From 298cb197fcb614894ea498695934eb5dbb418ea4 Mon Sep 17 00:00:00 2001 From: alexlan Date: Tue, 24 Apr 2007 05:15:44 +0000 Subject: [PATCH 01/42] Initial import. --- .cvsignore | 1 + sources | 1 + wise2-build.patch | 10 ++++++ wise2.spec | 79 +++++++++++++++++++++++++++++++++++++++++++++++ 4 files changed, 91 insertions(+) create mode 100644 wise2-build.patch create mode 100644 wise2.spec diff --git a/.cvsignore b/.cvsignore index e69de29..ba20b1d 100644 --- a/.cvsignore +++ b/.cvsignore @@ -0,0 +1 @@ +wise2.2.0.tar.gz diff --git a/sources b/sources index e69de29..8d1f2c3 100644 --- a/sources +++ b/sources @@ -0,0 +1 @@ +0584240f77885e37528e99e64535ab60 wise2.2.0.tar.gz diff --git a/wise2-build.patch b/wise2-build.patch new file mode 100644 index 0000000..1965c5b --- /dev/null +++ b/wise2-build.patch @@ -0,0 +1,10 @@ +--- src/makefile.orig 2007-04-11 07:52:41.000000000 -0700 ++++ src/makefile 2007-04-11 07:53:04.000000000 -0700 +@@ -89,7 +89,6 @@ + bin : + mkdir bin + mv models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/genomewise ./bin +- csh welcome.csh + + libs : + (cd base ; make CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a ) diff --git a/wise2.spec b/wise2.spec new file mode 100644 index 0000000..812d6f0 --- /dev/null +++ b/wise2.spec @@ -0,0 +1,79 @@ +Name: wise2 +Version: 2.2.0 +Release: 2%{?dist} +Summary: Tools for comparison of biopolymers + +Group: Applications/Engineering +License: GPL +URL: http://www.ebi.ac.uk/Wise2/ +Source0: ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/wise%{version}.tar.gz +Patch0: wise2-build.patch +BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) + +%description +Wise2 is a package focused on comparisons of biopolymers, commonly DNA +sequence and protein sequence. A strength of Wise2 is the +comparison of DNA sequence at the level of its protein +translation. This comparison allows the simultaneous prediction of +gene structure with homology based alignment. + +%prep +%setup -q -n wise%{version} + +## don't run "welcome.csh" +%patch0 -p0 + +## fix interpreter in examples +sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' docs/gettex.pl +## fix perms +chmod -x test_data/rrm.HMM + +## pull out licenses +for i in base dynlibsrc dyc +do + cp src/$i/LICENSE LICENSE.$i +done +cp src/models/GNULICENSE LICENSE.GPL + +%build +cd src +## removed "{?_smp_mflags}", does not support parallel build +make CC=gcc CFLAGS="-c $RPM_OPT_FLAGS" all + +%install +rm -rf $RPM_BUILD_ROOT +cd src/bin +%{__mkdir_p} $RPM_BUILD_ROOT%{_bindir} +for i in dba dnal estwise estwisedb genewise genewisedb genomewise psw pswdb +do + %{__install} $i $RPM_BUILD_ROOT/%{_bindir} +done +cd - +# install architecture-independent data and config files +%{__mkdir_p} $RPM_BUILD_ROOT%{_datadir}/wise2 +cd wisecfg +%{__install} -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2 + +# install scripts to automatically set the WISECONFIGDIR environment variable +%{__mkdir_p} $RPM_BUILD_ROOT%{_sysconfdir}/profile.d +echo "export WISECONFIGDIR=%{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.sh +echo "setenv WISECONFIGDIR %{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.csh + +%clean +rm -rf $RPM_BUILD_ROOT + + +%files +%defattr(-,root,root,-) +%doc docs test_data +%doc INSTALL LICENSE README LICENSE.base LICENSE.dynlibsrc LICENSE.dyc LICENSE.GPL +%{_bindir}/* +%{_datadir}/wise2 +%config(noreplace) %{_sysconfdir}/profile.d/* + +%changelog +* Mon Apr 12 2007 Alex Lancaster 2.2.0-2 +- Pass $RPM_OPT_FLAGS to compiler as per suggestion from Ralf Corsepius. + +* Mon Apr 11 2007 Alex Lancaster 2.2.0-1 +- Initial Fedora package. From ef1cc37177147004a9f6a860afb65fbc4df7a396 Mon Sep 17 00:00:00 2001 From: alexlan Date: Fri, 17 Aug 2007 05:47:58 +0000 Subject: [PATCH 02/42] - Clarify license as BSD and GPLv2+ --- wise2.spec | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/wise2.spec b/wise2.spec index 812d6f0..b4482cc 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,10 +1,13 @@ Name: wise2 Version: 2.2.0 -Release: 2%{?dist} +Release: 3%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering -License: GPL +## Everything is licensed under a BSD-style license except for +## the HMMer2 libraries and models directory which are GPLv2+ +## see LICENSE files for details. +License: BSD and GPLv2+ URL: http://www.ebi.ac.uk/Wise2/ Source0: ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/wise%{version}.tar.gz Patch0: wise2-build.patch @@ -72,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Thu Aug 16 2007 Alex Lancaster 2.2.0-3 +- Clarify license as BSD and GPLv2+ + * Mon Apr 12 2007 Alex Lancaster 2.2.0-2 - Pass $RPM_OPT_FLAGS to compiler as per suggestion from Ralf Corsepius. From 88f172edfcb82e61dd632dbcb45c6fa57caefba5 Mon Sep 17 00:00:00 2001 From: alexlan Date: Sun, 10 Feb 2008 05:05:12 +0000 Subject: [PATCH 03/42] rebuilt for GCC 4.3 as requested by Fedora Release Engineering --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index b4482cc..ecafb54 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,6 +1,6 @@ Name: wise2 Version: 2.2.0 -Release: 3%{?dist} +Release: 4%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering @@ -75,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Sat Feb 9 2008 Alex Lancaster - 2.2.0-4 +- rebuilt for GCC 4.3 as requested by Fedora Release Engineering + * Thu Aug 16 2007 Alex Lancaster 2.2.0-3 - Clarify license as BSD and GPLv2+ From 434bab1f820e977b79e0d71b36d70944590b93a0 Mon Sep 17 00:00:00 2001 From: Jesse Keating Date: Wed, 25 Feb 2009 18:49:07 +0000 Subject: [PATCH 04/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index ecafb54..ebcca56 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,6 +1,6 @@ Name: wise2 Version: 2.2.0 -Release: 4%{?dist} +Release: 5%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering @@ -75,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Wed Feb 25 2009 Fedora Release Engineering - 2.2.0-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild + * Sat Feb 9 2008 Alex Lancaster - 2.2.0-4 - rebuilt for GCC 4.3 as requested by Fedora Release Engineering From ded913fda31a2ba1057ee5a46cd0a6acd4f1d494 Mon Sep 17 00:00:00 2001 From: alexlan Date: Thu, 16 Jul 2009 06:17:22 +0000 Subject: [PATCH 05/42] - Add -D_POSIX_C_SOURCE=200112L to CFLAGS as a workaround to fix FTBFS (#511627) --- wise2.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/wise2.spec b/wise2.spec index ebcca56..3ec7fe3 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,6 +1,6 @@ Name: wise2 Version: 2.2.0 -Release: 5%{?dist} +Release: 6%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering @@ -41,7 +41,7 @@ cp src/models/GNULICENSE LICENSE.GPL %build cd src ## removed "{?_smp_mflags}", does not support parallel build -make CC=gcc CFLAGS="-c $RPM_OPT_FLAGS" all +make CC=gcc CFLAGS="-c $RPM_OPT_FLAGS -D_POSIX_C_SOURCE=200112L" all %install rm -rf $RPM_BUILD_ROOT @@ -75,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Thu Jul 16 2009 Alex Lancaster - 2.2.0-6 +- Add -D_POSIX_C_SOURCE=200112L to CFLAGS as a workaround to fix FTBFS (#511627) + * Wed Feb 25 2009 Fedora Release Engineering - 2.2.0-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild From 7dce0398d7d30b0e1d74251201943b5f0b25a881 Mon Sep 17 00:00:00 2001 From: Jesse Keating Date: Mon, 27 Jul 2009 07:18:48 +0000 Subject: [PATCH 06/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 3ec7fe3..24e27e4 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,6 +1,6 @@ Name: wise2 Version: 2.2.0 -Release: 6%{?dist} +Release: 7%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering @@ -75,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Mon Jul 27 2009 Fedora Release Engineering - 2.2.0-7 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild + * Thu Jul 16 2009 Alex Lancaster - 2.2.0-6 - Add -D_POSIX_C_SOURCE=200112L to CFLAGS as a workaround to fix FTBFS (#511627) From 30c6ada3dca1db6d60a69eb99042d89402d13b64 Mon Sep 17 00:00:00 2001 From: Bill Nottingham Date: Wed, 25 Nov 2009 22:43:15 +0000 Subject: [PATCH 07/42] Fix typo that causes a failure to update the common directory. (releng #2781) --- Makefile | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 6b22444..2f4e5ed 100644 --- a/Makefile +++ b/Makefile @@ -1,10 +1,10 @@ # Makefile for source rpm: wise2 -# $Id$ +# $Id: Makefile,v 1.1 2007/04/23 16:50:32 wtogami Exp $ NAME := wise2 SPECFILE = $(firstword $(wildcard *.spec)) define find-makefile-common -for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done +for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$d/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done endef MAKEFILE_COMMON := $(shell $(find-makefile-common)) From 919b6b52de9ac4f94872e4ccbf2635f7a1302db8 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 29 Jul 2010 15:22:08 +0000 Subject: [PATCH 08/42] dist-git conversion --- .cvsignore => .gitignore | 0 Makefile | 21 --------------------- 2 files changed, 21 deletions(-) rename .cvsignore => .gitignore (100%) delete mode 100644 Makefile diff --git a/.cvsignore b/.gitignore similarity index 100% rename from .cvsignore rename to .gitignore diff --git a/Makefile b/Makefile deleted file mode 100644 index 2f4e5ed..0000000 --- a/Makefile +++ /dev/null @@ -1,21 +0,0 @@ -# Makefile for source rpm: wise2 -# $Id: Makefile,v 1.1 2007/04/23 16:50:32 wtogami Exp $ -NAME := wise2 -SPECFILE = $(firstword $(wildcard *.spec)) - -define find-makefile-common -for d in common ../common ../../common ; do if [ -f $$d/Makefile.common ] ; then if [ -f $$d/CVS/Root -a -w $$d/Makefile.common ] ; then cd $$d ; cvs -Q update ; fi ; echo "$$d/Makefile.common" ; break ; fi ; done -endef - -MAKEFILE_COMMON := $(shell $(find-makefile-common)) - -ifeq ($(MAKEFILE_COMMON),) -# attept a checkout -define checkout-makefile-common -test -f CVS/Root && { cvs -Q -d $$(cat CVS/Root) checkout common && echo "common/Makefile.common" ; } || { echo "ERROR: I can't figure out how to checkout the 'common' module." ; exit -1 ; } >&2 -endef - -MAKEFILE_COMMON := $(shell $(checkout-makefile-common)) -endif - -include $(MAKEFILE_COMMON) From 1b9cb37834678ae1d7a03bf001d95b46a3e510b3 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Mon, 7 Feb 2011 20:46:28 -0600 Subject: [PATCH 09/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 24e27e4..333e417 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,6 +1,6 @@ Name: wise2 Version: 2.2.0 -Release: 7%{?dist} +Release: 8%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering @@ -75,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Mon Feb 07 2011 Fedora Release Engineering - 2.2.0-8 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild + * Mon Jul 27 2009 Fedora Release Engineering - 2.2.0-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild From 412b38f422bbc80ad62e13df6aaed8183808d5aa Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Sat, 14 Jan 2012 02:21:51 -0600 Subject: [PATCH 10/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 333e417..8bb9267 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,6 +1,6 @@ Name: wise2 Version: 2.2.0 -Release: 8%{?dist} +Release: 9%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering @@ -75,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Sat Jan 14 2012 Fedora Release Engineering - 2.2.0-9 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild + * Mon Feb 07 2011 Fedora Release Engineering - 2.2.0-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild From 1aa792acf4d28259ee72cb6fe9e034b93fc99f8a Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Sat, 21 Jul 2012 22:42:41 -0500 Subject: [PATCH 11/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 8bb9267..9162cff 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,6 +1,6 @@ Name: wise2 Version: 2.2.0 -Release: 9%{?dist} +Release: 10%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering @@ -75,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Sun Jul 22 2012 Fedora Release Engineering - 2.2.0-10 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild + * Sat Jan 14 2012 Fedora Release Engineering - 2.2.0-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild From 21dde59aa5ae389a9b923bd2298cfab2334401cf Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Thu, 14 Feb 2013 21:09:48 -0600 Subject: [PATCH 12/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 9162cff..69a16b6 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,6 +1,6 @@ Name: wise2 Version: 2.2.0 -Release: 10%{?dist} +Release: 11%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering @@ -75,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Fri Feb 15 2013 Fedora Release Engineering - 2.2.0-11 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild + * Sun Jul 22 2012 Fedora Release Engineering - 2.2.0-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild From 46bb27f9167ba09efec5220f23e3c217c97ea6ee Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Sun, 4 Aug 2013 02:02:33 -0500 Subject: [PATCH 13/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 69a16b6..5e62dcc 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,6 +1,6 @@ Name: wise2 Version: 2.2.0 -Release: 11%{?dist} +Release: 12%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering @@ -75,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Sun Aug 04 2013 Fedora Release Engineering - 2.2.0-12 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild + * Fri Feb 15 2013 Fedora Release Engineering - 2.2.0-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild From e3292c48756752c85084e57b96253279b9e13e61 Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Sat, 7 Jun 2014 23:39:02 -0500 Subject: [PATCH 14/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 5e62dcc..fb28f61 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,6 +1,6 @@ Name: wise2 Version: 2.2.0 -Release: 12%{?dist} +Release: 13%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering @@ -75,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Sun Jun 08 2014 Fedora Release Engineering - 2.2.0-13 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild + * Sun Aug 04 2013 Fedora Release Engineering - 2.2.0-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild From 6db296ccbbc9cd6e5d46aa5d2a61559911a6787c Mon Sep 17 00:00:00 2001 From: Peter Robinson Date: Mon, 18 Aug 2014 08:42:29 +0000 Subject: [PATCH 15/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index fb28f61..a92472e 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,6 +1,6 @@ Name: wise2 Version: 2.2.0 -Release: 13%{?dist} +Release: 14%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering @@ -75,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Mon Aug 18 2014 Fedora Release Engineering - 2.2.0-14 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild + * Sun Jun 08 2014 Fedora Release Engineering - 2.2.0-13 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild From 25e0ac3d5cad11c1428dcc23d38c0a732e0fb92a Mon Sep 17 00:00:00 2001 From: Dennis Gilmore Date: Fri, 19 Jun 2015 02:28:23 +0000 Subject: [PATCH 16/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index a92472e..668fdef 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,6 +1,6 @@ Name: wise2 Version: 2.2.0 -Release: 14%{?dist} +Release: 15%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering @@ -75,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Fri Jun 19 2015 Fedora Release Engineering - 2.2.0-15 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild + * Mon Aug 18 2014 Fedora Release Engineering - 2.2.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild From 1100d513dd2690a221f85ab6be0787c73d054240 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 5 Feb 2016 03:04:27 +0000 Subject: [PATCH 17/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 668fdef..c1a681b 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,6 +1,6 @@ Name: wise2 Version: 2.2.0 -Release: 15%{?dist} +Release: 16%{?dist} Summary: Tools for comparison of biopolymers Group: Applications/Engineering @@ -75,6 +75,9 @@ rm -rf $RPM_BUILD_ROOT %config(noreplace) %{_sysconfdir}/profile.d/* %changelog +* Fri Feb 05 2016 Fedora Release Engineering - 2.2.0-16 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild + * Fri Jun 19 2015 Fedora Release Engineering - 2.2.0-15 - Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild From e4aad30ae8d88cfe4f6407a471b02c58debbdf67 Mon Sep 17 00:00:00 2001 From: sagitter Date: Fri, 29 Jul 2016 21:41:57 +0200 Subject: [PATCH 18/42] Update to 2.4.1 --- .gitignore | 1 + sources | 2 +- wise2-build.patch | 21 +- wise2-getline.patch | 302 ++++++++++++++++ wise2-glib2.patch | 703 ++++++++++++++++++++++++++++++++++++++ wise2-isnumber.patch | 18 + wise2-ld--as-needed.patch | 54 +++ wise2-mayhem.patch | 99 ++++++ wise2.spec | 140 +++++--- 9 files changed, 1291 insertions(+), 49 deletions(-) create mode 100644 wise2-getline.patch create mode 100644 wise2-glib2.patch create mode 100755 wise2-isnumber.patch create mode 100644 wise2-ld--as-needed.patch create mode 100644 wise2-mayhem.patch diff --git a/.gitignore b/.gitignore index ba20b1d..075683e 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,2 @@ wise2.2.0.tar.gz +/wise2.4.1.tar.gz diff --git a/sources b/sources index 8d1f2c3..08acc43 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -0584240f77885e37528e99e64535ab60 wise2.2.0.tar.gz +d70c404c1dc40ceef7718757b11bdaa0 wise2.4.1.tar.gz diff --git a/wise2-build.patch b/wise2-build.patch index 1965c5b..d30904b 100644 --- a/wise2-build.patch +++ b/wise2-build.patch @@ -1,10 +1,21 @@ ---- src/makefile.orig 2007-04-11 07:52:41.000000000 -0700 -+++ src/makefile 2007-04-11 07:53:04.000000000 -0700 -@@ -89,7 +89,6 @@ +--- wise-2.4.0~/src/makefile 2007-07-15 23:39:24.000000000 +0200 ++++ wise-2.4.0/src/makefile 2007-07-15 23:41:11.000000000 +0200 +@@ -109,7 +109,7 @@ bin : mkdir bin - mv models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/genomewise ./bin + cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin - csh welcome.csh ++ ./welcome.csh libs : - (cd base ; make CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a ) + (cd base ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a ) +diff -urNad wise-2.4.0~/src/welcome.csh wise-2.4.0/src/welcome.csh +--- wise-2.4.0~/src/welcome.csh 2007-07-15 23:39:24.000000000 +0200 ++++ wise-2.4.0/src/welcome.csh 2007-07-15 23:40:46.000000000 +0200 +@@ -1,4 +1,4 @@ +-#!/bin/tcsh -f ++#!/bin/sh + + echo "" + echo "Welcome to Wise2.4" + diff --git a/wise2-getline.patch b/wise2-getline.patch new file mode 100644 index 0000000..0e2fd1a --- /dev/null +++ b/wise2-getline.patch @@ -0,0 +1,302 @@ +Index: wise-2.4.1/src/HMMer2/sqio.c +=================================================================== +--- wise-2.4.1.orig/src/HMMer2/sqio.c 2009-10-31 20:10:25.000000000 +0000 ++++ wise-2.4.1/src/HMMer2/sqio.c 2009-10-31 20:11:11.000000000 +0000 +@@ -213,7 +213,7 @@ + } + } + +-/* Function: getline() ++/* Function: getline_() + * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] + * + * Purpose: read a line from a sequence file into V->sbuffer. +@@ -229,7 +229,7 @@ + * Returns: (void) + */ + static void +-getline(struct ReadSeqVars *V) ++getline_(struct ReadSeqVars *V) + { + char *cp; + +@@ -299,7 +299,7 @@ + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ getline_(V); + /* feof() alone is a bug; files not necessarily \n terminated */ + if (*(V->sbuffer) == '\0' && feof(V->f)) + done = TRUE; +@@ -327,7 +327,7 @@ + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ getline_(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -336,7 +336,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ getline_(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -345,7 +345,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ getline_(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -359,7 +359,7 @@ + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ getline_(V); + } + + +@@ -377,7 +377,7 @@ + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ getline_(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -389,7 +389,7 @@ + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ getline_(V); + } + + static int +@@ -411,7 +411,7 @@ + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ getline_(V); + } + + if (! feof(V->f)) +@@ -420,7 +420,7 @@ + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ getline_(V); + } + + +@@ -438,7 +438,7 @@ + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ getline_(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -449,7 +449,7 @@ + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ getline_(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -482,11 +482,11 @@ + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ getline_(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ getline_(V); + } + + static int +@@ -515,7 +515,7 @@ + Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ getline_(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -535,7 +535,7 @@ + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ getline_(V); + } + + static int +@@ -555,12 +555,12 @@ + if ((sptr = strtok(NULL, "\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); + /* workaround for long NCBI NR lines */ +- while (V->longline && ! feof(V->f)) getline(V); ++ while (V->longline && ! feof(V->f)) getline_(V); + + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ getline_(V); + } + + +@@ -587,7 +587,7 @@ + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ getline_(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -596,7 +596,7 @@ + } + + do { +- getline(V); ++ getline_(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -620,7 +620,7 @@ + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ getline_(V); + } + + +@@ -636,7 +636,7 @@ + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ getline_(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -647,7 +647,7 @@ + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ getline_(V); + } + + static void +@@ -669,7 +669,7 @@ + + do { + done = feof(V->f); +- getline(V); ++ getline_(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -681,7 +681,7 @@ + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline_(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -689,7 +689,7 @@ + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ getline_(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -721,14 +721,14 @@ + while (1) + { + /* sequence line */ +- getline(V); ++ getline_(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ getline_(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -736,7 +736,7 @@ + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ getline_(V); + } + + +@@ -816,7 +816,7 @@ + + /* Load the first line. + */ +- getline(dbfp); ++ getline_(dbfp); + + return dbfp; + } +@@ -833,7 +833,7 @@ + Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); + + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ getline_(sqfp); + } + + +@@ -853,7 +853,7 @@ + if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; + else { + rewind(sqfp->f); +- getline(sqfp); ++ getline_(sqfp); + } + } + +@@ -949,7 +949,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ getline_(V); + } while (! feof(V->f)); + break; + diff --git a/wise2-glib2.patch b/wise2-glib2.patch new file mode 100644 index 0000000..8c8a448 --- /dev/null +++ b/wise2-glib2.patch @@ -0,0 +1,703 @@ +Author: Barry deFreese +Description: To build wise2 with the Glib version 2.0 instead of 1.2. +Forwarded: birney@sanger.ac.uk +--- a/src/makefile ++++ b/src/makefile +@@ -31,13 +31,13 @@ + + + # Intel icc flags +-# CFLAGS = -c -O3 -axWK -ipo `glib-config --cflags` ++# CFLAGS += -c -axWK -ipo `pkg-config --cflags glib-2.0` + + # alpha flags (-pthread) +-# CFLAGS = -c -O3 -pthread `glib-config --cflags` ++# CFLAGS += -c -pthread `pkg-config --cflags glib-2.0` + + # normal linux/bsd/mac flags +-CFLAGS = -c -O3 `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -c `pkg-config --cflags glib-2.0` + + + EXTRALIBS = -lm +--- a/src/snp/makefile ++++ b/src/snp/makefile +@@ -5,9 +5,9 @@ + CC = cc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -16,7 +16,7 @@ + $(CC) $(CFLAGS) $(INCFLAGS) $? + + test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o +- $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) ++ $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LDFLAGS) + + INCFLAGS = -I../base/ -I../dynlibsrc/ + DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn +--- a/src/corba/makefile ++++ b/src/corba/makefile +@@ -3,9 +3,9 @@ + CC = cc + INCFLAGS = -I../base/ -I../dynlibsrc + #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/ +-CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` +-LFLAGS = -L../base/ -lm -lpthread ++#CFLAGS += -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/ ++CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` ++LDFLAGS += -L../base/ -lm -lpthread + AR_OPTIONS = ru + + +@@ -14,18 +14,18 @@ + orbit-idl hspscan_corba.idl + + test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o +- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o +- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +--- a/src/models/makefile ++++ b/src/models/makefile +@@ -62,46 +62,46 @@ + # $(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) wise2xhmmer2.c + + testgenestat : testgenestat.o genestats.o pwmdna.o +- $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) + + test_aligng : test_aligng.o aligngenemodel.o pwmdna.o +- $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) + + makepwm : makepwm.o pwmdna.o +- $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) + + testwise2xhmmer2.o : testwise2xhmmer2.c + $(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) testwise2xhmmer2.c + + testwise2xhmmer2 : testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o +- $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LFLAGS) ++ $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LDFLAGS) + + plan7test.o : plan7test.c + $(CC) $(CFLAGS) -I../HMMer2/ plan7test.c + + plan7test : plan7test.o plan7.o wise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o +- $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LFLAGS) ++ $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LDFLAGS) + + seqstat : seqstat.o +- $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LDFLAGS) + + mutatedna : mutatedna.o +- $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LDFLAGS) + + revcomp : revcomp.o +- $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LDFLAGS) + + stupid_motif_scan : stupid_motif_scan.o +- $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LDFLAGS) + + seqtrunc : seqtrunc.o +- $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LDFLAGS) + + seqlist : seqlist.o +- $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LDFLAGS) + + testpwm : testpwm.o pwmdna.o +- $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) -lefence ++ $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) -lefence + + + threestate : $(MODELOBJ) +@@ -111,29 +111,29 @@ + pwise : $(MODELOBJ) threestatemat.o threestatedisplay.o + + test : test.o proteinsw.o protprotdis.o +- $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LFLAGS) ++ $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LDFLAGS) + + testanc : testanc.o proteinsw.o abc.o pba.o sw_wrap.o +- $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + test_tf : test_transfactor.o transfactor.o pwmdna.o +- $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LDFLAGS) -ldyna -lwisebase + + motifwise : motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o +- $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase + + motifcluster : motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o +- $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase + + motifdiff : motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o +- $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase + + + cdtest : cdtest.o cdna2genomic.o d2d_display.o +- $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LDFLAGS) + + prob2bits : prob2bits.o +- $(CC) -o prob2bits $(LFLAGS) -ldyna_glib -ldyna -lwisebase ++ $(CC) -o prob2bits $(LDFLAGS) -ldyna_glib -ldyna -lwisebase + + quick : + cc -O -c -I../dynlibsrc/ -I../base/ genewise6.c +@@ -180,161 +180,161 @@ + $(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. + + oldpostwise : oldpostwise.o $(NEWG) +- $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase ++ $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase + + testdna : testdna.o dnaalign.o seqaligndisplay.o +- $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + dnal : dnal.o dnaalign.o seqaligndisplay.o +- $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o +- $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + scanwisep.o : scanwisep.c +- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $? + + hsp2aln_sw.o : hsp2aln_sw.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? + + scanwisep_mysql.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c + + scanwisep_mysql : scanwisep_mysql.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o $(LFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) -lpthread -lZ ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o $(LDFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) $(LDFLAGS) -lpthread -lZ + + + scanwisep_corba.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_CORBA -I../corba -I../external/mott `orbit-config --cflags server` scanwisep.c + + scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LDFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread + + + scanwisep_wiseserver.o : scanwisep.c + $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c + + scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread ++ $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread + + scanwisep_compress.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c + + scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread + + + + scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + test_gwhsp : test_gwhsp.o genewisehsp.o +- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + localcishit.o : localcishit.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? + + promoterwise.o : promoterwise.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? + + promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o +- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o +- $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread ++ $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread + + pswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o +- $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + efpswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o +- $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS) ++ $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS) + + dba : dbac.o dba.o slimdba.o bigdba.o dbadisplay.o +- $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + lba : lba.o largeblockdp.o seqaligndisplay.o +- $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + fastdba : fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o +- $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + evopairwise : evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o +- $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + test_threestatehsp : test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o threestatehsp.o +- $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + makerandomdb : makerandomdb.o +- $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + genewise : genewise.o $(NEWG) +- $(CC) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + cdnawise : cdnawise.o $(NEWG) cdnawise10.o +- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o +- $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase ++ $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase + + + efgw : genewise.o $(NEWG) +- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence ++ $(CC) -g -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + + + genewisedb : genewisedb.o $(NEWG) +- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + estwisedb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + edb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence ++ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + + estwise : estwise.o $(NEWG) +- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o +- $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o +- $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o +- $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + test_splice : test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o +- $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + pseudowise : pseudowise.o pseudowise7.o $(NEWG) +- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o +- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + HMMER_LIBS = ../HMMer2/ +@@ -345,11 +345,11 @@ + CC = cc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` +-#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` +-#LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ ++CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` ++#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` ++#LDFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ + +-LFLAGS = -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs` ++LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -360,7 +360,7 @@ + + + #test : test.o libwisedb.a +-# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LFLAGS) ++# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LDFLAGS) + + + # +--- a/src/dnaindex/makefile ++++ b/src/dnaindex/makefile +@@ -27,53 +27,53 @@ + + + kwise : kwise.o $(ASSEMBLY_OBJ) +- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` + + arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) +- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` + + + findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) +- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` + + make_shotgun : make_shotgun.o shotgun.o +- $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LDFLAGS) + + test_dnanumber : test_dnanumber.o dnanumber.o +- $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) + + test_linkindex : test_linkindex.o linkindex.o dnanumber.o +- $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) + + test_forwardindex : test_forwardindex.o forwardindex.o +- $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LDFLAGS) + + test_euler : test_euler.o eulerindex.o singleseqspace.o +- $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) + + test_kmer : test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_contig.o kmer_assembly_error.o assembly.o +- $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LDFLAGS) + + kmer_stat : kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o +- $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LDFLAGS) + + test_compara : test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o +- $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) + + bigseqwise : bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o +- $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) + + + + + show_euler : show_euler.o eulerindex.o singleseqspace.o +- $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) + + CC = cc +-CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` + + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm + + + .c.o : +--- a/src/dnaindex/assembly/makefile ++++ b/src/dnaindex/assembly/makefile +@@ -3,33 +3,33 @@ + .SUFFIXES : .dy + + test_basegraph : test_basegraph.o basegraph.o +- $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LDFLAGS) -ldyna -lwisebase + + test_assemblygraph : test_assemblygraph.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + + test_graphtangle : test_graphtangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o +- $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LDFLAGS) -ldyna -lwisebase + + + pathwise : pathwise.o supertangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o grapherror.o graphmanager.o depthmanager.o +- $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LDFLAGS) -ldyna -lwisebase + + + badkmer : badkmer.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + + + CC = cc +-CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0` + + +-LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm + + + .c.o : +--- a/src/dynlibsrc/makefile ++++ b/src/dynlibsrc/makefile +@@ -84,11 +84,11 @@ + CC = cc + INCFLAGS = -I../base/ + #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-CFLAGS = -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` +-#CFLAGS = -Wall -g3 -pg -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` +-#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` ++#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` ++#CFLAGS += -c -pthread -DUNIX -I../base/ `pkg-config --cflags glib-2.0` + #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ +-LFLAGS = -g -L../base/ -lm ++LDFLAGS += -g -L../base/ -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -133,47 +133,47 @@ + # + + test_genomic : genomic.o test_genomic.o sequence.o codon.o +- $(CC) -o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS)-o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm + + test_tree : tree.o test_tree.o +- $(CC) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm + + test_intallocator : intallocator.o test_intallocator.o +- $(CC) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm + + test_psi : test_psi.o proteinstreamedindex.o +- $(CC) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm + + test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a +- $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm + + test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a +- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o test_seqhash `pkg-config --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm + + test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` + + test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` + + + testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o +- $(CC) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm + + testseqalign : seqalign.o testseqalign.o sequence.o codon.o +- $(CC) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm + + testanc : libdyna.a +- $(CC) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm + + testdb : testdb.o sequencedb.o sequence.o codon.o probability.o +- $(CC) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm + + testpdb : testpdb.o protein.o proteindb.o complexevalset.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o histogram.o +- $(CC) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm + + testpb : testpairbase.o pairbase.o pairbaseseq.o sequence.o seqalign.o codon.o probability.o complexsequence.o complexevalset.o +- $(CC) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +--- a/src/network/makefile ++++ b/src/network/makefile +@@ -3,8 +3,8 @@ + + CC = cc + INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex +-CFLAGS = -O2 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags` +-LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs` ++CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -13,7 +13,7 @@ + + + scanwise_server : wise_proteinindex_server.o net_hspscan.o ../dynlibsrc/libdyna.a ../dynlibsrc/libdyna_glib.a ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o +- $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LFLAGS) -lpthread ++ $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LDFLAGS) -lpthread + + + .c.o : +--- a/src/other_programs/makefile ++++ b/src/other_programs/makefile +@@ -3,8 +3,8 @@ + .SUFFIXES : .dy + + CC = cc +-CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `glib-config --cflags` +-LFLAGS = -g -L../base/ -L../dynlibsrc -lm `glib-config --libs` ++CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `pkg-config --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +--- a/src/base/makefile ++++ b/src/base/makefile +@@ -19,9 +19,9 @@ + + + +-#CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH +-CFLAGS = -c -O2 -DUNIX -pthread +-LFLAGS = -g -lm ++#CFLAGS += -c -g -DUNIX -DWISE_MEMORY_WATCH ++CFLAGS += $(CPPFLAGS) -c -DUNIX -pthread ++LDFLAGS += -g -lm + DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D + AR_OPTIONS = ru + +--- a/src/HMMer2/Makefile ++++ b/src/HMMer2/Makefile +@@ -13,7 +13,7 @@ + ## your compiler and compiler flags + # + CC = cc +-CFLAGS = -g ++CFLAGS += $(CPPFLAGS) -g + + ## machine specific definitions + # +@@ -75,25 +75,25 @@ + all: $(PROGS) + + hmmalign: $(OBJ) hmmalign.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) + + hmmbuild: $(OBJ) hmmbuild.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) + + hmmcalibrate: $(OBJ) hmmcalibrate.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) + + hmmconvert: $(OBJ) hmmconvert.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) + + hmmemit: $(OBJ) hmmemit.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) + + hmmpfam: $(OBJ) hmmpfam.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) + + hmmsearch: $(OBJ) hmmsearch.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) + + ####### + ## Target used in making Shiva test suite diff --git a/wise2-isnumber.patch b/wise2-isnumber.patch new file mode 100755 index 0000000..c678582 --- /dev/null +++ b/wise2-isnumber.patch @@ -0,0 +1,18 @@ +#! /bin/sh /usr/share/dpatch/dpatch-run +## 02_isnumber.dpatch by Philipp Benner +## +## DP: Replace isnumber() (which does not exist on linux) by isdigit(). + +@DPATCH@ +diff -urNad wise-2.4.0~/src/models/phasemodel.c wise-2.4.0/src/models/phasemodel.c +--- wise-2.4.0~/src/models/phasemodel.c 2007-07-01 22:44:39.000000000 +0200 ++++ wise-2.4.0/src/models/phasemodel.c 2007-07-16 00:24:16.000000000 +0200 +@@ -20,7 +20,7 @@ + if( line[0] == '#' ) { + continue; + } +- if( !isnumber(line[0]) ) { ++ if( !isdigit(line[0]) ) { + warn("Bad looking line in intron file, %s",line); + continue; + } diff --git a/wise2-ld--as-needed.patch b/wise2-ld--as-needed.patch new file mode 100644 index 0000000..b8db369 --- /dev/null +++ b/wise2-ld--as-needed.patch @@ -0,0 +1,54 @@ +Description: Fix FTBFS with ld --as-needed. +Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935 + +diff --git a/src/models/makefile b/src/models/makefile +index 1766fee..e4634b5 100644 +--- a/src/models/makefile ++++ b/src/models/makefile +@@ -215,7 +215,7 @@ scanwisep_wiseserver.o : scanwisep.c + $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c + + scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread ++ $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread $(LDFLAGS) + + scanwisep_compress.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c +@@ -275,7 +275,7 @@ makerandomdb : makerandomdb.o + $(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + genewise : genewise.o $(NEWG) +- $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + cdnawise : cdnawise.o $(NEWG) cdnawise10.o + $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) +@@ -300,16 +300,16 @@ efgw : genewise.o $(NEWG) + + + genewisedb : genewisedb.o $(NEWG) +- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + estwisedb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + edb : estwisedb.o $(NEWG) + $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + + estwise : estwise.o $(NEWG) +- $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + + amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o +@@ -331,7 +331,7 @@ statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o + $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + pseudowise : pseudowise.o pseudowise7.o $(NEWG) +- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o + $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) diff --git a/wise2-mayhem.patch b/wise2-mayhem.patch new file mode 100644 index 0000000..f4b7724 --- /dev/null +++ b/wise2-mayhem.patch @@ -0,0 +1,99 @@ +--- a/src/models/dbac.c ++++ b/src/models/dbac.c +@@ -535,8 +535,12 @@ + * + */ + +- one = read_fasta_file_Sequence(*argv++); +- two = read_fasta_file_Sequence(*argv++); ++ if( (one = read_fasta_file_Sequence(*argv++)) == NULL ) { ++ fatal("Unable to read the sequence in file"); ++ } ++ if( (two = read_fasta_file_Sequence(*argv++)) == NULL ) { ++ fatal("Unable to read the sequence in file"); ++ } + + uppercase_Sequence(one); + uppercase_Sequence(two); +--- a/src/models/estwise.c ++++ b/src/models/estwise.c +@@ -313,7 +313,7 @@ + } + } + +- if( reverse == TRUE ) { ++ if( cdna && reverse == TRUE ) { + if( tstart > tend ) { + warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend); + } +@@ -323,7 +323,7 @@ + cdna = cdna_temp; + } + +- if( target_abs == TRUE ) { ++ if( cdna && target_abs == TRUE ) { + cdna->baseseq->offset = 1; + cdna->baseseq->end = strlen(cdna->baseseq->seq); + } +@@ -472,8 +472,11 @@ + } + + cp = flat_cDNAParser(indel_error); +- cm = flat_CodonMapper(ct); +- sprinkle_errors_over_CodonMapper(cm,subs_error); ++ ++ if( ct ) { ++ cm = flat_CodonMapper(ct); ++ sprinkle_errors_over_CodonMapper(cm,subs_error); ++ } + + return ret; + +--- a/src/models/genewise.c ++++ b/src/models/genewise.c +@@ -550,8 +550,10 @@ + ret = FALSE; + } + +- gen->baseseq->offset = 1; +- gen->baseseq->end = strlen(gen->baseseq->seq); ++ if ( gen ) { ++ gen->baseseq->offset = 1; ++ gen->baseseq->end = strlen(gen->baseseq->seq); ++ } + } + + if( alg_str != NULL ) { +--- a/src/models/estwisedb.c ++++ b/src/models/estwisedb.c +@@ -688,8 +688,11 @@ + + + cps = flat_cDNAParser(indel_error); +- cm = flat_CodonMapper(ct); +- sprinkle_errors_over_CodonMapper(cm,subs_error); ++ ++ if( ct ) { ++ cm = flat_CodonMapper(ct); ++ sprinkle_errors_over_CodonMapper(cm,subs_error); ++ } + + return ret; + +--- a/src/models/promoterwise.c ++++ b/src/models/promoterwise.c +@@ -147,8 +147,12 @@ + + lchs = standard_LocalCisHitScore(NMaskType_VARIABLE); + +- query = read_fasta_file_Sequence(argv[1]); +- target = read_fasta_file_Sequence(argv[2]); ++ if( (query = read_fasta_file_Sequence(argv[1])) == NULL ) { ++ fatal("Unable to read the sequence in query file"); ++ } ++ if( (target = read_fasta_file_Sequence(argv[2])) == NULL ) { ++ fatal("Unable to read the sequence in target file"); ++ } + + for(i=0;ilen;i++) { + query->seq[i] = toupper(query->seq[i]); diff --git a/wise2.spec b/wise2.spec index c1a681b..1bf328f 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,30 +1,67 @@ +%if 0%{?epel} < 7 +%{!?__global_ldflags: %global __global_ldflags -Wl,-z,relro} +%endif + Name: wise2 -Version: 2.2.0 -Release: 16%{?dist} -Summary: Tools for comparison of biopolymers +Version: 2.4.1 +Release: 1%{?dist} +Summary: Tools for comparison of bio-polymers Group: Applications/Engineering ## Everything is licensed under a BSD-style license except for ## the HMMer2 libraries and models directory which are GPLv2+ ## see LICENSE files for details. License: BSD and GPLv2+ -URL: http://www.ebi.ac.uk/Wise2/ -Source0: ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/wise%{version}.tar.gz -Patch0: wise2-build.patch -BuildRoot: %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n) +URL: http://www.ebi.ac.uk/~birney/%{name}/ +Source0: http://www.ebi.ac.uk/~birney/%{name}/wise%{version}.tar.gz + +## Patches from Debian package. Thanks to Philipp Benner +Patch0: %{name}-build.patch +Patch1: %{name}-isnumber.patch +Patch2: %{name}-glib2.patch +Patch3: %{name}-getline.patch +Patch4: %{name}-ld--as-needed.patch +Patch5: %{name}-mayhem.patch + +BuildRequires: glib2-devel +BuildRequires: strace +BuildRequires: pkgconfig %description -Wise2 is a package focused on comparisons of biopolymers, commonly DNA +Wise2 is a package focused on comparisons of bio-polymers, commonly DNA sequence and protein sequence. A strength of Wise2 is the comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of gene structure with homology based alignment. +%package doc +Summary: Wise2 documentation +Group: Development/Libraries +BuildArch: noarch +%description doc +Wise2, Wise2api and Dynamite documentation files. + +%package examples +Summary: Wise2 examples +Group: Development/Libraries +Requires: %{name}%{?_isa} = %{version}-%{release} +%description examples +Here are some examples that you might want to try out. The +Wise2 executables of course should be installed before. + %prep %setup -q -n wise%{version} +%patch0 -p1 +%patch1 -p1 +%patch2 -p1 +%patch3 -p1 +%patch4 -p1 -## don't run "welcome.csh" -%patch0 -p0 +# Remove spurious-executable-perm +chmod a-x src/external/mott/mott_api.c +chmod a-x src/external/mott/mott_api.h +chmod a-x src/external/mott/gaplib.c +chmod a-x src/external/mott/gapstat.h ## fix interpreter in examples sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' docs/gettex.pl @@ -39,53 +76,70 @@ done cp src/models/GNULICENSE LICENSE.GPL %build -cd src ## removed "{?_smp_mflags}", does not support parallel build -make CC=gcc CFLAGS="-c $RPM_OPT_FLAGS -D_POSIX_C_SOURCE=200112L" all +export LDFLAGS="%{__global_ldflags}" +make -C src CC=gcc \ + CFLAGS=" -c $RPM_OPT_FLAGS -pthread -D_GNU_SOURCE %(pkg-config --cflags glib-2.0) -D_POSIX_C_SOURCE=200112L" all %install -rm -rf $RPM_BUILD_ROOT -cd src/bin -%{__mkdir_p} $RPM_BUILD_ROOT%{_bindir} -for i in dba dnal estwise estwisedb genewise genewisedb genomewise psw pswdb +pushd src/bin +mkdir -p $RPM_BUILD_ROOT%{_bindir} +for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb do - %{__install} $i $RPM_BUILD_ROOT/%{_bindir} + install -pm 755 $i $RPM_BUILD_ROOT%{_bindir} done -cd - +popd + # install architecture-independent data and config files -%{__mkdir_p} $RPM_BUILD_ROOT%{_datadir}/wise2 -cd wisecfg -%{__install} -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2 +mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2 +pushd wisecfg +install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2 +popd + +# install architecture-independent files to run example tests +mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2/examples +pushd test_data +install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2/examples +popd # install scripts to automatically set the WISECONFIGDIR environment variable -%{__mkdir_p} $RPM_BUILD_ROOT%{_sysconfdir}/profile.d +mkdir -p $RPM_BUILD_ROOT%{_sysconfdir}/profile.d echo "export WISECONFIGDIR=%{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.sh echo "setenv WISECONFIGDIR %{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.csh -%clean -rm -rf $RPM_BUILD_ROOT - +%check +export WISECONFIGDIR=$PWD/wisecfg +make -C src test %files -%defattr(-,root,root,-) -%doc docs test_data -%doc INSTALL LICENSE README LICENSE.base LICENSE.dynlibsrc LICENSE.dyc LICENSE.GPL -%{_bindir}/* -%{_datadir}/wise2 +%doc README +%license LICENSE LICENSE.base LICENSE.dynlibsrc LICENSE.dyc LICENSE.GPL +%{_bindir}/genewisedb +%{_bindir}/estwisedb +%{_bindir}/genewise +%{_bindir}/estwise +%{_bindir}/scanwise +%{_bindir}/promoterwise +%{_bindir}/pswdb +%{_bindir}/dba +%{_bindir}/psw +%{_bindir}/scanwise_server +%{_bindir}/dnal +%{_datadir}/wise2/ %config(noreplace) %{_sysconfdir}/profile.d/* +%files doc +%license LICENSE +%doc docs + +%files examples +%doc test_data/README +%{_datadir}/wise2/examples/ + %changelog -* Fri Feb 05 2016 Fedora Release Engineering - 2.2.0-16 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild - -* Fri Jun 19 2015 Fedora Release Engineering - 2.2.0-15 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild - -* Mon Aug 18 2014 Fedora Release Engineering - 2.2.0-14 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild - -* Sun Jun 08 2014 Fedora Release Engineering - 2.2.0-13 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild +* Tue May 05 2015 Antonio Trande - 2.4.1-1 +- Update to 2.4.1 +- Fix compiler flags * Sun Aug 04 2013 Fedora Release Engineering - 2.2.0-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild @@ -117,8 +171,8 @@ rm -rf $RPM_BUILD_ROOT * Thu Aug 16 2007 Alex Lancaster 2.2.0-3 - Clarify license as BSD and GPLv2+ -* Mon Apr 12 2007 Alex Lancaster 2.2.0-2 +* Thu Apr 12 2007 Alex Lancaster 2.2.0-2 - Pass $RPM_OPT_FLAGS to compiler as per suggestion from Ralf Corsepius. -* Mon Apr 11 2007 Alex Lancaster 2.2.0-1 +* Wed Apr 11 2007 Alex Lancaster 2.2.0-1 - Initial Fedora package. From e4d46ef8cfce931f4b29dda56d3475499b89f0c7 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 11 Feb 2017 17:26:59 +0000 Subject: [PATCH 19/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 1bf328f..10651a2 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 1%{?dist} +Release: 2%{?dist} Summary: Tools for comparison of bio-polymers Group: Applications/Engineering @@ -137,6 +137,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Sat Feb 11 2017 Fedora Release Engineering - 2.4.1-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild + * Tue May 05 2015 Antonio Trande - 2.4.1-1 - Update to 2.4.1 - Fix compiler flags From d4bc1956a89368562834ed4f11b5a7493ed032f2 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 27 Jul 2017 21:40:35 +0000 Subject: [PATCH 20/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 10651a2..d9860bc 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 2%{?dist} +Release: 3%{?dist} Summary: Tools for comparison of bio-polymers Group: Applications/Engineering @@ -137,6 +137,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Thu Jul 27 2017 Fedora Release Engineering - 2.4.1-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild + * Sat Feb 11 2017 Fedora Release Engineering - 2.4.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild From d9b70c237749bf995cb87a8393dcc7d03d44f599 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 3 Aug 2017 10:19:44 +0000 Subject: [PATCH 21/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index d9860bc..840f8be 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 3%{?dist} +Release: 4%{?dist} Summary: Tools for comparison of bio-polymers Group: Applications/Engineering @@ -137,6 +137,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Thu Aug 03 2017 Fedora Release Engineering - 2.4.1-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild + * Thu Jul 27 2017 Fedora Release Engineering - 2.4.1-3 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild From 06a40b08352e665ec6688dfe6760615d1a9e3138 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 9 Feb 2018 21:01:41 +0000 Subject: [PATCH 22/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 840f8be..7a8c3e8 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 4%{?dist} +Release: 5%{?dist} Summary: Tools for comparison of bio-polymers Group: Applications/Engineering @@ -137,6 +137,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Fri Feb 09 2018 Fedora Release Engineering - 2.4.1-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild + * Thu Aug 03 2017 Fedora Release Engineering - 2.4.1-4 - Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild From d3bc51e3c41c4c0e82416d9424e2c2ef8807389b Mon Sep 17 00:00:00 2001 From: sagitter Date: Thu, 22 Feb 2018 22:15:31 +0100 Subject: [PATCH 23/42] Add gcc perl BR --- wise2.spec | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/wise2.spec b/wise2.spec index 7a8c3e8..d06cf5c 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 5%{?dist} +Release: 6%{?dist} Summary: Tools for comparison of bio-polymers Group: Applications/Engineering @@ -23,7 +23,7 @@ Patch3: %{name}-getline.patch Patch4: %{name}-ld--as-needed.patch Patch5: %{name}-mayhem.patch -BuildRequires: glib2-devel +BuildRequires: glib2-devel, gcc, perl BuildRequires: strace BuildRequires: pkgconfig @@ -36,14 +36,12 @@ gene structure with homology based alignment. %package doc Summary: Wise2 documentation -Group: Development/Libraries BuildArch: noarch %description doc Wise2, Wise2api and Dynamite documentation files. %package examples Summary: Wise2 examples -Group: Development/Libraries Requires: %{name}%{?_isa} = %{version}-%{release} %description examples Here are some examples that you might want to try out. The @@ -137,6 +135,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Thu Feb 22 2018 Antonio Trande - 2.4.1-6 +- Add gcc perl BR + * Fri Feb 09 2018 Fedora Release Engineering - 2.4.1-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild From 384da2a9ced293eb9669927bfd3f57d1744cc78d Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 14 Jul 2018 08:54:38 +0000 Subject: [PATCH 24/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index d06cf5c..c8666b7 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 6%{?dist} +Release: 7%{?dist} Summary: Tools for comparison of bio-polymers Group: Applications/Engineering @@ -135,6 +135,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Sat Jul 14 2018 Fedora Release Engineering - 2.4.1-7 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild + * Thu Feb 22 2018 Antonio Trande - 2.4.1-6 - Add gcc perl BR From 701f411d3f09b0aea632f69eea92d19b96b1e082 Mon Sep 17 00:00:00 2001 From: Igor Gnatenko Date: Mon, 28 Jan 2019 20:18:30 +0100 Subject: [PATCH 25/42] Remove obsolete Group tag References: https://fedoraproject.org/wiki/Changes/Remove_Group_Tag --- wise2.spec | 1 - 1 file changed, 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index c8666b7..4f73f92 100644 --- a/wise2.spec +++ b/wise2.spec @@ -7,7 +7,6 @@ Version: 2.4.1 Release: 7%{?dist} Summary: Tools for comparison of bio-polymers -Group: Applications/Engineering ## Everything is licensed under a BSD-style license except for ## the HMMer2 libraries and models directory which are GPLv2+ ## see LICENSE files for details. From 383d887ce4504642cb0768830f8a1af845a03abf Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sun, 3 Feb 2019 11:48:41 +0000 Subject: [PATCH 26/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 4f73f92..d9fe6e3 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 7%{?dist} +Release: 8%{?dist} Summary: Tools for comparison of bio-polymers ## Everything is licensed under a BSD-style license except for @@ -134,6 +134,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Sun Feb 03 2019 Fedora Release Engineering - 2.4.1-8 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild + * Sat Jul 14 2018 Fedora Release Engineering - 2.4.1-7 - Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild From 029ec6f33dcb7c0d5bca4716c4e7f0c9b32647dd Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 27 Jul 2019 03:34:24 +0000 Subject: [PATCH 27/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index d9fe6e3..183813a 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 8%{?dist} +Release: 9%{?dist} Summary: Tools for comparison of bio-polymers ## Everything is licensed under a BSD-style license except for @@ -134,6 +134,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Sat Jul 27 2019 Fedora Release Engineering - 2.4.1-9 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild + * Sun Feb 03 2019 Fedora Release Engineering - 2.4.1-8 - Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild From dd6055412743075640853a0feedf23cef3413d82 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 31 Jan 2020 03:48:24 +0000 Subject: [PATCH 28/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 183813a..0163bf8 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 9%{?dist} +Release: 10%{?dist} Summary: Tools for comparison of bio-polymers ## Everything is licensed under a BSD-style license except for @@ -134,6 +134,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Fri Jan 31 2020 Fedora Release Engineering - 2.4.1-10 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild + * Sat Jul 27 2019 Fedora Release Engineering - 2.4.1-9 - Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild From 4bc0e0b4303b4d0eee5ee4d8808569918104402e Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 29 Jul 2020 14:12:53 +0000 Subject: [PATCH 29/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 0163bf8..88a21f5 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 10%{?dist} +Release: 11%{?dist} Summary: Tools for comparison of bio-polymers ## Everything is licensed under a BSD-style license except for @@ -134,6 +134,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Wed Jul 29 2020 Fedora Release Engineering - 2.4.1-11 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild + * Fri Jan 31 2020 Fedora Release Engineering - 2.4.1-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild From 7715bf55986926ac004ec66ccb751c41fb491a92 Mon Sep 17 00:00:00 2001 From: Tom Stellard Date: Sat, 9 Jan 2021 00:57:22 +0000 Subject: [PATCH 30/42] Add BuildRequires: make https://fedoraproject.org/wiki/Changes/Remove_make_from_BuildRoot --- wise2.spec | 1 + 1 file changed, 1 insertion(+) diff --git a/wise2.spec b/wise2.spec index 88a21f5..678138f 100644 --- a/wise2.spec +++ b/wise2.spec @@ -22,6 +22,7 @@ Patch3: %{name}-getline.patch Patch4: %{name}-ld--as-needed.patch Patch5: %{name}-mayhem.patch +BuildRequires: make BuildRequires: glib2-devel, gcc, perl BuildRequires: strace BuildRequires: pkgconfig From 670c2a612d1a3d04e27f77d9a6c8970cdcd88ffe Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 27 Jan 2021 23:33:53 +0000 Subject: [PATCH 31/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 678138f..bfda0eb 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 11%{?dist} +Release: 12%{?dist} Summary: Tools for comparison of bio-polymers ## Everything is licensed under a BSD-style license except for @@ -135,6 +135,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Wed Jan 27 2021 Fedora Release Engineering - 2.4.1-12 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild + * Wed Jul 29 2020 Fedora Release Engineering - 2.4.1-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild From 53c3469bd22e7f0941ae15930893a15c419c411f Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Fri, 23 Jul 2021 21:01:07 +0000 Subject: [PATCH 32/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index bfda0eb..3e1b2e7 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 12%{?dist} +Release: 13%{?dist} Summary: Tools for comparison of bio-polymers ## Everything is licensed under a BSD-style license except for @@ -135,6 +135,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Fri Jul 23 2021 Fedora Release Engineering - 2.4.1-13 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild + * Wed Jan 27 2021 Fedora Release Engineering - 2.4.1-12 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild From 2bdc7c1bfdc59b62daeed211ac24bd1b83f588b9 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 22 Jan 2022 04:32:48 +0000 Subject: [PATCH 33/42] - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 3e1b2e7..5140c77 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 13%{?dist} +Release: 14%{?dist} Summary: Tools for comparison of bio-polymers ## Everything is licensed under a BSD-style license except for @@ -135,6 +135,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Sat Jan 22 2022 Fedora Release Engineering - 2.4.1-14 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild + * Fri Jul 23 2021 Fedora Release Engineering - 2.4.1-13 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild From 12bf79194f6608f05431eae91edd1c8132e17b34 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 23 Jul 2022 12:30:05 +0000 Subject: [PATCH 34/42] Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 5140c77..0da1bcf 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 14%{?dist} +Release: 15%{?dist} Summary: Tools for comparison of bio-polymers ## Everything is licensed under a BSD-style license except for @@ -135,6 +135,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Sat Jul 23 2022 Fedora Release Engineering - 2.4.1-15 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild + * Sat Jan 22 2022 Fedora Release Engineering - 2.4.1-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild From 2f5e7a25cfa5c358b638a5d0f1b40e8c0de00dba Mon Sep 17 00:00:00 2001 From: Peter Fordham Date: Fri, 23 Dec 2022 07:40:08 +0000 Subject: [PATCH 35/42] Port source code to C99 by adding missing system includes. No upstream bug tracker so tracked here: https://bugzilla.redhat.com/show_bug.cgi?id=2155977 https://fedoraproject.org/wiki/Toolchain/PortingToModernC --- wise2-c99.patch | 29 +++++++++++++++++++++++++++++ wise2.spec | 7 ++++++- 2 files changed, 35 insertions(+), 1 deletion(-) create mode 100644 wise2-c99.patch diff --git a/wise2-c99.patch b/wise2-c99.patch new file mode 100644 index 0000000..4e2074f --- /dev/null +++ b/wise2-c99.patch @@ -0,0 +1,29 @@ +No upstream bug tracking so tracked here: +https://bugzilla.redhat.com/show_bug.cgi?id=2155977 + +diff --git a/src/HMMer2/prior.c b/src/HMMer2/prior.c +index a40eb9c..76517e2 100644 +--- a/src/HMMer2/prior.c ++++ b/src/HMMer2/prior.c +@@ -4,6 +4,8 @@ + * Support for Dirichlet prior data structure, p7prior_s. + */ + ++#include ++ + #include "config.h" + #include "structs.h" + #include "funcs.h" +diff --git a/src/external/mott/mott_api.c b/src/external/mott/mott_api.c +index a42ab5b..4466095 100644 +--- a/src/external/mott/mott_api.c ++++ b/src/external/mott/mott_api.c +@@ -1,6 +1,8 @@ + #include + #include + #include ++#include ++#include + #include"gapstat.h" + + double default_lambda0, default_K0, default_Kplus, default_H, default_r, default_s, default_alpha; diff --git a/wise2.spec b/wise2.spec index 0da1bcf..43de326 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 15%{?dist} +Release: 16%{?dist} Summary: Tools for comparison of bio-polymers ## Everything is licensed under a BSD-style license except for @@ -21,6 +21,7 @@ Patch2: %{name}-glib2.patch Patch3: %{name}-getline.patch Patch4: %{name}-ld--as-needed.patch Patch5: %{name}-mayhem.patch +Patch6: %{name}-c99.patch BuildRequires: make BuildRequires: glib2-devel, gcc, perl @@ -54,6 +55,7 @@ Wise2 executables of course should be installed before. %patch2 -p1 %patch3 -p1 %patch4 -p1 +%patch6 -p1 # Remove spurious-executable-perm chmod a-x src/external/mott/mott_api.c @@ -135,6 +137,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Fri Dec 23 2022 Peter Fordham - 2.4.1-16 +- Fix build for C99 compliance by adding missing headers. + * Sat Jul 23 2022 Fedora Release Engineering - 2.4.1-15 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild From 1b8eeab14fc547b4ad455b72b50dd2f918309a6d Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 21 Jan 2023 06:52:44 +0000 Subject: [PATCH 36/42] Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 43de326..4007433 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 16%{?dist} +Release: 17%{?dist} Summary: Tools for comparison of bio-polymers ## Everything is licensed under a BSD-style license except for @@ -137,6 +137,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Sat Jan 21 2023 Fedora Release Engineering - 2.4.1-17 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild + * Fri Dec 23 2022 Peter Fordham - 2.4.1-16 - Fix build for C99 compliance by adding missing headers. From e6979f69155efc3f71961260452c769134aa400f Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 22 Jul 2023 18:15:48 +0000 Subject: [PATCH 37/42] Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- wise2.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 4007433..d51323d 100644 --- a/wise2.spec +++ b/wise2.spec @@ -4,7 +4,7 @@ Name: wise2 Version: 2.4.1 -Release: 17%{?dist} +Release: 18%{?dist} Summary: Tools for comparison of bio-polymers ## Everything is licensed under a BSD-style license except for @@ -137,6 +137,9 @@ make -C src test %{_datadir}/wise2/examples/ %changelog +* Sat Jul 22 2023 Fedora Release Engineering - 2.4.1-18 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild + * Sat Jan 21 2023 Fedora Release Engineering - 2.4.1-17 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild From 819b94be4f4a5ede769655fee97ee63423a723fc Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Sun, 24 Dec 2023 21:47:15 +0100 Subject: [PATCH 38/42] Modernize SPEC file --- wise2.spec | 124 +++++++---------------------------------------------- 1 file changed, 15 insertions(+), 109 deletions(-) diff --git a/wise2.spec b/wise2.spec index d51323d..6416291 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,16 +1,12 @@ -%if 0%{?epel} < 7 -%{!?__global_ldflags: %global __global_ldflags -Wl,-z,relro} -%endif - Name: wise2 Version: 2.4.1 -Release: 18%{?dist} +Release: %autorelease Summary: Tools for comparison of bio-polymers ## Everything is licensed under a BSD-style license except for ## the HMMer2 libraries and models directory which are GPLv2+ ## see LICENSE files for details. -License: BSD and GPLv2+ +License: BSD-3-Clause AND GPL-2.0-or-later URL: http://www.ebi.ac.uk/~birney/%{name}/ Source0: http://www.ebi.ac.uk/~birney/%{name}/wise%{version}.tar.gz @@ -23,10 +19,11 @@ Patch4: %{name}-ld--as-needed.patch Patch5: %{name}-mayhem.patch Patch6: %{name}-c99.patch -BuildRequires: make -BuildRequires: glib2-devel, gcc, perl -BuildRequires: strace -BuildRequires: pkgconfig +BuildRequires: make +BuildRequires: glib2-devel +BuildRequires: gcc +BuildRequires: perl +BuildRequires: strace %description Wise2 is a package focused on comparisons of bio-polymers, commonly DNA @@ -35,27 +32,25 @@ comparison of DNA sequence at the level of its protein translation. This comparison allows the simultaneous prediction of gene structure with homology based alignment. + %package doc Summary: Wise2 documentation BuildArch: noarch + %description doc Wise2, Wise2api and Dynamite documentation files. + %package examples Summary: Wise2 examples Requires: %{name}%{?_isa} = %{version}-%{release} + %description examples Here are some examples that you might want to try out. The Wise2 executables of course should be installed before. %prep -%setup -q -n wise%{version} -%patch0 -p1 -%patch1 -p1 -%patch2 -p1 -%patch3 -p1 -%patch4 -p1 -%patch6 -p1 +%autosetup -p1 -n wise%{version} # Remove spurious-executable-perm chmod a-x src/external/mott/mott_api.c @@ -77,9 +72,9 @@ cp src/models/GNULICENSE LICENSE.GPL %build ## removed "{?_smp_mflags}", does not support parallel build -export LDFLAGS="%{__global_ldflags}" make -C src CC=gcc \ - CFLAGS=" -c $RPM_OPT_FLAGS -pthread -D_GNU_SOURCE %(pkg-config --cflags glib-2.0) -D_POSIX_C_SOURCE=200112L" all + LDFLAGS="%{__global_ldflags}" \ + CFLAGS=" -c %{build_cflags} -pthread -D_GNU_SOURCE %(pkg-config --cflags glib-2.0) -D_POSIX_C_SOURCE=200112L" all %install pushd src/bin @@ -137,93 +132,4 @@ make -C src test %{_datadir}/wise2/examples/ %changelog -* Sat Jul 22 2023 Fedora Release Engineering - 2.4.1-18 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild - -* Sat Jan 21 2023 Fedora Release Engineering - 2.4.1-17 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild - -* Fri Dec 23 2022 Peter Fordham - 2.4.1-16 -- Fix build for C99 compliance by adding missing headers. - -* Sat Jul 23 2022 Fedora Release Engineering - 2.4.1-15 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild - -* Sat Jan 22 2022 Fedora Release Engineering - 2.4.1-14 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild - -* Fri Jul 23 2021 Fedora Release Engineering - 2.4.1-13 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild - -* Wed Jan 27 2021 Fedora Release Engineering - 2.4.1-12 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild - -* Wed Jul 29 2020 Fedora Release Engineering - 2.4.1-11 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild - -* Fri Jan 31 2020 Fedora Release Engineering - 2.4.1-10 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild - -* Sat Jul 27 2019 Fedora Release Engineering - 2.4.1-9 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild - -* Sun Feb 03 2019 Fedora Release Engineering - 2.4.1-8 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild - -* Sat Jul 14 2018 Fedora Release Engineering - 2.4.1-7 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild - -* Thu Feb 22 2018 Antonio Trande - 2.4.1-6 -- Add gcc perl BR - -* Fri Feb 09 2018 Fedora Release Engineering - 2.4.1-5 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild - -* Thu Aug 03 2017 Fedora Release Engineering - 2.4.1-4 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild - -* Thu Jul 27 2017 Fedora Release Engineering - 2.4.1-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild - -* Sat Feb 11 2017 Fedora Release Engineering - 2.4.1-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild - -* Tue May 05 2015 Antonio Trande - 2.4.1-1 -- Update to 2.4.1 -- Fix compiler flags - -* Sun Aug 04 2013 Fedora Release Engineering - 2.2.0-12 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild - -* Fri Feb 15 2013 Fedora Release Engineering - 2.2.0-11 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild - -* Sun Jul 22 2012 Fedora Release Engineering - 2.2.0-10 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild - -* Sat Jan 14 2012 Fedora Release Engineering - 2.2.0-9 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_17_Mass_Rebuild - -* Mon Feb 07 2011 Fedora Release Engineering - 2.2.0-8 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild - -* Mon Jul 27 2009 Fedora Release Engineering - 2.2.0-7 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild - -* Thu Jul 16 2009 Alex Lancaster - 2.2.0-6 -- Add -D_POSIX_C_SOURCE=200112L to CFLAGS as a workaround to fix FTBFS (#511627) - -* Wed Feb 25 2009 Fedora Release Engineering - 2.2.0-5 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild - -* Sat Feb 9 2008 Alex Lancaster - 2.2.0-4 -- rebuilt for GCC 4.3 as requested by Fedora Release Engineering - -* Thu Aug 16 2007 Alex Lancaster 2.2.0-3 -- Clarify license as BSD and GPLv2+ - -* Thu Apr 12 2007 Alex Lancaster 2.2.0-2 -- Pass $RPM_OPT_FLAGS to compiler as per suggestion from Ralf Corsepius. - -* Wed Apr 11 2007 Alex Lancaster 2.2.0-1 -- Initial Fedora package. +%autochangelog From 10fe1c9a49a6f1b271b0a365b5f5561bcb3de023 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Sun, 24 Dec 2023 21:58:54 +0100 Subject: [PATCH 39/42] Exporting LDFLAGS --- wise2.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/wise2.spec b/wise2.spec index 6416291..1c2e423 100644 --- a/wise2.spec +++ b/wise2.spec @@ -72,8 +72,8 @@ cp src/models/GNULICENSE LICENSE.GPL %build ## removed "{?_smp_mflags}", does not support parallel build +export LDFLAGS="%{__global_ldflags}" make -C src CC=gcc \ - LDFLAGS="%{__global_ldflags}" \ CFLAGS=" -c %{build_cflags} -pthread -D_GNU_SOURCE %(pkg-config --cflags glib-2.0) -D_POSIX_C_SOURCE=200112L" all %install From 05f8f6e430d2a5fa56eb1ddf9cb7a76decfb3b4f Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Sun, 24 Dec 2023 22:22:14 +0100 Subject: [PATCH 40/42] Disable LTO flags --- wise2.spec | 2 ++ 1 file changed, 2 insertions(+) diff --git a/wise2.spec b/wise2.spec index 1c2e423..846e652 100644 --- a/wise2.spec +++ b/wise2.spec @@ -1,3 +1,5 @@ +%define _lto_cflags %{nil} + Name: wise2 Version: 2.4.1 Release: %autorelease From 6b79847170f7c725540ab168b1ed63802aba35b3 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 27 Jan 2024 08:53:28 +0000 Subject: [PATCH 41/42] Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild From a15e828eabdb414aa4238ca2e10beec4a3951998 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Sun, 4 Feb 2024 12:39:58 +0100 Subject: [PATCH 42/42] Orphaned by upstream; no longer needed in Fedora --- .gitignore | 2 - dead.package | 1 + sources | 1 - wise2-build.patch | 21 -- wise2-c99.patch | 29 -- wise2-getline.patch | 302 ---------------- wise2-glib2.patch | 703 -------------------------------------- wise2-isnumber.patch | 18 - wise2-ld--as-needed.patch | 54 --- wise2-mayhem.patch | 99 ------ wise2.spec | 137 -------- 11 files changed, 1 insertion(+), 1366 deletions(-) delete mode 100644 .gitignore create mode 100644 dead.package delete mode 100644 sources delete mode 100644 wise2-build.patch delete mode 100644 wise2-c99.patch delete mode 100644 wise2-getline.patch delete mode 100644 wise2-glib2.patch delete mode 100755 wise2-isnumber.patch delete mode 100644 wise2-ld--as-needed.patch delete mode 100644 wise2-mayhem.patch delete mode 100644 wise2.spec diff --git a/.gitignore b/.gitignore deleted file mode 100644 index 075683e..0000000 --- a/.gitignore +++ /dev/null @@ -1,2 +0,0 @@ -wise2.2.0.tar.gz -/wise2.4.1.tar.gz diff --git a/dead.package b/dead.package new file mode 100644 index 0000000..995362e --- /dev/null +++ b/dead.package @@ -0,0 +1 @@ +Orphaned by upstream; no longer needed in Fedora diff --git a/sources b/sources deleted file mode 100644 index 08acc43..0000000 --- a/sources +++ /dev/null @@ -1 +0,0 @@ -d70c404c1dc40ceef7718757b11bdaa0 wise2.4.1.tar.gz diff --git a/wise2-build.patch b/wise2-build.patch deleted file mode 100644 index d30904b..0000000 --- a/wise2-build.patch +++ /dev/null @@ -1,21 +0,0 @@ ---- wise-2.4.0~/src/makefile 2007-07-15 23:39:24.000000000 +0200 -+++ wise-2.4.0/src/makefile 2007-07-15 23:41:11.000000000 +0200 -@@ -109,7 +109,7 @@ - bin : - mkdir bin - cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin -- csh welcome.csh -+ ./welcome.csh - - libs : - (cd base ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a ) -diff -urNad wise-2.4.0~/src/welcome.csh wise-2.4.0/src/welcome.csh ---- wise-2.4.0~/src/welcome.csh 2007-07-15 23:39:24.000000000 +0200 -+++ wise-2.4.0/src/welcome.csh 2007-07-15 23:40:46.000000000 +0200 -@@ -1,4 +1,4 @@ --#!/bin/tcsh -f -+#!/bin/sh - - echo "" - echo "Welcome to Wise2.4" - diff --git a/wise2-c99.patch b/wise2-c99.patch deleted file mode 100644 index 4e2074f..0000000 --- a/wise2-c99.patch +++ /dev/null @@ -1,29 +0,0 @@ -No upstream bug tracking so tracked here: -https://bugzilla.redhat.com/show_bug.cgi?id=2155977 - -diff --git a/src/HMMer2/prior.c b/src/HMMer2/prior.c -index a40eb9c..76517e2 100644 ---- a/src/HMMer2/prior.c -+++ b/src/HMMer2/prior.c -@@ -4,6 +4,8 @@ - * Support for Dirichlet prior data structure, p7prior_s. - */ - -+#include -+ - #include "config.h" - #include "structs.h" - #include "funcs.h" -diff --git a/src/external/mott/mott_api.c b/src/external/mott/mott_api.c -index a42ab5b..4466095 100644 ---- a/src/external/mott/mott_api.c -+++ b/src/external/mott/mott_api.c -@@ -1,6 +1,8 @@ - #include - #include - #include -+#include -+#include - #include"gapstat.h" - - double default_lambda0, default_K0, default_Kplus, default_H, default_r, default_s, default_alpha; diff --git a/wise2-getline.patch b/wise2-getline.patch deleted file mode 100644 index 0e2fd1a..0000000 --- a/wise2-getline.patch +++ /dev/null @@ -1,302 +0,0 @@ -Index: wise-2.4.1/src/HMMer2/sqio.c -=================================================================== ---- wise-2.4.1.orig/src/HMMer2/sqio.c 2009-10-31 20:10:25.000000000 +0000 -+++ wise-2.4.1/src/HMMer2/sqio.c 2009-10-31 20:11:11.000000000 +0000 -@@ -213,7 +213,7 @@ - } - } - --/* Function: getline() -+/* Function: getline_() - * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] - * - * Purpose: read a line from a sequence file into V->sbuffer. -@@ -229,7 +229,7 @@ - * Returns: (void) - */ - static void --getline(struct ReadSeqVars *V) -+getline_(struct ReadSeqVars *V) - { - char *cp; - -@@ -299,7 +299,7 @@ - V->seqlen = 0; - if (addfirst) addseq(V->sbuffer, V); - do { -- getline(V); -+ getline_(V); - /* feof() alone is a bug; files not necessarily \n terminated */ - if (*(V->sbuffer) == '\0' && feof(V->f)) - done = TRUE; -@@ -327,7 +327,7 @@ - char *sptr; - /* load first line of entry */ - while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) -- getline(V); -+ getline_(V); - if (feof(V->f)) return; - - if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) -@@ -336,7 +336,7 @@ - SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); - } - do { -- getline(V); -+ getline_(V); - if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) - SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); - else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) -@@ -345,7 +345,7 @@ - SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); - } - } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); -- getline(V); /* skip next line, coords */ -+ getline_(V); /* skip next line, coords */ - - readLoop(0, endPIR, V); - -@@ -359,7 +359,7 @@ - /* get next line - */ - while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) -- getline(V); -+ getline_(V); - } - - -@@ -377,7 +377,7 @@ - char *nm; - /* position past ';' comments */ - do { -- getline(V); -+ getline_(V); - } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); - - if (!feof(V->f)) -@@ -389,7 +389,7 @@ - } - - while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) -- getline(V); -+ getline_(V); - } - - static int -@@ -411,7 +411,7 @@ - if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) - SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); - } -- getline(V); -+ getline_(V); - } - - if (! feof(V->f)) -@@ -420,7 +420,7 @@ - /* load next line - */ - while ((!feof(V->f)) && (*V->sbuffer != ';')) -- getline(V); -+ getline_(V); - } - - -@@ -438,7 +438,7 @@ - int in_definition; - - while (strncmp(V->sbuffer, "LOCUS", 5) != 0) -- getline(V); -+ getline_(V); - - if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) - { -@@ -449,7 +449,7 @@ - in_definition = FALSE; - while (! feof(V->f)) - { -- getline(V); -+ getline_(V); - if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) - { - if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) -@@ -482,11 +482,11 @@ - - - while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) -- getline(V); -+ getline_(V); - /* SRE: V->s now holds "//", so sequential - reads are wedged: fixed Tue Jul 13 1993 */ - while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) -- getline(V); -+ getline_(V); - } - - static int -@@ -515,7 +515,7 @@ - Die("bogus GCGdata format? %s", V->sbuffer); - - /* second line contains free text description */ -- getline(V); -+ getline_(V); - SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); - - if (binary) { -@@ -535,7 +535,7 @@ - else readLoop(0, endGCGdata, V); - - while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) -- getline(V); -+ getline_(V); - } - - static int -@@ -555,12 +555,12 @@ - if ((sptr = strtok(NULL, "\n")) != NULL) - SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); - /* workaround for long NCBI NR lines */ -- while (V->longline && ! feof(V->f)) getline(V); -+ while (V->longline && ! feof(V->f)) getline_(V); - - readLoop(0, endPearson, V); - - while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) -- getline(V); -+ getline_(V); - } - - -@@ -587,7 +587,7 @@ - - /* make sure we have first line */ - while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) -- getline(V); -+ getline_(V); - - if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) - { -@@ -596,7 +596,7 @@ - } - - do { -- getline(V); -+ getline_(V); - if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) - { - if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) -@@ -620,7 +620,7 @@ - - /* load next record's ID line */ - while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) -- getline(V); -+ getline_(V); - } - - -@@ -636,7 +636,7 @@ - { - char *sptr; - -- getline(V); /*s == "seqLen seqid string..."*/ -+ getline_(V); /*s == "seqLen seqid string..."*/ - - if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) - SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); -@@ -647,7 +647,7 @@ - readLoop(0, endZuker, V); - - while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) -- getline(V); -+ getline_(V); - } - - static void -@@ -669,7 +669,7 @@ - - do { - done = feof(V->f); -- getline(V); -+ getline_(V); - if (! done) addseq(V->sbuffer, V); - } while (!done); - } -@@ -681,7 +681,7 @@ - char *sptr; - int dostruc = FALSE; - -- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); -+ while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline_(V); - - if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) - SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); -@@ -689,7 +689,7 @@ - /*CONSTCOND*/ - while (1) - { -- getline(V); -+ getline_(V); - if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } - - if (strncmp(V->sbuffer, "SRC ", 4) == 0) -@@ -721,14 +721,14 @@ - while (1) - { - /* sequence line */ -- getline(V); -+ getline_(V); - if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) - break; - addseq(V->sbuffer, V); - /* structure line */ - if (dostruc) - { -- getline(V); -+ getline_(V); - if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } - addstruc(V->sbuffer, V); - } -@@ -736,7 +736,7 @@ - - - while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) -- getline(V); -+ getline_(V); - } - - -@@ -816,7 +816,7 @@ - - /* Load the first line. - */ -- getline(dbfp); -+ getline_(dbfp); - - return dbfp; - } -@@ -833,7 +833,7 @@ - Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); - - fseek(sqfp->f, offset, SEEK_SET); -- getline(sqfp); -+ getline_(sqfp); - } - - -@@ -853,7 +853,7 @@ - if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; - else { - rewind(sqfp->f); -- getline(sqfp); -+ getline_(sqfp); - } - } - -@@ -949,7 +949,7 @@ - do { /* skip leading comments on GCG file */ - gotuw = (strstr(V->sbuffer,"..") != NULL); - if (gotuw) readUWGCG(V); -- getline(V); -+ getline_(V); - } while (! feof(V->f)); - break; - diff --git a/wise2-glib2.patch b/wise2-glib2.patch deleted file mode 100644 index 8c8a448..0000000 --- a/wise2-glib2.patch +++ /dev/null @@ -1,703 +0,0 @@ -Author: Barry deFreese -Description: To build wise2 with the Glib version 2.0 instead of 1.2. -Forwarded: birney@sanger.ac.uk ---- a/src/makefile -+++ b/src/makefile -@@ -31,13 +31,13 @@ - - - # Intel icc flags --# CFLAGS = -c -O3 -axWK -ipo `glib-config --cflags` -+# CFLAGS += -c -axWK -ipo `pkg-config --cflags glib-2.0` - - # alpha flags (-pthread) --# CFLAGS = -c -O3 -pthread `glib-config --cflags` -+# CFLAGS += -c -pthread `pkg-config --cflags glib-2.0` - - # normal linux/bsd/mac flags --CFLAGS = -c -O3 `glib-config --cflags` -+CFLAGS += $(CPPFLAGS) -c `pkg-config --cflags glib-2.0` - - - EXTRALIBS = -lm ---- a/src/snp/makefile -+++ b/src/snp/makefile -@@ -5,9 +5,9 @@ - CC = cc - #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ - #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. --CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` -+CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` - --LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm -+LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm - AR_OPTIONS = ru - - RANLIB_NEEDED = 0 -@@ -16,7 +16,7 @@ - $(CC) $(CFLAGS) $(INCFLAGS) $? - - test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o -- $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) -+ $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LDFLAGS) - - INCFLAGS = -I../base/ -I../dynlibsrc/ - DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn ---- a/src/corba/makefile -+++ b/src/corba/makefile -@@ -3,9 +3,9 @@ - CC = cc - INCFLAGS = -I../base/ -I../dynlibsrc - #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ --#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/ --CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` --LFLAGS = -L../base/ -lm -lpthread -+#CFLAGS += -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/ -+CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` -+LDFLAGS += -L../base/ -lm -lpthread - AR_OPTIONS = ru - - -@@ -14,18 +14,18 @@ - orbit-idl hspscan_corba.idl - - test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o -- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread -+ cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread - - scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o -- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread -+ cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread - - - test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o -- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread -+ cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread - - - test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o -- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread -+ cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread - - .c.o : - $(CC) $(CFLAGS) $(INCFLAGS) $? ---- a/src/models/makefile -+++ b/src/models/makefile -@@ -62,46 +62,46 @@ - # $(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) wise2xhmmer2.c - - testgenestat : testgenestat.o genestats.o pwmdna.o -- $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) - - test_aligng : test_aligng.o aligngenemodel.o pwmdna.o -- $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) - - makepwm : makepwm.o pwmdna.o -- $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) - - testwise2xhmmer2.o : testwise2xhmmer2.c - $(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) testwise2xhmmer2.c - - testwise2xhmmer2 : testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -- $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LFLAGS) -+ $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LDFLAGS) - - plan7test.o : plan7test.c - $(CC) $(CFLAGS) -I../HMMer2/ plan7test.c - - plan7test : plan7test.o plan7.o wise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -- $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LFLAGS) -+ $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LDFLAGS) - - seqstat : seqstat.o -- $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LDFLAGS) - - mutatedna : mutatedna.o -- $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LDFLAGS) - - revcomp : revcomp.o -- $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LDFLAGS) - - stupid_motif_scan : stupid_motif_scan.o -- $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LDFLAGS) - - seqtrunc : seqtrunc.o -- $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LDFLAGS) - - seqlist : seqlist.o -- $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LDFLAGS) - - testpwm : testpwm.o pwmdna.o -- $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) -lefence -+ $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) -lefence - - - threestate : $(MODELOBJ) -@@ -111,29 +111,29 @@ - pwise : $(MODELOBJ) threestatemat.o threestatedisplay.o - - test : test.o proteinsw.o protprotdis.o -- $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LFLAGS) -+ $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LDFLAGS) - - testanc : testanc.o proteinsw.o abc.o pba.o sw_wrap.o -- $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - test_tf : test_transfactor.o transfactor.o pwmdna.o -- $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LFLAGS) -ldyna -lwisebase -+ $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LDFLAGS) -ldyna -lwisebase - - motifwise : motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o -- $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase -+ $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase - - motifcluster : motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o -- $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase -+ $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase - - motifdiff : motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o -- $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase -+ $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase - - - cdtest : cdtest.o cdna2genomic.o d2d_display.o -- $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LDFLAGS) - - prob2bits : prob2bits.o -- $(CC) -o prob2bits $(LFLAGS) -ldyna_glib -ldyna -lwisebase -+ $(CC) -o prob2bits $(LDFLAGS) -ldyna_glib -ldyna -lwisebase - - quick : - cc -O -c -I../dynlibsrc/ -I../base/ genewise6.c -@@ -180,161 +180,161 @@ - $(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. - - oldpostwise : oldpostwise.o $(NEWG) -- $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase -+ $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase - - testdna : testdna.o dnaalign.o seqaligndisplay.o -- $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - dnal : dnal.o dnaalign.o seqaligndisplay.o -- $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o -- $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - scanwisep.o : scanwisep.c -- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $? -+ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $? - - hsp2aln_sw.o : hsp2aln_sw.c -- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? -+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? - - scanwisep_mysql.o : scanwisep.c - $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c - - scanwisep_mysql : scanwisep_mysql.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o -- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o $(LFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) -lpthread -lZ -+ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o $(LDFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) $(LDFLAGS) -lpthread -lZ - - - scanwisep_corba.o : scanwisep.c - $(CC) $(CFLAGS) -DSCAN_CORBA -I../corba -I../external/mott `orbit-config --cflags server` scanwisep.c - - scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o -- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread -+ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LDFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread - - - scanwisep_wiseserver.o : scanwisep.c - $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c - - scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o -- $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread -+ $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread - - scanwisep_compress.o : scanwisep.c - $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c - - scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o -- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread -+ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread - - - - scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o -- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread -+ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread - - test_gwhsp : test_gwhsp.o genewisehsp.o -- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread -+ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread - - localcishit.o : localcishit.c -- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? -+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? - - promoterwise.o : promoterwise.c -- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? -+ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? - - promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o -- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread -+ $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread - - test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o -- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread -+ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread - - promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o -- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread -+ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread - - dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o -- $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread -+ $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread - - pswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o -- $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - efpswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o -- $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS) -+ $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS) - - dba : dbac.o dba.o slimdba.o bigdba.o dbadisplay.o -- $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - lba : lba.o largeblockdp.o seqaligndisplay.o -- $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - - fastdba : fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o -- $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - evopairwise : evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o -- $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - test_threestatehsp : test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o threestatehsp.o -- $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - makerandomdb : makerandomdb.o -- $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - genewise : genewise.o $(NEWG) -- $(CC) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - cdnawise : cdnawise.o $(NEWG) cdnawise10.o -- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o -- $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - - fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o -- $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o -- $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - - editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o -- $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -+ $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase - - - efgw : genewise.o $(NEWG) -- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence -+ $(CC) -g -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence - - - genewisedb : genewisedb.o $(NEWG) -- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - estwisedb : estwisedb.o $(NEWG) -- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - edb : estwisedb.o $(NEWG) -- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence -+ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence - - estwise : estwise.o $(NEWG) -- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - - amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o -- $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o -- $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o -- $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o -- $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - test_splice : test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o -- $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o -- $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - pseudowise : pseudowise.o pseudowise7.o $(NEWG) -- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o -- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - - HMMER_LIBS = ../HMMer2/ -@@ -345,11 +345,11 @@ - CC = cc - #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ - #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. --CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` --#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` --#LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ -+CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` -+#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` -+#LDFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ - --LFLAGS = -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs` -+LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0` - AR_OPTIONS = ru - - RANLIB_NEEDED = 0 -@@ -360,7 +360,7 @@ - - - #test : test.o libwisedb.a --# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LFLAGS) -+# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LDFLAGS) - - - # ---- a/src/dnaindex/makefile -+++ b/src/dnaindex/makefile -@@ -27,53 +27,53 @@ - - - kwise : kwise.o $(ASSEMBLY_OBJ) -- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` -+ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` - - arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) -- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` -+ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` - - - findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) -- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` -+ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` - - make_shotgun : make_shotgun.o shotgun.o -- $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LDFLAGS) - - test_dnanumber : test_dnanumber.o dnanumber.o -- $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) - - test_linkindex : test_linkindex.o linkindex.o dnanumber.o -- $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) - - test_forwardindex : test_forwardindex.o forwardindex.o -- $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LDFLAGS) - - test_euler : test_euler.o eulerindex.o singleseqspace.o -- $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) - - test_kmer : test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_contig.o kmer_assembly_error.o assembly.o -- $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LDFLAGS) - - kmer_stat : kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -- $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LDFLAGS) - - test_compara : test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -- $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) - - bigseqwise : bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -- $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) - - - - - show_euler : show_euler.o eulerindex.o singleseqspace.o -- $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) -+ $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) - - CC = cc --CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` -+CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` - - --LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm -+LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm - - - .c.o : ---- a/src/dnaindex/assembly/makefile -+++ b/src/dnaindex/assembly/makefile -@@ -3,33 +3,33 @@ - .SUFFIXES : .dy - - test_basegraph : test_basegraph.o basegraph.o -- $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LFLAGS) -ldyna -lwisebase -+ $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LDFLAGS) -ldyna -lwisebase - - test_assemblygraph : test_assemblygraph.o assemblygraph.o assemblystats.o basegraph.o -- $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase -+ $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase - - - test_graphtangle : test_graphtangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o -- $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LFLAGS) -ldyna -lwisebase -+ $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LDFLAGS) -ldyna -lwisebase - - - pathwise : pathwise.o supertangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o grapherror.o graphmanager.o depthmanager.o -- $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LFLAGS) -ldyna -lwisebase -+ $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LDFLAGS) -ldyna -lwisebase - - - badkmer : badkmer.o assemblygraph.o assemblystats.o basegraph.o -- $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase -+ $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase - - arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o -- $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase -+ $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase - - - - CC = cc --CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags` -+CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0` - - --LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm -+LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm - - - .c.o : ---- a/src/dynlibsrc/makefile -+++ b/src/dynlibsrc/makefile -@@ -84,11 +84,11 @@ - CC = cc - INCFLAGS = -I../base/ - #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ --CFLAGS = -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` --#CFLAGS = -Wall -g3 -pg -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` --#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags` -+CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -+#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -+#CFLAGS += -c -pthread -DUNIX -I../base/ `pkg-config --cflags glib-2.0` - #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ --LFLAGS = -g -L../base/ -lm -+LDFLAGS += -g -L../base/ -lm - AR_OPTIONS = ru - - RANLIB_NEEDED = 0 -@@ -133,47 +133,47 @@ - # - - test_genomic : genomic.o test_genomic.o sequence.o codon.o -- $(CC) -o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm -+ $(CC) $(LDFLAGS)-o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm - - test_tree : tree.o test_tree.o -- $(CC) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm -+ $(CC) $(LDFLAGS) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm - - test_intallocator : intallocator.o test_intallocator.o -- $(CC) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm -+ $(CC) $(LDFLAGS) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm - - test_psi : test_psi.o proteinstreamedindex.o -- $(CC) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm -+ $(CC) $(LDFLAGS) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm - - test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a -- $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm -+ $(CC) $(LDFLAGS) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm - - test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a -- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm -+ $(CC) $(LDFLAGS) -g -o test_seqhash `pkg-config --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm - - test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o -- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` -+ $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` - - test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o -- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` -+ $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` - - - testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o -- $(CC) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm -+ $(CC) $(LDFLAGS) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm - - testseqalign : seqalign.o testseqalign.o sequence.o codon.o -- $(CC) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm -+ $(CC) $(LDFLAGS) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm - - testanc : libdyna.a -- $(CC) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm -+ $(CC) $(LDFLAGS) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm - - testdb : testdb.o sequencedb.o sequence.o codon.o probability.o -- $(CC) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm -+ $(CC) $(LDFLAGS) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm - - testpdb : testpdb.o protein.o proteindb.o complexevalset.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o histogram.o -- $(CC) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm -+ $(CC) $(LDFLAGS) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm - - testpb : testpairbase.o pairbase.o pairbaseseq.o sequence.o seqalign.o codon.o probability.o complexsequence.o complexevalset.o -- $(CC) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm -+ $(CC) $(LDFLAGS) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm - - .c.o : - $(CC) $(CFLAGS) $(INCFLAGS) $? ---- a/src/network/makefile -+++ b/src/network/makefile -@@ -3,8 +3,8 @@ - - CC = cc - INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex --CFLAGS = -O2 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags` --LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs` -+CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0` -+LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` - AR_OPTIONS = ru - - RANLIB_NEEDED = 0 -@@ -13,7 +13,7 @@ - - - scanwise_server : wise_proteinindex_server.o net_hspscan.o ../dynlibsrc/libdyna.a ../dynlibsrc/libdyna_glib.a ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -- $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LFLAGS) -lpthread -+ $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LDFLAGS) -lpthread - - - .c.o : ---- a/src/other_programs/makefile -+++ b/src/other_programs/makefile -@@ -3,8 +3,8 @@ - .SUFFIXES : .dy - - CC = cc --CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `glib-config --cflags` --LFLAGS = -g -L../base/ -L../dynlibsrc -lm `glib-config --libs` -+CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0` -+LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `pkg-config --libs glib-2.0` - AR_OPTIONS = ru - - RANLIB_NEEDED = 0 ---- a/src/base/makefile -+++ b/src/base/makefile -@@ -19,9 +19,9 @@ - - - --#CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH --CFLAGS = -c -O2 -DUNIX -pthread --LFLAGS = -g -lm -+#CFLAGS += -c -g -DUNIX -DWISE_MEMORY_WATCH -+CFLAGS += $(CPPFLAGS) -c -DUNIX -pthread -+LDFLAGS += -g -lm - DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D - AR_OPTIONS = ru - ---- a/src/HMMer2/Makefile -+++ b/src/HMMer2/Makefile -@@ -13,7 +13,7 @@ - ## your compiler and compiler flags - # - CC = cc --CFLAGS = -g -+CFLAGS += $(CPPFLAGS) -g - - ## machine specific definitions - # -@@ -75,25 +75,25 @@ - all: $(PROGS) - - hmmalign: $(OBJ) hmmalign.o -- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) - - hmmbuild: $(OBJ) hmmbuild.o -- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) - - hmmcalibrate: $(OBJ) hmmcalibrate.o -- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) - - hmmconvert: $(OBJ) hmmconvert.o -- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) - - hmmemit: $(OBJ) hmmemit.o -- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) - - hmmpfam: $(OBJ) hmmpfam.o -- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) - - hmmsearch: $(OBJ) hmmsearch.o -- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) - - ####### - ## Target used in making Shiva test suite diff --git a/wise2-isnumber.patch b/wise2-isnumber.patch deleted file mode 100755 index c678582..0000000 --- a/wise2-isnumber.patch +++ /dev/null @@ -1,18 +0,0 @@ -#! /bin/sh /usr/share/dpatch/dpatch-run -## 02_isnumber.dpatch by Philipp Benner -## -## DP: Replace isnumber() (which does not exist on linux) by isdigit(). - -@DPATCH@ -diff -urNad wise-2.4.0~/src/models/phasemodel.c wise-2.4.0/src/models/phasemodel.c ---- wise-2.4.0~/src/models/phasemodel.c 2007-07-01 22:44:39.000000000 +0200 -+++ wise-2.4.0/src/models/phasemodel.c 2007-07-16 00:24:16.000000000 +0200 -@@ -20,7 +20,7 @@ - if( line[0] == '#' ) { - continue; - } -- if( !isnumber(line[0]) ) { -+ if( !isdigit(line[0]) ) { - warn("Bad looking line in intron file, %s",line); - continue; - } diff --git a/wise2-ld--as-needed.patch b/wise2-ld--as-needed.patch deleted file mode 100644 index b8db369..0000000 --- a/wise2-ld--as-needed.patch +++ /dev/null @@ -1,54 +0,0 @@ -Description: Fix FTBFS with ld --as-needed. -Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935 - -diff --git a/src/models/makefile b/src/models/makefile -index 1766fee..e4634b5 100644 ---- a/src/models/makefile -+++ b/src/models/makefile -@@ -215,7 +215,7 @@ scanwisep_wiseserver.o : scanwisep.c - $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c - - scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o -- $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread -+ $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread $(LDFLAGS) - - scanwisep_compress.o : scanwisep.c - $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c -@@ -275,7 +275,7 @@ makerandomdb : makerandomdb.o - $(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - genewise : genewise.o $(NEWG) -- $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) - - cdnawise : cdnawise.o $(NEWG) cdnawise10.o - $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -@@ -300,16 +300,16 @@ efgw : genewise.o $(NEWG) - - - genewisedb : genewisedb.o $(NEWG) -- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) - - estwisedb : estwisedb.o $(NEWG) -- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) - - edb : estwisedb.o $(NEWG) - $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence - - estwise : estwise.o $(NEWG) -- $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) - - - amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o -@@ -331,7 +331,7 @@ statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o - $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) - - pseudowise : pseudowise.o pseudowise7.o $(NEWG) -- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -+ $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) - - clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o - $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) diff --git a/wise2-mayhem.patch b/wise2-mayhem.patch deleted file mode 100644 index f4b7724..0000000 --- a/wise2-mayhem.patch +++ /dev/null @@ -1,99 +0,0 @@ ---- a/src/models/dbac.c -+++ b/src/models/dbac.c -@@ -535,8 +535,12 @@ - * - */ - -- one = read_fasta_file_Sequence(*argv++); -- two = read_fasta_file_Sequence(*argv++); -+ if( (one = read_fasta_file_Sequence(*argv++)) == NULL ) { -+ fatal("Unable to read the sequence in file"); -+ } -+ if( (two = read_fasta_file_Sequence(*argv++)) == NULL ) { -+ fatal("Unable to read the sequence in file"); -+ } - - uppercase_Sequence(one); - uppercase_Sequence(two); ---- a/src/models/estwise.c -+++ b/src/models/estwise.c -@@ -313,7 +313,7 @@ - } - } - -- if( reverse == TRUE ) { -+ if( cdna && reverse == TRUE ) { - if( tstart > tend ) { - warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend); - } -@@ -323,7 +323,7 @@ - cdna = cdna_temp; - } - -- if( target_abs == TRUE ) { -+ if( cdna && target_abs == TRUE ) { - cdna->baseseq->offset = 1; - cdna->baseseq->end = strlen(cdna->baseseq->seq); - } -@@ -472,8 +472,11 @@ - } - - cp = flat_cDNAParser(indel_error); -- cm = flat_CodonMapper(ct); -- sprinkle_errors_over_CodonMapper(cm,subs_error); -+ -+ if( ct ) { -+ cm = flat_CodonMapper(ct); -+ sprinkle_errors_over_CodonMapper(cm,subs_error); -+ } - - return ret; - ---- a/src/models/genewise.c -+++ b/src/models/genewise.c -@@ -550,8 +550,10 @@ - ret = FALSE; - } - -- gen->baseseq->offset = 1; -- gen->baseseq->end = strlen(gen->baseseq->seq); -+ if ( gen ) { -+ gen->baseseq->offset = 1; -+ gen->baseseq->end = strlen(gen->baseseq->seq); -+ } - } - - if( alg_str != NULL ) { ---- a/src/models/estwisedb.c -+++ b/src/models/estwisedb.c -@@ -688,8 +688,11 @@ - - - cps = flat_cDNAParser(indel_error); -- cm = flat_CodonMapper(ct); -- sprinkle_errors_over_CodonMapper(cm,subs_error); -+ -+ if( ct ) { -+ cm = flat_CodonMapper(ct); -+ sprinkle_errors_over_CodonMapper(cm,subs_error); -+ } - - return ret; - ---- a/src/models/promoterwise.c -+++ b/src/models/promoterwise.c -@@ -147,8 +147,12 @@ - - lchs = standard_LocalCisHitScore(NMaskType_VARIABLE); - -- query = read_fasta_file_Sequence(argv[1]); -- target = read_fasta_file_Sequence(argv[2]); -+ if( (query = read_fasta_file_Sequence(argv[1])) == NULL ) { -+ fatal("Unable to read the sequence in query file"); -+ } -+ if( (target = read_fasta_file_Sequence(argv[2])) == NULL ) { -+ fatal("Unable to read the sequence in target file"); -+ } - - for(i=0;ilen;i++) { - query->seq[i] = toupper(query->seq[i]); diff --git a/wise2.spec b/wise2.spec deleted file mode 100644 index 846e652..0000000 --- a/wise2.spec +++ /dev/null @@ -1,137 +0,0 @@ -%define _lto_cflags %{nil} - -Name: wise2 -Version: 2.4.1 -Release: %autorelease -Summary: Tools for comparison of bio-polymers - -## Everything is licensed under a BSD-style license except for -## the HMMer2 libraries and models directory which are GPLv2+ -## see LICENSE files for details. -License: BSD-3-Clause AND GPL-2.0-or-later -URL: http://www.ebi.ac.uk/~birney/%{name}/ -Source0: http://www.ebi.ac.uk/~birney/%{name}/wise%{version}.tar.gz - -## Patches from Debian package. Thanks to Philipp Benner -Patch0: %{name}-build.patch -Patch1: %{name}-isnumber.patch -Patch2: %{name}-glib2.patch -Patch3: %{name}-getline.patch -Patch4: %{name}-ld--as-needed.patch -Patch5: %{name}-mayhem.patch -Patch6: %{name}-c99.patch - -BuildRequires: make -BuildRequires: glib2-devel -BuildRequires: gcc -BuildRequires: perl -BuildRequires: strace - -%description -Wise2 is a package focused on comparisons of bio-polymers, commonly DNA -sequence and protein sequence. A strength of Wise2 is the -comparison of DNA sequence at the level of its protein -translation. This comparison allows the simultaneous prediction of -gene structure with homology based alignment. - - -%package doc -Summary: Wise2 documentation -BuildArch: noarch - -%description doc -Wise2, Wise2api and Dynamite documentation files. - - -%package examples -Summary: Wise2 examples -Requires: %{name}%{?_isa} = %{version}-%{release} - -%description examples -Here are some examples that you might want to try out. The -Wise2 executables of course should be installed before. - -%prep -%autosetup -p1 -n wise%{version} - -# Remove spurious-executable-perm -chmod a-x src/external/mott/mott_api.c -chmod a-x src/external/mott/mott_api.h -chmod a-x src/external/mott/gaplib.c -chmod a-x src/external/mott/gapstat.h - -## fix interpreter in examples -sed -i 's#/usr/local/bin/perl#/usr/bin/perl#' docs/gettex.pl -## fix perms -chmod -x test_data/rrm.HMM - -## pull out licenses -for i in base dynlibsrc dyc -do - cp src/$i/LICENSE LICENSE.$i -done -cp src/models/GNULICENSE LICENSE.GPL - -%build -## removed "{?_smp_mflags}", does not support parallel build -export LDFLAGS="%{__global_ldflags}" -make -C src CC=gcc \ - CFLAGS=" -c %{build_cflags} -pthread -D_GNU_SOURCE %(pkg-config --cflags glib-2.0) -D_POSIX_C_SOURCE=200112L" all - -%install -pushd src/bin -mkdir -p $RPM_BUILD_ROOT%{_bindir} -for i in dba dnal estwise estwisedb genewise genewisedb promoterwise scanwise scanwise_server psw pswdb -do - install -pm 755 $i $RPM_BUILD_ROOT%{_bindir} -done -popd - -# install architecture-independent data and config files -mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2 -pushd wisecfg -install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2 -popd - -# install architecture-independent files to run example tests -mkdir -p $RPM_BUILD_ROOT%{_datadir}/wise2/examples -pushd test_data -install -pm 644 * $RPM_BUILD_ROOT%{_datadir}/wise2/examples -popd - -# install scripts to automatically set the WISECONFIGDIR environment variable -mkdir -p $RPM_BUILD_ROOT%{_sysconfdir}/profile.d -echo "export WISECONFIGDIR=%{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.sh -echo "setenv WISECONFIGDIR %{_datadir}/wise2/" > $RPM_BUILD_ROOT%{_sysconfdir}/profile.d/wise2.csh - -%check -export WISECONFIGDIR=$PWD/wisecfg -make -C src test - -%files -%doc README -%license LICENSE LICENSE.base LICENSE.dynlibsrc LICENSE.dyc LICENSE.GPL -%{_bindir}/genewisedb -%{_bindir}/estwisedb -%{_bindir}/genewise -%{_bindir}/estwise -%{_bindir}/scanwise -%{_bindir}/promoterwise -%{_bindir}/pswdb -%{_bindir}/dba -%{_bindir}/psw -%{_bindir}/scanwise_server -%{_bindir}/dnal -%{_datadir}/wise2/ -%config(noreplace) %{_sysconfdir}/profile.d/* - -%files doc -%license LICENSE -%doc docs - -%files examples -%doc test_data/README -%{_datadir}/wise2/examples/ - -%changelog -%autochangelog