Bug in segment size checks

Makefile.in

@@ -221,7 +221,6 @@ LDFLAGS = @LDFLAGS@
 LIBOBJS = @LIBOBJS@
 LIBS = @LIBS@
 LTLIBOBJS = @LTLIBOBJS@
-MAINT = @MAINT@
 MAKEINFO = @MAKEINFO@
 MKDIR_P = @MKDIR_P@
 OBJEXT = @OBJEXT@
@@ -288,7 +287,7 @@ all: config.h
 .SUFFIXES:
 am--refresh: Makefile
 	@:
-$(srcdir)/Makefile.in: @MAINTAINER_MODE_TRUE@ $(srcdir)/Makefile.am  $(am__configure_deps)
+$(srcdir)/Makefile.in:  $(srcdir)/Makefile.am  $(am__configure_deps)
 	@for dep in $?; do \
 	  case '$(am__configure_deps)' in \
 	    *$$dep*) \
@@ -315,9 +314,9 @@ Makefile: $(srcdir)/Makefile.in $(top_builddir)/config.status
 $(top_builddir)/config.status: $(top_srcdir)/configure $(CONFIG_STATUS_DEPENDENCIES)
 	$(SHELL) ./config.status --recheck
 
-$(top_srcdir)/configure: @MAINTAINER_MODE_TRUE@ $(am__configure_deps)
+$(top_srcdir)/configure:  $(am__configure_deps)
 	$(am__cd) $(srcdir) && $(AUTOCONF)
-$(ACLOCAL_M4): @MAINTAINER_MODE_TRUE@ $(am__aclocal_m4_deps)
+$(ACLOCAL_M4):  $(am__aclocal_m4_deps)
 	$(am__cd) $(srcdir) && $(ACLOCAL) $(ACLOCAL_AMFLAGS)
 $(am__aclocal_m4_deps):
 
@@ -328,7 +327,7 @@ config.h: stamp-h1
 stamp-h1: $(srcdir)/config.h.in $(top_builddir)/config.status
 	@rm -f stamp-h1
 	cd $(top_builddir) && $(SHELL) ./config.status config.h
-$(srcdir)/config.h.in: @MAINTAINER_MODE_TRUE@ $(am__configure_deps) 
+$(srcdir)/config.h.in:  $(am__configure_deps) 
 	($(am__cd) $(top_srcdir) && $(AUTOHEADER))
 	rm -f stamp-h1
 	touch $@

aclocal.m4

@@ -642,42 +642,6 @@ fi
 rmdir .tst 2>/dev/null
 AC_SUBST([am__leading_dot])])
 
-# Add --enable-maintainer-mode option to configure.         -*- Autoconf -*-
-# From Jim Meyering
-
-# Copyright (C) 1996-2013 Free Software Foundation, Inc.
-#
-# This file is free software; the Free Software Foundation
-# gives unlimited permission to copy and/or distribute it,
-# with or without modifications, as long as this notice is preserved.
-
-# AM_MAINTAINER_MODE([DEFAULT-MODE])
-# ----------------------------------
-# Control maintainer-specific portions of Makefiles.
-# Default is to disable them, unless 'enable' is passed literally.
-# For symmetry, 'disable' may be passed as well.  Anyway, the user
-# can override the default with the --enable/--disable switch.
-AC_DEFUN([AM_MAINTAINER_MODE],
-[m4_case(m4_default([$1], [disable]),
-       [enable], [m4_define([am_maintainer_other], [disable])],
-       [disable], [m4_define([am_maintainer_other], [enable])],
-       [m4_define([am_maintainer_other], [enable])
-        m4_warn([syntax], [unexpected argument to AM@&t@_MAINTAINER_MODE: $1])])
-AC_MSG_CHECKING([whether to enable maintainer-specific portions of Makefiles])
-  dnl maintainer-mode's default is 'disable' unless 'enable' is passed
-  AC_ARG_ENABLE([maintainer-mode],
-    [AS_HELP_STRING([--]am_maintainer_other[-maintainer-mode],
-      am_maintainer_other[ make rules and dependencies not useful
-      (and sometimes confusing) to the casual installer])],
-    [USE_MAINTAINER_MODE=$enableval],
-    [USE_MAINTAINER_MODE=]m4_if(am_maintainer_other, [enable], [no], [yes]))
-  AC_MSG_RESULT([$USE_MAINTAINER_MODE])
-  AM_CONDITIONAL([MAINTAINER_MODE], [test $USE_MAINTAINER_MODE = yes])
-  MAINT=$MAINTAINER_MODE_TRUE
-  AC_SUBST([MAINT])dnl
-]
-)
-
 # Check to see how 'make' treats includes.	            -*- Autoconf -*-
 
 # Copyright (C) 2001-2013 Free Software Foundation, Inc.

config.log

@@ -4,7 +4,7 @@ running configure, to aid debugging if configure makes a mistake.
 It was created by fgwas configure 0.03, which was
 generated by GNU Autoconf 2.69.  Invocation command line was
 
-  $ ./configure 
+  $ ./configure LDFLAGS=-L/opt/local/lib --no-create --no-recursion
 
 ## --------- ##
 ## Platform. ##
@@ -30,8 +30,8 @@ Kernel configured for up to 4 processors.
 Processor type: i486 (Intel 80486)
 Processors active: 0 1 2 3
 Primary memory available: 4.00 gigabytes
-Default processor set: 190 tasks, 1005 threads, 4 processors
-Load average: 1.00, Mach factor: 2.99
+Default processor set: 177 tasks, 876 threads, 4 processors
+Load average: 1.27, Mach factor: 2.72
 /bin/machine           = unknown
 /usr/bin/oslevel       = unknown
 /bin/universe          = unknown
@@ -79,17 +79,17 @@ configure:2020: g++ -qversion >&5
 clang: error: no input files
 configure:2031: $? = 1
 configure:2051: checking whether the C++ compiler works
-configure:2073: g++    conftest.cpp  >&5
+configure:2073: g++   -L/opt/local/lib conftest.cpp  >&5
 configure:2077: $? = 0
 configure:2125: result: yes
 configure:2128: checking for C++ compiler default output file name
 configure:2130: result: a.out
 configure:2136: checking for suffix of executables
-configure:2143: g++ -o conftest    conftest.cpp  >&5
+configure:2143: g++ -o conftest   -L/opt/local/lib conftest.cpp  >&5
 configure:2147: $? = 0
 configure:2169: result: 
 configure:2191: checking whether we are cross compiling
-configure:2199: g++ -o conftest    conftest.cpp  >&5
+configure:2199: g++ -o conftest   -L/opt/local/lib conftest.cpp  >&5
 configure:2203: $? = 0
 configure:2210: ./conftest
 configure:2214: $? = 0
@@ -185,11 +185,11 @@ configure:3872: result: yes
 configure:3891: checking dependency style of gcc
 configure:4002: result: gcc3
 configure:4018: checking for gzopen in -lz
-configure:4043: gcc -o conftest -g -O2   conftest.c -lz   >&5
+configure:4043: gcc -o conftest -g -O2  -L/opt/local/lib conftest.c -lz   >&5
 configure:4043: $? = 0
 configure:4052: result: yes
 configure:4065: checking for cos in -lm
-configure:4090: gcc -o conftest -g -O2   conftest.c -lm  -lz  >&5
+configure:4090: gcc -o conftest -g -O2  -L/opt/local/lib conftest.c -lm  -lz  >&5
 conftest.c:19:6: warning: incompatible redeclaration of library function 'cos' [-Wincompatible-library-redeclaration]
 char cos ();
      ^
@@ -198,40 +198,20 @@ conftest.c:19:6: note: 'cos' is a builtin with type 'double (double)'
 configure:4090: $? = 0
 configure:4099: result: yes
 configure:4110: checking for cblas_dgemm in -lgslcblas
-configure:4135: gcc -o conftest -g -O2   conftest.c -lgslcblas  -lm -lz  >&5
-ld: library not found for -lgslcblas
-clang: error: linker command failed with exit code 1 (use -v to see invocation)
-configure:4135: $? = 1
-configure: failed program was:
-| /* confdefs.h */
-| #define PACKAGE_NAME "fgwas"
-| #define PACKAGE_TARNAME "fgwas"
-| #define PACKAGE_VERSION "0.03"
-| #define PACKAGE_STRING "fgwas 0.03"
-| #define PACKAGE_BUGREPORT "[email protected]"
-| #define PACKAGE_URL "http://gwas.googlecode.com/"
-| #define PACKAGE "fgwas"
-| #define VERSION "0.03"
-| #define HAVE_LIBZ 1
-| #define HAVE_LIBM 1
-| /* end confdefs.h.  */
-| 
-| /* Override any GCC internal prototype to avoid an error.
-|    Use char because int might match the return type of a GCC
-|    builtin and then its argument prototype would still apply.  */
-| #ifdef __cplusplus
-| extern "C"
-| #endif
-| char cblas_dgemm ();
-| int
-| main ()
-| {
-| return cblas_dgemm ();
-|   ;
-|   return 0;
-| }
-configure:4144: result: no
-configure:4154: error: could not find GSL BLAS
+configure:4135: gcc -o conftest -g -O2  -L/opt/local/lib conftest.c -lgslcblas  -lm -lz  >&5
+configure:4135: $? = 0
+configure:4144: result: yes
+configure:4157: checking for gsl_blas_dgemm in -lgsl
+configure:4182: gcc -o conftest -g -O2  -L/opt/local/lib conftest.c -lgsl  -lgslcblas -lm -lz  >&5
+configure:4182: $? = 0
+configure:4191: result: yes
+configure:4292: checking for boostlib >= 1.42
+configure:4361: g++ -c -g -O2  -I/opt/local/include conftest.cpp >&5
+configure:4361: $? = 0
+configure:4363: result: yes
+configure:4621: checking that generated files are newer than configure
+configure:4627: result: done
+configure:4654: creating ./config.status
 
 ## ---------------- ##
 ## Cache variables. ##
@@ -251,8 +231,8 @@ ac_cv_env_CXXFLAGS_set=
 ac_cv_env_CXXFLAGS_value=
 ac_cv_env_CXX_set=
 ac_cv_env_CXX_value=
-ac_cv_env_LDFLAGS_set=
-ac_cv_env_LDFLAGS_value=
+ac_cv_env_LDFLAGS_set=set
+ac_cv_env_LDFLAGS_value=-L/opt/local/lib
 ac_cv_env_LIBS_set=
 ac_cv_env_LIBS_value=
 ac_cv_env_build_alias_set=
@@ -261,7 +241,8 @@ ac_cv_env_host_alias_set=
 ac_cv_env_host_alias_value=
 ac_cv_env_target_alias_set=
 ac_cv_env_target_alias_value=
-ac_cv_lib_gslcblas_cblas_dgemm=no
+ac_cv_lib_gsl_gsl_blas_dgemm=yes
+ac_cv_lib_gslcblas_cblas_dgemm=yes
 ac_cv_lib_m_cos=yes
 ac_cv_lib_z_gzopen=yes
 ac_cv_objext=o
@@ -296,17 +277,17 @@ AUTOCONF='${SHELL} /Users/jkpickrell/Documents/workspace/GWAS/missing autoconf'
 AUTOHEADER='${SHELL} /Users/jkpickrell/Documents/workspace/GWAS/missing autoheader'
 AUTOMAKE='${SHELL} /Users/jkpickrell/Documents/workspace/GWAS/missing automake-1.14'
 AWK='awk'
-BOOST_CPPFLAGS=''
-BOOST_LDFLAGS=''
+BOOST_CPPFLAGS='-I/opt/local/include'
+BOOST_LDFLAGS='-L/opt/local/lib'
 CC='gcc'
 CCDEPMODE='depmode=gcc3'
 CFLAGS='-g -O2'
-CPPFLAGS=''
+CPPFLAGS=' -I/opt/local/include'
 CXX='g++'
 CXXDEPMODE='depmode=gcc3'
 CXXFLAGS='-g -O2'
 CYGPATH_W='echo'
-DEFS=''
+DEFS='-DHAVE_CONFIG_H'
 DEPDIR='.deps'
 ECHO_C='\c'
 ECHO_N=''
@@ -316,9 +297,9 @@ INSTALL_DATA='${INSTALL} -m 644'
 INSTALL_PROGRAM='${INSTALL}'
 INSTALL_SCRIPT='${INSTALL}'
 INSTALL_STRIP_PROGRAM='$(install_sh) -c -s'
-LDFLAGS=''
+LDFLAGS='-L/opt/local/lib'
 LIBOBJS=''
-LIBS='-lm -lz '
+LIBS='-lgsl -lgslcblas -lm -lz '
 LTLIBOBJS=''
 MAKEINFO='${SHELL} /Users/jkpickrell/Documents/workspace/GWAS/missing makeinfo'
 MKDIR_P='./install-sh -c -d'
@@ -338,7 +319,7 @@ VERSION='0.03'
 ac_ct_CC='gcc'
 ac_ct_CXX='g++'
 am__EXEEXT_FALSE=''
-am__EXEEXT_TRUE=''
+am__EXEEXT_TRUE='#'
 am__fastdepCC_FALSE='#'
 am__fastdepCC_TRUE=''
 am__fastdepCXX_FALSE='#'
@@ -356,7 +337,7 @@ datadir='${datarootdir}'
 datarootdir='${prefix}/share'
 docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
 dvidir='${docdir}'
-exec_prefix='NONE'
+exec_prefix='${prefix}'
 host_alias=''
 htmldir='${docdir}'
 includedir='${prefix}/include'
@@ -370,7 +351,7 @@ mandir='${datarootdir}/man'
 mkdir_p='$(MKDIR_P)'
 oldincludedir='/usr/include'
 pdfdir='${docdir}'
-prefix='NONE'
+prefix='/usr/local'
 program_transform_name='s,x,x,'
 psdir='${docdir}'
 sbindir='${exec_prefix}/sbin'
@@ -393,5 +374,47 @@ target_alias=''
 #define VERSION "0.03"
 #define HAVE_LIBZ 1
 #define HAVE_LIBM 1
+#define HAVE_LIBGSLCBLAS 1
+#define HAVE_LIBGSL 1
+#define HAVE_BOOST /**/
 
-configure: exit 1
+configure: exit 0
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by fgwas config.status 0.03, which was
+generated by GNU Autoconf 2.69.  Invocation command line was
+
+  CONFIG_FILES    = 
+  CONFIG_HEADERS  = 
+  CONFIG_LINKS    = 
+  CONFIG_COMMANDS = 
+  $ ./config.status 
+
+on jkpickrell01
+
+config.status:854: creating Makefile
+config.status:854: creating src/Makefile
+config.status:854: creating config.h
+config.status:1035: config.h is unchanged
+config.status:1083: executing depfiles commands
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by fgwas config.status 0.03, which was
+generated by GNU Autoconf 2.69.  Invocation command line was
+
+  CONFIG_FILES    = 
+  CONFIG_HEADERS  = 
+  CONFIG_LINKS    = 
+  CONFIG_COMMANDS = 
+  $ ./config.status config.h
+
+on jkpickrell01
+
+config.status:854: creating config.h
+config.status:1035: config.h is unchanged

configure

@@ -596,9 +596,6 @@ CCDEPMODE
 ac_ct_CC
 CFLAGS
 CC
-MAINT
-MAINTAINER_MODE_FALSE
-MAINTAINER_MODE_TRUE
 AM_BACKSLASH
 AM_DEFAULT_VERBOSITY
 AM_DEFAULT_V
@@ -686,7 +683,6 @@ ac_user_opts='
 enable_option_checking
 enable_dependency_tracking
 enable_silent_rules
-enable_maintainer_mode
 with_boost
 with_boost_libdir
 '
@@ -1321,9 +1317,6 @@ Optional Features:
                           speeds up one-time build
   --enable-silent-rules   less verbose build output (undo: "make V=1")
   --disable-silent-rules  verbose build output (undo: "make V=0")
-  --enable-maintainer-mode
-                          enable make rules and dependencies not useful (and
-                          sometimes confusing) to the casual installer
 
 Optional Packages:
   --with-PACKAGE[=ARG]    use PACKAGE [ARG=yes]
@@ -3295,29 +3288,6 @@ END
 fi
 ac_config_headers="$ac_config_headers config.h"
 
-
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether to enable maintainer-specific portions of Makefiles" >&5
-$as_echo_n "checking whether to enable maintainer-specific portions of Makefiles... " >&6; }
-    # Check whether --enable-maintainer-mode was given.
-if test "${enable_maintainer_mode+set}" = set; then :
-  enableval=$enable_maintainer_mode; USE_MAINTAINER_MODE=$enableval
-else
-  USE_MAINTAINER_MODE=no
-fi
-
-  { $as_echo "$as_me:${as_lineno-$LINENO}: result: $USE_MAINTAINER_MODE" >&5
-$as_echo "$USE_MAINTAINER_MODE" >&6; }
-   if test $USE_MAINTAINER_MODE = yes; then
-  MAINTAINER_MODE_TRUE=
-  MAINTAINER_MODE_FALSE='#'
-else
-  MAINTAINER_MODE_TRUE='#'
-  MAINTAINER_MODE_FALSE=
-fi
-
-  MAINT=$MAINTAINER_MODE_TRUE
-
-
 ac_ext=c
 ac_cpp='$CPP $CPPFLAGS'
 ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
@@ -4672,10 +4642,6 @@ else
   am__EXEEXT_FALSE=
 fi
 
-if test -z "${MAINTAINER_MODE_TRUE}" && test -z "${MAINTAINER_MODE_FALSE}"; then
-  as_fn_error $? "conditional \"MAINTAINER_MODE\" was never defined.
-Usually this means the macro was only invoked conditionally." "$LINENO" 5
-fi
 if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then
   as_fn_error $? "conditional \"am__fastdepCC\" was never defined.
 Usually this means the macro was only invoked conditionally." "$LINENO" 5