[lilac] updated to 3.0.2-2

4 files changed, 66 insertions, 50 deletions

diff --git a/.SRCINFO b/.SRCINFO
index 336e1182935a..8ebc9ceff24c 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,19 +1,21 @@
 pkgbase = spaln
 	pkgdesc = Splicing-aware transcript (cDNA/EST or protein sequences) alignment to genomic DNA
-	pkgver = 2.4.13f
-	pkgrel = 1
+	pkgver = 3.0.2
+	pkgrel = 2
 	url = https://github.com/ogotoh/spaln
 	arch = x86_64
 	license = GPL2
 	depends = zlib
 	depends = perl
-	source = spaln-2.4.13f.tar.gz::https://github.com/ogotoh/spaln/archive/refs/tags/ver.2.4.13f.tar.gz
+	depends = glibc
+	depends = gcc-libs
+	source = spaln-3.0.2.tar.gz::https://github.com/ogotoh/spaln/archive/refs/tags/ver3.0.2.tar.gz
 	source = spaln.sh
 	source = spaln.csh
-	source = destdir.patch
-	sha256sums = 024fdcf58e38373983092280a7e10ff9c7e246e7d2465c165e158512e686225e
+	source = harden.patch
+	sha256sums = 830e02617c90cd9f245b406e29d4ab03fe29712832eff837ce24431db14a5555
 	sha256sums = 9a0b4fa808ab2d88d277cbe5d49b6ed02eff768c45409cba70d4132230ca676d
 	sha256sums = 9b77f3a31dd260703a8cefc6416794fc0ddb04999cd5078be9c5a287664561d1
-	sha256sums = b78d8bf6c79cee8aa0a06e5aa61098041d46a468275fda911883d356866f8a8f
+	sha256sums = b369eb6f01b17f5f165660a464033595afde8e222084d3deb9b77763deaa4aa5
 
 pkgname = spaln
diff --git a/PKGBUILD b/PKGBUILD
index cff9e4e0829b..5f8a208566dd 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,42 +1,45 @@
-# Maintainer: Bipin Kumar <bipin@ccmb.res.in>
+# Maintainer: Bipin Kumar <kbipinkumar@pm.me>
 
 pkgname=spaln
-pkgver=2.4.13f
-pkgrel=1
+pkgver=3.0.2
+pkgrel=2
 pkgdesc='Splicing-aware transcript (cDNA/EST or protein sequences) alignment to genomic DNA'
 arch=('x86_64')
 url='https://github.com/ogotoh/spaln'
 license=('GPL2')
-depends=('zlib' 'perl')
-source=("${pkgname}-${pkgver}.tar.gz::https://github.com/ogotoh/spaln/archive/refs/tags/ver.${pkgver}.tar.gz"
+depends=('zlib' 'perl' 'glibc' 'gcc-libs')
+source=("${pkgname}-${pkgver}.tar.gz::https://github.com/ogotoh/spaln/archive/refs/tags/ver${pkgver}.tar.gz"
         "spaln.sh"
         "spaln.csh"
-        "destdir.patch")
-sha256sums=('024fdcf58e38373983092280a7e10ff9c7e246e7d2465c165e158512e686225e'
+        "harden.patch")
+sha256sums=('830e02617c90cd9f245b406e29d4ab03fe29712832eff837ce24431db14a5555'
             '9a0b4fa808ab2d88d277cbe5d49b6ed02eff768c45409cba70d4132230ca676d'
             '9b77f3a31dd260703a8cefc6416794fc0ddb04999cd5078be9c5a287664561d1'
-            'b78d8bf6c79cee8aa0a06e5aa61098041d46a468275fda911883d356866f8a8f')
+            'b369eb6f01b17f5f165660a464033595afde8e222084d3deb9b77763deaa4aa5')
 
 prepare() {
-  cp destdir.patch ${pkgname}-ver.${pkgver}/src
-  cp spaln.* ${pkgname}-ver.${pkgver}/src
-  cd ${pkgname}-ver.${pkgver}/src
-  # patch to enable support for GNU make's staged install process
-  patch -p1 < destdir.patch 
-  CXX=g++ CFLAGS="-O2" ./configure --exec_prefix=/usr/bin --table_dir=/usr/share/spaln/table --alndbs_dir=/usr/share/spaln/seqdb --use_zlib=1
+  cd ${pkgname}-ver${pkgver}/src
+  patch -p2 < "${srcdir}"/harden.patch
+  CFLAGS=${CFLAGS} ./configure --exec_prefix=/usr/bin --table_dir=/usr/share/spaln/table --alndbs_dir=/usr/share/spaln/seqdb
+  
 }
 
 build() {
-  cd ${pkgname}-ver.${pkgver}/src
+  cd ${pkgname}-ver${pkgver}/src 
   make -j1
+  
 }
 
 package() {
-  cd ${pkgname}-ver.${pkgver}/src
+  cd ${pkgname}-ver${pkgver}/src
   make DESTDIR=${pkgdir} install
   # set paths to tables and alndbs
   install -dm755 "${pkgdir}"/etc/profile.d/
-  install -Dm644 spaln.sh -t "${pkgdir}"/etc/profile.d/
-  install -Dm644 spaln.csh -t "${pkgdir}"/etc/profile.d/
+  install -Dm644 "${srcdir}"/spaln.sh -t "${pkgdir}"/etc/profile.d/
+  install -Dm644 "${srcdir}"/spaln.csh -t "${pkgdir}"/etc/profile.d/
+  cd ..
+  # man page
+    install -Dm0644 "spaln.1" -t "$pkgdir/usr/share/man/man1"
+    install -Dm0644 "sortgrcd.1" -t "$pkgdir/usr/share/man/man1"
 
 }
diff --git a/destdir.patch b/destdir.patch
deleted file mode 100644
index 06e14460db05..000000000000
--- a/destdir.patch
+++ /dev/null
@@ -1,26 +0,0 @@
---- a/Makefile.in	2023-01-11 17:27:09.000000000 +0530
-+++ b/Makefile.in	2023-02-26 23:12:50.488085410 +0530
-@@ -53,16 +53,16 @@
- 	tar cvf Sources.tar $$Pnm
- 
- install:
--	test -d $(exec_prefix) || mkdir -p $(exec_prefix)
--	cp $(PROG) $(exec_prefix)
--	test -d $(table_dir) || mkdir -p $(table_dir)
-+	test -d $(DESTDIR)$(exec_prefix) || mkdir -p $(DESTDIR)$(exec_prefix)
-+	cp $(PROG) $(DESTDIR)$(exec_prefix)
-+	test -d $(DESTDIR)$(table_dir) || mkdir -p $(DESTDIR)$(table_dir)
- 	@if test "$(table_dir)" != "$(PWD)/../table"; then \
--		cp -pfR ../table/* $(table_dir); \
-+		cp -pfR ../table/* $(DESTDIR)$(table_dir); \
- 	fi
--	./makmdm $(table_dir)
--	test -d $(alndbs_dir) || mkdir -p $(alndbs_dir)
-+	./makmdm $(DESTDIR)$(table_dir)
-+	test -d $(DESTDIR)$(alndbs_dir) || mkdir -p $(DESTDIR)$(alndbs_dir)
- 	@if test "$(alndbs_dir)" != "$(PWD)/../seqdb"; then \
--		cp -pfR ../seqdb/????* $(alndbs_dir); \
-+		cp -pfR ../seqdb/????* $(DESTDIR)$(alndbs_dir); \
- 	fi
- 
- uninstall uninst:
diff --git a/harden.patch b/harden.patch
new file mode 100644
index 000000000000..214fe133fae3
--- /dev/null
+++ b/harden.patch
@@ -0,0 +1,37 @@
+--- spaln-ver3.0.2.orig/src/Makefile.in	2023-10-31 07:23:58.000000000 +0530
++++ spaln-ver3.0.2.new/src/Makefile.in	2023-11-17 00:07:42.903202161 +0530
+@@ -6,14 +6,14 @@
+ alndbs_dir = /db/seqdb
+ CXX  = g++
+ #CXX  = clang++
+-CFLAGS = -O3 -march=native
++CFLAGS += -O3 -march=native
+ RANLIB = ranlib
+ LD  = g++
+ AR = ar ru
+ DEL = rm -f
+ DEFLT = -DM_THREAD=1
+ 
+-CXX := $(CXX) $(CFLAGS) $(DEFLT)
++CXX := $(CXX) $(CFLAGS) $(CPPFLAGS) $(DEFLT)
+ 
+ .SUFFIXES: .o .cc .h .sh
+ 
+@@ -88,13 +88,13 @@
+ 	ls $(SRC) $(HDR)
+ 
+ spaln:	spaln.cc blksrc.o $(SLIB)
+-	$(CXX) -o $@ spaln.cc blksrc.o $(SLIB) $(ILIB)
++	$(CXX) -o $@ spaln.cc blksrc.o $(SLIB) $(ILIB) $(LDFLAGS)
+ sortgrcd:	sortgrcd.cc $(SLIB)
+-	$(CXX) -o $@ sortgrcd.cc $(SLIB) $(ILIB)
++	$(CXX) -o $@ sortgrcd.cc $(SLIB) $(ILIB) $(LDFLAGS)
+ makdbs: makdbs.cc dbs.h seq.h bitpat.h $(SLIB)
+-	$(CXX) -o $@ makdbs.cc $(SLIB) $(ILIB)
++	$(CXX) -o $@ makdbs.cc $(SLIB) $(ILIB) $(LDFLAGS)
+ makmdm: makmdm.cc mdm.h $(CLIB)
+-	$(CXX) -o $@ makmdm.cc $(CLIB) $(ILIB)
++	$(CXX) -o $@ makmdm.cc $(CLIB) $(ILIB) $(LDFLAGS)
+ 
+ dvn:	dvn.cc autocomp.h $(ULIB)
+ 	$(CXX) -o $@ dvn.cc $(ULIB) $(ILIB)