binaries/src/ViennaRNA/m4/package.m4

   1 # This file is part of Autoconf.                       -*- Autoconf -*-
   2
   3 # ViennaRNA Package 2011 Ronny Lorenz
   4 #
   5
   6 ##-----------------##
   7 ## Private macros. ##
   8 ##-----------------##
   9
  10 AC_DEFUN([AC_RNA_TEST_FILE],[
  11 AC_MSG_CHECKING([for $1])
  12 if test -f $1 ; then
  13   AC_MSG_RESULT([yes])
  14   $2
  15 else
  16   AC_MSG_RESULT([no])
  17   $3
  18 fi
  19 ])
  20
  21 AC_DEFUN([AC_RNA_PACKAGE_IF_ENABLED],[
  22 if test "x$with_$1" != xno; then
  23   $2
  24 fi
  25 ])
  26
  27 #
  28 # AC_RNA_ADD_PACKAGE( package-name,
  29 #                     package-description,
  30 #                     default-on,
  31 #                     [action-if-not-default],
  32 #                     [action-if-default],
  33 #                     [files to check for])
  34 #
  35 # This macro handles additional package inclusion
  36 # Parameters:
  37 #       package-name:       a lowercase name of the optional package
  38 #                           which is used for $with_package_name variables
  39 #                           and --with[out]-package-name options in
  40 #                           configure script
  41 #                           The package_name must consist of alphanumeric
  42 #                           characters including the dash only! Every
  43 #                           occuring dash will be replaced by a '-' char
  44 #                           in the --with[out]-package-name option
  45 #
  46 #       package-desciption: a very brief description used for the package
  47 #                           specific help output in configure script
  48 #
  49 #       default-on:         package build | installed by default
  50 #                           Values: "yes" or "no"
  51 #
  52 # Example: AC_RNA_ADD_PACKAGE([foo], [the incredible Foo program], [yes], [with_foo=no], [with_foo=yes], [file1 file2])
  53 #
  54
  55 AC_DEFUN([AC_RNA_ADD_PACKAGE],[
  56
  57 # announce the option to include it in configure script
  58 AC_ARG_WITH(m4_translit([[$1]], [_], [-]),
  59             [ifelse([$3], [yes],
  60               [AS_HELP_STRING([--without-m4_translit([$1], [_], [-])], [do not build | install $2])],
  61               [AS_HELP_STRING([--with-m4_translit([$1], [_], [-])], [build | install $2])])],
  62             [$4],
  63             [$5])
  64
  65 # check if enabling the package makes sense at configure-time
  66 # and deactivate it if not
  67
  68 AC_RNA_PACKAGE_IF_ENABLED([$1],[
  69   for i in $6; do
  70     AC_RNA_TEST_FILE([$i],
  71       [with_$1=$with_$1],
  72       [with_$1=no])
  73   done
  74 ])
  75
  76 ])
  77
  78
  79 # AC_RNA_DOCUMENTATION_INIT(PROJECT_NAME, [config-file], [documentation-output-directory])
  80 #
  81 #
  82 AC_DEFUN([AC_RNA_DOCUMENTATION_INIT],[
  83
  84 AC_PATH_PROG(doxygen, [doxygen],no)
  85 AC_PATH_PROG(pdflatex,[pdflatex],no)
  86 AC_PATH_PROG(latex,[latex],no)
  87 AC_PATH_PROG(makeindex,[makeindex],no)
  88 AC_PATH_PROG(dot,[dot],no)
  89 AC_PATH_PROG(egrep,[egrep],no)
  90 AC_PATH_PROG(perl,[perl],no)
  91
  92 DOXYGEN_PDFLATEX_WORKARROUND=yes
  93
  94 # check whether we are able to generate the doxygen documentation
  95 AC_RNA_PACKAGE_IF_ENABLED([doc],[
  96   if test "x$doxygen" != xno;
  97   then
  98     # test for programs necessary in order to use doxygen
  99
 100     if test "x$DOXYGEN_PDFLATEX_WORKARROUND" = xno;
 101     then
 102     # this is a workarround for older versions of doxygen as installed e.g. in fc12 where
 103     # pdflatex usage does not work
 104
 105       if test "x$pdflatex" = xno;
 106       then
 107         if test "x$latex" = xno;
 108         then
 109           AC_MSG_WARN([neither latex or pdflatex exists on your system!])
 110           AC_MSG_WARN([deactivating automatic (re)generation of reference manual!])
 111           doxygen=no
 112         else
 113           _latex_cmd=$latex
 114         fi
 115       else
 116         _latex_cmd=$pdflatex
 117       fi
 118     else
 119       if test "x$latex" = xno;
 120       then
 121         AC_MSG_WARN([neither latex or pdflatex exists on your system!])
 122         AC_MSG_WARN([deactivating automatic (re)generation of reference manual!])
 123         doxygen=no
 124         _latex_cmd=
 125       else
 126         AC_MSG_WARN([due to a bug in older versions of doxygen, latex will be used for reference manual generation even if pdflatex is available])
 127         _latex_cmd=$latex
 128         pdflatex=no
 129       fi
 130     fi
 131
 132     if test "x$makeindex" = xno;
 133     then
 134       AC_MSG_WARN([makeindex command not found on your system!])
 135       AC_MSG_WARN([deactivating automatic (re)generation of reference manual!])
 136       doxygen=no
 137     fi
 138
 139     if test "x$egrep" = xno;
 140     then
 141       AC_MSG_WARN([egrep command not found on your system!])
 142       AC_MSG_WARN([deactivating automatic (re)generation of reference manual!])
 143       doxygen=no
 144     fi
 145
 146     if test "x$dot" = xno;
 147     then
 148       AC_MSG_WARN([dot command not found on your system!])
 149       AC_MSG_WARN([deactivating graph output in reference manual!])
 150     fi
 151
 152     if test "x$perl" = xno;
 153     then
 154       AC_MSG_WARN([perl command not found on your system!])
 155       AC_MSG_WARN([deactivating automatic (re)generation of reference manual!])
 156       doxygen=no
 157     fi
 158
 159   fi
 160 ])
 161
 162
 163 # setup everything in order to generate the doxygen configfile
 164
 165 AC_RNA_PACKAGE_IF_ENABLED([doc],[
 166
 167   AC_SUBST([DOXYGEN_PROJECT_NAME], [$1-$PACKAGE_VERSION])
 168   AC_SUBST([DOXYGEN_SRCDIR], [$srcdir])
 169   AC_SUBST([DOXYGEN_DOCDIR], [ifelse([$3], [], [doc], [$3])])
 170   AC_SUBST([DOXYGEN_CONF], [ifelse([$2], [], [doxygen.conf], [$2])])
 171
 172
 173 # prepare the config file for doxygen if we are able to generate a reference manual
 174   if test "x$doxygen" != xno;
 175   then
 176
 177     AC_SUBST([DOXYGEN_CMD_LATEX], [$_latex_cmd])
 178     AC_SUBST([DOXYGEN_CMD_MAKEINDEX], [$makeindex])
 179     AC_SUBST([DOXYGEN_HAVE_DOT],[ifelse([$dot], [no], [NO], [YES])])
 180     AC_SUBST([DOXYGEN_WITH_PDFLATEX], [ifelse([$pdflatex],[no],[NO],[YES])])
 181     AC_SUBST([DOXYGEN_GENERATE_HTML], [ifelse([$with_doc_html], [no], [NO], [YES])])
 182     AC_SUBST([DOXYGEN_GENERATE_LATEX], [ifelse([$with_doc_pdf], [no], [NO], [YES])])
 183
 184     AC_CONFIG_FILES([${DOXYGEN_DOCDIR}/${DOXYGEN_CONF}])
 185
 186   else
 187
 188 # otherwise check if a generated reference manual already exists
 189
 190     AC_RNA_PACKAGE_IF_ENABLED([doc_pdf],[
 191       AC_RNA_TEST_FILE( [$DOXYGEN_DOCDIR/$DOXYGEN_PROJECT_NAME.pdf],
 192                         [with_doc_pdf=yes],
 193                         [with_doc_pdf=no])])
 194
 195     AC_RNA_PACKAGE_IF_ENABLED([doc_html],[
 196       AC_RNA_TEST_FILE( [$DOXYGEN_DOCDIR/html/index.html],
 197                         [with_doc_html=yes],
 198                         [with_doc_html=no])])
 199
 200     if test "x$with_doc_pdf" = "x$with_doc_html";
 201     then
 202       if test "x$with_doc_pdf" = xno;
 203       then
 204         with_doc=no
 205       fi
 206     fi
 207   fi
 208 ])
 209
 210 AC_SUBST([REFERENCE_MANUAL_PDF_NAME], [ifelse([$with_doc_pdf],
 211                                               [no],
 212                                               [],
 213                                               [$DOXYGEN_PROJECT_NAME.pdf])])
 214 AC_SUBST([REFERENCE_MANUAL_TAGFILE],  [ifelse([$doxygen],
 215                                               [no],
 216                                               [],
 217                                               [$DOXYGEN_PROJECT_NAME.tag])])
 218
 219
 220 # setup variables used in Makefile.am
 221 AM_CONDITIONAL(WITH_REFERENCE_MANUAL, test "x$with_doc" != xno)
 222 AM_CONDITIONAL(WITH_REFERENCE_MANUAL_BUILD, test "x$doxygen" != xno)
 223 AM_CONDITIONAL(WITH_REFERENCE_MANUAL_PDF, test "x$with_doc_pdf" != xno)
 224 AM_CONDITIONAL(WITH_REFERENCE_MANUAL_HTML, test "x$with_doc_html" != xno)
 225
 226 ])
 227
 228 ##----------------##
 229 ## Public macros. ##
 230 ##----------------##
 231
 232 AC_DEFUN([AC_RNA_INIT],[
 233
 234 SVM_VERSION=2.91
 235 with_pf_float=no
 236
 237 dnl add packages to the configure process
 238
 239 AC_RNA_ADD_PACKAGE( [perl],
 240                     [Perl interface],
 241                     [yes],
 242                     [with_perl=no],
 243                     [with_perl=yes],
 244                     [interfaces/Perl/Makefile.am])
 245 AC_RNA_ADD_PACKAGE( [python],
 246                     [Python interface],
 247                     [no],
 248                     [with_python=yes],
 249                     [with_python=no],
 250                     [interfaces/Python/Makefile.am])
 251 AC_RNA_ADD_PACKAGE( [ruby],
 252                     [Ruby interface],
 253                     [no],
 254                     [with_ruby=yes],
 255                     [with_ruby=no],
 256                     [interfaces/Ruby/Makefile.am])
 257 AC_RNA_ADD_PACKAGE( [kinfold],
 258                     [Kinfold program],
 259                     [yes],
 260                     [with_kinfold=no],
 261                     [with_kinfold=yes],
 262                     [Kinfold/Makefile.am])
 263 AC_RNA_ADD_PACKAGE( [forester],
 264                     [RNAforester program],
 265                     [yes],
 266                     [with_forester=no],
 267                     [with_forester=yes],
 268                     [RNAforester/Makefile.am])
 269 AC_RNA_ADD_PACKAGE( [cluster],
 270                     [AnalyseSeqs and AnalyseDists],
 271                     [no],
 272                     [with_cluster=yes],
 273                     [with_cluster=no],
 274                     [Cluster/Makefile.am])
 275 AC_RNA_ADD_PACKAGE( [svm],
 276                     [svm classifiers],
 277                     [yes],
 278                     [with_svm=no],
 279                     [with_svm=yes],
 280                     [libsvm-${SVM_VERSION}/svm.cpp libsvm-${SVM_VERSION}/svm.h])
 281 AC_RNA_ADD_PACKAGE( [doc_pdf],
 282                     [PDF RNAlib reference manual],
 283                     [yes],
 284                     [with_doc_pdf=no],
 285                     [with_doc_pdf=yes])
 286 AC_RNA_ADD_PACKAGE( [doc_html],
 287                     [HTML RNAlib reference manual],
 288                     [yes],
 289                     [with_doc_html=no],
 290                     [with_doc_html=yes])
 291 AC_RNA_ADD_PACKAGE( [doc],
 292                     [RNAlib reference manual],
 293                     [yes],
 294                     [ with_doc=no
 295                       with_doc_pdf=no
 296                       with_doc_html=no],
 297                     [with_doc=yes])
 298
 299 ## begin with initialization according to configure-time specific options
 300
 301 ## The following test ensures the right type for FLT_OR_DBL in the SWIG RNAlib interface
 302 AC_MSG_CHECKING([whether float precision is used for partition function arrays instead of double precision])
 303 bla=`${GREP} "^#define LARGE_PF" H/data_structures.h`
 304 if test "x$bla" = "x";
 305 then
 306   with_pf_float=yes
 307 fi
 308 AC_MSG_RESULT([$with_pf_float])
 309
 310 # check prerequisites for Perl interface
 311 AC_PATH_PROG(PerlCmd, perl)
 312 ifelse([$PerlCmd], [],[
 313   AC_MSG_WARN([No suitable Perl found -- will not build Perl module])
 314   AC_MSG_WARN([You may set the PerlCmd environment variable to point to
 315               a suitable perl binary])
 316   with_perl="no"
 317 ],[
 318   if $PerlCmd -e 'require 5.004'; then :
 319   else
 320     AC_MSG_WARN([You need Perl version 5.004 or higher for the Perl module])
 321     with_perl="no"
 322   fi
 323 ])
 324
 325
 326 # prepare all files for perl interface
 327 AC_RNA_PACKAGE_IF_ENABLED([perl],[
 328   AC_DEFINE([WITH_PERL_INTERFACE], [1], [Create the perl interface to RNAlib])
 329   AC_SUBST([PERL_INTERFACE], [Perl])
 330   AC_CONFIG_FILES([interfaces/Perl/Makefile interfaces/Perl/Makefile.PL])
 331 ])
 332
 333 # check prerequisites for Python interface
 334 AC_PATH_PROG(PythonCmd, python)
 335 ifelse([$PythonCmd], [], [
 336   AC_MSG_WARN([No suitable Python found -- will not build Python extension])
 337   AC_MSG_WARN([You may set the PythonCmd environment variable to point to
 338                 a suitable python binary])
 339   with_python="no"
 340 ],[
 341   version_test=`$PythonCmd interfaces/Python/version_test.py`
 342   if test "x$version_test" = "xok"; then :
 343   else
 344     AC_MSG_WARN([You need Python >= 2.5 and < 3.0 to build the Python extension])
 345     AC_MSG_WARN([You may set the PythonCmd environment variable to point to
 346                 a suitable python binary])
 347     with_python="no"
 348   fi
 349 ])
 350
 351 # prepare all files for python interface
 352 AC_RNA_PACKAGE_IF_ENABLED([python],[
 353   AC_DEFINE([WITH_PYTHON_INTERFACE], [1], [Create the python interface to RNAlib])
 354   AC_SUBST([PYTHON_INTERFACE], [Python])
 355   AC_CONFIG_FILES([interfaces/Python/Makefile interfaces/Python/setup.py])
 356 ])
 357
 358
 359 AC_RNA_PACKAGE_IF_ENABLED([kinfold],[
 360   AC_CONFIG_SUBDIRS([Kinfold])
 361 ])
 362
 363 AC_RNA_PACKAGE_IF_ENABLED([forester],[
 364   AC_CONFIG_SUBDIRS([RNAforester])
 365 ])
 366
 367 AC_RNA_PACKAGE_IF_ENABLED([cluster],[
 368   AC_DEFINE([WITH_CLUSTER], [1], [Analyse{Dists,Seqs}])
 369   AC_SUBST([CLUSTER_DIR], [Cluster])
 370   AC_CONFIG_FILES([Cluster/Makefile])
 371 ])
 372
 373 AC_RNA_PACKAGE_IF_ENABLED([svm],[
 374   AC_SUBST([LIBSVM_DIR], [libsvm-${SVM_VERSION}])
 375   AC_SUBST([CXXLD],[${CXX}]) # this is rather a hack for RNALfold.c linking correctly
 376   AC_DEFINE([USE_SVM], [1], [Compute z-scores for RNALfold])
 377 ])
 378
 379 AM_CONDITIONAL(WITH_LARGE_PF, test "$with_pf_float" != "yes")
 380 AM_CONDITIONAL(MAKE_KINFOLD, test "$with_kinfold" != "no")
 381 AM_CONDITIONAL(MAKE_FORESTER, test "$with_forester" != "no")
 382 AM_CONDITIONAL(MAKE_CLUSTER, test "$with_cluster" = "yes")
 383 AM_CONDITIONAL(WITH_LIBSVM, test "$with_svm" != "no")
 384
 385 AC_RNA_DOCUMENTATION_INIT([RNAlib])
 386
 387 AC_CONFIG_FILES([misc/Makefile misc/ViennaRNA.spec misc/PKGBUILD])
 388 AC_CONFIG_FILES([interfaces/Makefile])
 389 AC_CONFIG_FILES([Makefile RNAlib2.pc Utils/Makefile Progs/Makefile lib/Makefile man/Makefile H/Makefile doc/Makefile])
 390
 391 AC_CONFIG_FILES([man/cmdlopt.sh],[chmod +x man/cmdlopt.sh])
 392
 393 ])
 394
 395 AC_DEFUN([AC_RNA_NOTICE],[
 396
 397 # get directory paths
 398
 399 eval _bindir=$(eval printf "%s" $bindir)
 400 eval _libdir=$(eval printf "%s" $libdir)
 401 eval _includedir=$(eval printf "%s" $includedir)
 402 eval _datadir=$(eval printf "%s" $datadir)
 403 eval _mandir=$(eval printf "%s" $mandir)
 404 eval _docdir=$(eval printf "%s" $docdir)
 405 eval _htmldir=$(eval printf "%s" $htmldir)
 406 eval _pdfdir=$(eval printf "%s" $pdfdir)
 407
 408 # Notify the user
 409
 410 AC_MSG_NOTICE(
 411 [
 412 Configure successful with the following options:
 413
 414 RNAlib Interfaces:
 415   Perl Interface:       ${with_perl:-yes}
 416   Python Interface:     ${with_python:-yes}
 417   Ruby Interface:       ${with_ruby:-yes}
 418
 419 Extra Programs:
 420   Analyse{Dists,Seqs}:  ${with_cluster:-no}
 421   Kinfold:              ${with_kinfold:-yes}
 422   RNAforester:          ${with_forester:-yes}
 423
 424 Other Options:
 425   SVM:                  ${with_svm:-yes}
 426   Documentation:        ${with_doc:-no}
 427     (HTML):             ${with_doc_html:-no}
 428     (PDF):              ${with_doc_pdf:-no}
 429 -
 430 Files will be installed in the following directories:
 431
 432   Executables:    $_bindir
 433   Libraries:      $_libdir
 434   Header files:   $_includedir
 435   Extra Data:     $_datadir
 436   Man pages:      $_mandir
 437   Documentation:  $_docdir
 438     (HTML):       $(eval printf "%s" $_htmldir)/html
 439     (PDF):        $(eval printf "%s" $_pdfdir)
 440 ])
 441
 442 ])
 443
 444
 445