Proper Autotools use for Boost library for gzip input

- Add a ./configure option --with-boost-iostreams (enabled by default)
- Add a ./configure option --with-boost-include-path so the user can
  tell configure where to find the libraries if they are not in the
  default locations
- Add an Automake option WITH_BOOST_IOSTREAMS that is true if the lib
  can be found (well, if the gzip.hpp file can be found) and use this to
  add the LDADD flags for the binaries that need it. This option is also
  used in the C++ code to switch between compiling with or without
  Boost::iostreams.
- Print the version of the Boost library if Boost is used
- In gendata.cpp keep the option open to read files when the library is
  not present. Unfortunately this does leave the code more ugly with a
  bunch of #ifdefs...

configure.ac

@@ -88,6 +88,37 @@ if test x$ac_cv_header_Eigen_Dense = xno; then
 fi
 
 
+# See if we can use the Boost IOstreams libraries for reading gzipped
+# files
+AC_ARG_WITH([boost-iostreams],
+ AS_HELP_STRING([--with-boost-iostreams], [Use the Boost Iostreams library to
+ allow reading from gzipped files. This is enabled by default]
+               )
+)
+
+if test "x$with_boost_iostreams" != "xno"; then
+    AC_MSG_NOTICE([building using the Boost IOstreams library enabled])
+
+    AC_ARG_WITH([boost-include-path],
+        [AS_HELP_STRING([--with-boost-include-path],
+          [location of the Boost headers, defaults to /usr/include/boost])],
+        [CPPFLAGS+=" -I${withval}"],
+        [CPPFLAGS+=' -I/usr/include/'])
+
+    # Check for the Boost IOstreams header files
+    AC_CHECK_HEADER([boost/iostreams/filter/gzip.hpp],
+        [],
+        [AC_MSG_ERROR([Could not find the Boost IOstreams header files. Did \
+you specify --with-boost-include-path correctly? Or use --without-boost \
+to disable the reading of gzipped files.])]
+    )
+else
+   AC_MSG_NOTICE([not using the Boost IOstreams libraries, so input \
+from gzipped files is not possible])
+fi
+AM_CONDITIONAL([WITH_BOOST_IOSTREAMS], test "x$with_boost_iostreams" != "xno")
+
+
 # Checks for typedefs, structures, and compiler characteristics.
 AC_HEADER_STDBOOL
 AC_C_INLINE

src/Makefile.am

@@ -37,8 +37,6 @@ RHEADERS = include/R.h include/Rmath.h include/R_ext/Arith.h		\
  include/R_ext/Print.h include/R_ext/Random.h include/R_ext/Utils.h	\
  include/R_ext/RS.h
 
-LDADD = -lboost_iostreams -lz 
-
 bin_PROGRAMS =
 if BUILD_palinear
 bin_PROGRAMS += palinear
@@ -62,19 +60,32 @@ endif
 
 palinear_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
 palinear_CPPFLAGS = -DLINEAR $(AM_CPPFLAGS)
+palinear_LDADD =
 palinear_SOURCES += $(EIGENFILES)
 
 palogist_SOURCES = $(REGFILES) $(FVSRC) $(FVHEADERS)
 palogist_CPPFLAGS = -DLOGISTIC $(AM_CPPFLAGS)
+palogist_LDADD =
 palogist_SOURCES += $(EIGENFILES)
 
 pacoxph_SOURCES = $(COXSRC) $(REGFILES) $(FVSRC) $(FVHEADERS)	\
  $(RHEADERS) survS.h survproto.h coxph_data.h coxph_data.cpp
 pacoxph_CXXFLAGS = -I $(top_srcdir)/src/include $(AM_CXXFLAGS)
 pacoxph_CPPFLAGS = -DCOXPH $(AM_CPPFLAGS)
 pacoxph_CFLAGS = -I $(top_srcdir)/src/include $(AM_CFLAGS)
+pacoxph_LDADD =
 pacoxph_SOURCES += $(EIGENFILES)
 
+if WITH_BOOST_IOSTREAMS
+palinear_CPPFLAGS += -DWITH_BOOST_IOSTREAMS
+palinear_LDADD += -lboost_iostreams -lz
+palogist_CPPFLAGS += -DWITH_BOOST_IOSTREAMS
+palogist_LDADD += -lboost_iostreams -lz
+pacoxph_CPPFLAGS += -DWITH_BOOST_IOSTREAMS
+pacoxph_LDADD += -lboost_iostreams -lz
+endif
+
+
 extract_snp_SOURCES = extract-snp.cpp $(FVSRC) $(FVHEADERS)
 
 ## Install these scripts in the bin directory as well:

src/gendata.cpp

@@ -36,9 +36,11 @@
 #include "utilities.h"
 #include <iostream>
 #include <fstream>
+
+#if WITH_BOOST_IOSTREAMS
 #include <boost/iostreams/filtering_stream.hpp>
 #include <boost/iostreams/filter/gzip.hpp>
-
+#endif
 
 void gendata::mldose_line_to_matrix(const int k,
                                     const char *all_numbers,
@@ -251,9 +253,15 @@ void gendata::re_gendata(const char * fname,
 
     G.reinit(nids, (nsnps * ngpreds));
 
+#if WITH_BOOST_IOSTREAMS
     std::ifstream file(fname, std::ios_base::in | std::ios_base::binary);
     boost::iostreams::filtering_istream infile;
     std::string filename = fname;
+    // Note: a better check would be to read the first two bytes of
+    // the file and check for the gzip signature: 0x1f8b
+    // W.r.t. endianness and bytt width: compare each byte separately,
+    // see the comment to this SE answer:
+    // http://stackoverflow.com/a/6059342/881084
     if (filename.compare(filename.length() - 2, 2, "gz") == 0)
     {
         infile.push(boost::iostreams::gzip_decompressor());
@@ -263,8 +271,16 @@ void gendata::re_gendata(const char * fname,
         std::cout << "no gziped:" << ":\n";
     }
     infile.push(file);
+#else
+    std::ifstream infile;
+    infile.open(fname);
+#endif
 
+#if WITH_BOOST_IOSTREAMS
     if (!file)
+#else
+    if (!infile)
+#endif
     {
         std::cerr << "gendata: cannot open file " << fname << endl;
         exit(1);
@@ -297,7 +313,11 @@ void gendata::re_gendata(const char * fname,
                     cerr << "phenotype file and dose or probability file "
                             << "did not match at line " << i + 2 << " ("
                             << tmpid << " != " << idnames[k] << ")" << endl;
+#if WITH_BOOST_IOSTREAMS
                     file.close();
+#else
+                    infile.close();
+#endif
                     exit(1);
                 }
             }
@@ -327,7 +347,11 @@ void gendata::re_gendata(const char * fname,
         }
     }
 
+#if WITH_BOOST_IOSTREAMS
     file.close();
+#else
+    infile.close();
+#endif
 }
 
 // HERE NEED A NEW CONSTRUCTOR BASED ON DATABELBASECPP OBJECT

src/usage.cpp

@@ -31,6 +31,10 @@
 #include "config.h"
 #endif
 
+#if WITH_BOOST_IOSTREAMS
+#include <boost/version.hpp>
+#endif
+
 #include "eigen_mematrix.h"
 
 
@@ -103,6 +107,10 @@ void print_version(void) {
     cout << "Using EIGEN version " << EIGEN_WORLD_VERSION
          << "." << EIGEN_MAJOR_VERSION << "." << EIGEN_MINOR_VERSION
          << " for matrix operations\n";
+#if WITH_BOOST_IOSTREAMS
+    cout << "Using Boost libraries version " << BOOST_LIB_VERSION << endl;
+#endif
+
 }