build-system/r: Update to Bioconductor 3.7. - guix

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author	Ricardo Wurmus <rekado@elephly.net>	2018-06-05 09:57:05 +0200
committer	Ricardo Wurmus <rekado@elephly.net>	2018-06-05 09:58:52 +0200
commit	0ebef06dbe5e53025670a76ff98f05e8c093f013 (patch)
tree	568250b8a4b3bfc84f242fec3a229141aa8623da /guix.scm
parent	4bf0a1f8d13e00dd436349b943cbab9c6d8d8f8b (diff)
download	guix-0ebef06dbe5e53025670a76ff98f05e8c093f013.tar.gz guix-0ebef06dbe5e53025670a76ff98f05e8c093f013.zip

build-system/r: Update to Bioconductor 3.7.

This is a follow-up to 41f17554d88795bf35fbfc3e05301a6d2f64cca0. * guix/build-system/r.scm (bioconductor-uri): Update to version 3.7.

Diffstat (limited to 'guix.scm')

0 files changed, 0 insertions, 0 deletions

# -*- Autoconf -*- # Process this file with autoconf to produce a configure script. AC_PREREQ([2.69]) AC_INIT([GNU Guix], [m4_esyscmd([build-aux/git-version-gen .tarball-version])], [bug-guix@gnu.org], [guix], [https://www.gnu.org/software/guix/]) AC_CONFIG_AUX_DIR([build-aux]) AM_INIT_AUTOMAKE([1.14 gnu tar-ustar silent-rules subdir-objects \ color-tests parallel-tests -Woverride -Wno-portability]) # Enable silent rules by default. AM_SILENT_RULES([yes]) AC_CONFIG_SRCDIR([guix.scm]) AC_CONFIG_MACRO_DIR([m4]) dnl For the C++ code. This must be used early. AC_USE_SYSTEM_EXTENSIONS AM_GNU_GETTEXT([external]) AM_GNU_GETTEXT_VERSION([0.19.1]) GUIX_SYSTEM_TYPE GUIX_ASSERT_SUPPORTED_SYSTEM GUIX_CHANNEL_METADATA AM_CONDITIONAL([CROSS_COMPILING], [test "x$cross_compiling" = "xyes"]) AC_ARG_WITH(store-dir, AS_HELP_STRING([--with-store-dir=PATH], [file name of the store (defaults to /gnu/store)]), [storedir="$withval"], [storedir="/gnu/store"]) AC_SUBST(storedir) AC_ARG_WITH([bash-completion-dir], AS_HELP_STRING([--with-bash-completion-dir=DIR], [name of the Bash completion directory]), [bashcompletiondir="$withval"], [bashcompletiondir='${sysconfdir}/bash_completion.d']) AC_SUBST([bashcompletiondir]) AC_ARG_WITH([zsh-completion-dir], AS_HELP_STRING([--with-zsh-completion-dir=DIR], [name of the Zsh completion directory]), [zshcompletiondir="$withval"], [zshcompletiondir='${datadir}/zsh/site-functions']) AC_SUBST([zshcompletiondir]) AC_ARG_WITH([fish-completion-dir], AS_HELP_STRING([--with-fish-completion-dir=DIR], [name of the Fish completion directory]), [fishcompletiondir="$withval"], [fishcompletiondir='${datadir}/fish/vendor_completions.d']) AC_SUBST([fishcompletiondir]) AC_ARG_WITH([selinux-policy-dir], AS_HELP_STRING([--with-selinux-policy-dir=DIR], [name of the SELinux policy directory]), [selinux_policydir="$withval"], [selinux_policydir='${datadir}/selinux/']) AC_SUBST([selinux_policydir]) dnl Better be verbose. AC_MSG_CHECKING([for the store directory]) AC_MSG_RESULT([$storedir]) AC_ARG_ENABLE([daemon], [AS_HELP_STRING([--disable-daemon], [do not build the Nix daemon (C++)])], [guix_build_daemon="$enableval"], [guix_build_daemon="yes"]) # Prepare a version of $localstatedir & co. that does not contain references # to shell variables. guix_prefix="`eval echo $prefix | sed -e"s|NONE|/usr/local|g"`" guix_localstatedir="`eval echo $localstatedir | sed -e "s|NONE|$guix_prefix|g"`" guix_sysconfdir="`eval echo $sysconfdir | sed -e "s|NONE|$guix_prefix|g"`" guix_sbindir="`eval echo $sbindir | sed -e "s|NONE|$guix_prefix|g"`" AC_SUBST([guix_localstatedir]) AC_SUBST([guix_sysconfdir]) AC_SUBST([guix_sbindir]) GUIX_CHECK_FILE_NAME_LIMITS([can_run_tests]) AM_CONDITIONAL([CAN_RUN_TESTS], [test "x$can_run_tests" = "xyes"]) dnl We require pkg.m4 (from pkg-config) and guile.m4 (from Guile.) dnl Make sure they are available. m4_pattern_forbid([PKG_CHECK_MODULES]) m4_pattern_forbid([GUILE_MODULE_AVAILABLE]) m4_pattern_forbid([^GUILE_P]) m4_pattern_allow([^GUILE_PKG_ERRORS]) m4_pattern_forbid([^GUIX_]) dnl Search for 'guile' and 'guild'. This macro defines dnl 'GUILE_EFFECTIVE_VERSION'. GUILE_PKG([3.0]) GUILE_PROGS if test "x$GUILD" = "x"; then AC_MSG_ERROR(['guild' binary not found; please check your Guile installation.]) fi dnl (guix ui), notably, requires 'default-optimization-level' added in 3.0.3. PKG_CHECK_MODULES([GUILE], [guile-3.0 >= 3.0.3]) dnl Get CFLAGS and LDFLAGS for libguile. GUILE_FLAGS dnl Installation directories for .scm and .go files. guilemoduledir="${datarootdir}/guile/site/$GUILE_EFFECTIVE_VERSION" guileobjectdir="${libdir}/guile/$GUILE_EFFECTIVE_VERSION/site-ccache" AC_SUBST([guilemoduledir]) AC_SUBST([guileobjectdir]) dnl The GnuTLS bindings are necessary for substitutes over HTTPS and for 'guix dnl pull', among other things. GUILE_MODULE_AVAILABLE([have_gnutls], [(gnutls)]) if test "x$have_gnutls" != "xyes"; then AC_MSG_ERROR([The Guile bindings of GnuTLS are missing; please install them.]) fi dnl Check for Guile-Git. GUILE_MODULE_AVAILABLE([have_guile_git], [(git)]) if test "x$have_guile_git" != "xyes"; then AC_MSG_ERROR([Guile-Git is missing; please install it.]) fi dnl Check for Guile-JSON. GUIX_CHECK_GUILE_JSON if test "x$guix_cv_have_recent_guile_json" != "xyes"; then AC_MSG_ERROR([Guile-JSON is missing; please install it.]) fi dnl Guile-Sqlite3 is used by the (guix store ...) modules. GUIX_CHECK_GUILE_SQLITE3 if test "x$guix_cv_have_recent_guile_sqlite3" != "xyes"; then AC_MSG_ERROR([A recent Guile-SQLite3 could not be found; please install it.]) fi GUIX_CHECK_GUILE_GCRYPT if test "x$guix_cv_have_recent_guile_gcrypt" != "xyes"; then AC_MSG_ERROR([A recent Guile-Gcrypt could not be found; please install it.]) fi GUIX_CHECK_GUILE_GIT if test "x$guix_cv_have_recent_guile_git" != "xyes"; then AC_MSG_ERROR([A recent Guile-Git could not be found; please install it.]) fi dnl Check for the optional Guile-Lib. GUILE_MODULE_EXPORTS([have_guile_lib], [(htmlprag)], [%strict-tokenizer?]) AM_CONDITIONAL([HAVE_GUILE_LIB], [test "x$have_guile_lib" = "xyes"]) AM_COND_IF(HAVE_GUILE_LIB,, [AC_MSG_WARN([The Guile-Lib requirement was not satisfied (>= 0.2.7); Some features such as the Go importer will not be usable.])]) dnl Check for Guile-zlib. GUIX_CHECK_GUILE_ZLIB if test "x$guix_cv_have_recent_guile_zlib" != "xyes"; then AC_MSG_ERROR([A recent Guile-zlib could not be found; please install it.]) fi dnl Check for Guile-lzlib. GUILE_MODULE_AVAILABLE([have_guile_lzlib], [(lzlib)]) if test "x$have_guile_lzlib" != "xyes"; then AC_MSG_ERROR([Guile-lzlib is missing; please install it.]) fi dnl Check for Guile-Avahi. GUILE_MODULE_AVAILABLE([have_guile_avahi], [(avahi)]) AM_CONDITIONAL([HAVE_GUILE_AVAHI], [test "x$have_guile_avahi" = "xyes"]) dnl Guile-newt is used by the graphical installer. GUILE_MODULE_AVAILABLE([have_guile_newt], [(newt)]) AC_ARG_ENABLE([installer], AS_HELP_STRING([--enable-installer], [Build the graphical installer sources.])) AS_IF([test "x$enable_installer" = "xyes"], [ if test "x$have_guile_newt" != "xyes"; then AC_MSG_ERROR([Guile-newt could not be found; please install it.]) fi ]) AM_CONDITIONAL([ENABLE_INSTALLER], [test "x$enable_installer" = "xyes"]) dnl Make sure we have a full-fledged Guile. GUIX_ASSERT_GUILE_FEATURES([regex posix socket net-db threads]) AC_PROG_SED dnl Decompressors, for use by the substituter and other modules. AC_PATH_PROG([GZIP], [gzip]) AC_PATH_PROG([BZIP2], [bzip2]) AC_PATH_PROG([XZ], [xz]) AC_SUBST([GZIP]) AC_SUBST([BZIP2]) AC_SUBST([XZ]) LIBGCRYPT_LIBDIR="no" LIBGCRYPT_PREFIX="no" AC_ARG_WITH([libgcrypt-prefix], [AS_HELP_STRING([--with-libgcrypt-prefix=DIR], [search for GNU libgcrypt in DIR])], [case "$withval" in yes|no) ;; *) LIBGCRYPT_PREFIX="$withval" LIBGCRYPT_LIBDIR="$withval/lib" ;; esac]) AC_ARG_WITH([libgcrypt-libdir], [AS_HELP_STRING([--with-libgcrypt-libdir=DIR], [search for GNU libgcrypt's shared library in DIR])], [case "$withval" in yes|no) LIBGCRYPT_LIBDIR="no" ;; *) LIBGCRYPT_LIBDIR="$withval" ;; esac]) dnl If none of the --with-libgcrypt-* options was used, try to determine the dnl the library directory. case "x$LIBGCRYPT_PREFIX$LIBGCRYPT_LIBDIR" in xnono) GUIX_LIBGCRYPT_LIBDIR([LIBGCRYPT_LIBDIR]) ;; esac AC_SUBST([LIBGCRYPT_PREFIX]) AC_SUBST([LIBGCRYPT_LIBDIR]) dnl Check for Guile-SSH, for the (guix ssh) module. GUIX_CHECK_GUILE_SSH AM_CONDITIONAL([HAVE_GUILE_SSH], [test "x$guix_cv_have_recent_guile_ssh" = "xyes"]) AC_CACHE_SAVE m4_include([config-daemon.ac]) dnl `dot' (from the Graphviz package) is only needed for maintainers. dnl See `Building from Git' in the manual for more info. AM_MISSING_PROG([DOT], [dot]) dnl Manual pages. AM_MISSING_PROG([HELP2MAN], [help2man]) dnl Documentation translation. AM_MISSING_PROG([PO4A_TRANSLATE], [po4a-translate]) AM_MISSING_PROG([PO4A_UPDATEPO], [po4a-updatepo]) case "$storedir" in /gnu/store) ;; *) AC_MSG_WARN([Using a store directory other than '/gnu/store' will prevent you]) AC_MSG_WARN([from downloading substitutes from gnu.org.]) ;; esac AC_CONFIG_FILES([Makefile po/guix/Makefile.in po/packages/Makefile.in etc/guix-daemon.cil guix/config.scm]) AC_CONFIG_FILES([etc/committer.scm], [chmod +x etc/committer.scm]) AC_CONFIG_FILES([test-env:build-aux/test-env.in], [chmod +x test-env]) AC_CONFIG_FILES([pre-inst-env:build-aux/pre-inst-env.in], [chmod +x pre-inst-env]) AC_OUTPUT


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