3.1.1, which was
 generated by GNU Autoconf 2.71.  Invocation command line was
 
   CONFIG_FILES    = $CONFIG_FILES
@@ -2372,7 +2423,7 @@ ac_cs_config_escaped=`printf "%s\n" "$ac_cs_config" | sed "s/^ //; s/'/'\\\\\\\\
 cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
 ac_cs_config='$ac_cs_config_escaped'
 ac_cs_version="\\
-abn config.status 3.0.7
+abn config.status 3.1.1
 configured by $0, generated by GNU Autoconf 2.71,
   with options \\"\$ac_cs_config\\"
 

configure.ac

@@ -17,5 +17,11 @@ fi
 AC_SUBST(GSL_CFLAGS)
 AC_SUBST(GSL_LIBS)
 
+## Check for non-standard programs: JAGS
+AC_PATH_PROG([JAGS], [jags])
+if test "${JAGS}" = ""; then
+    AC_MSG_ERROR([jags not found, is JAGS installed?])
+fi
+
 AC_CONFIG_FILES([src/Makevars])
 AC_OUTPUT