Update to fix compile error related to ToUpper()

3 files changed, 47 insertions, 12 deletions

diff --git a/.SRCINFO b/.SRCINFO
index d0681fdc95b8..bebb11d64c22 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,12 +1,13 @@
+# Generated by mksrcinfo v8
+# Sat Apr  8 18:40:29 UTC 2017
 pkgbase = dnaa
 	pkgdesc = An analysis package for short reads from next-generation sequencing
 	pkgver = 0.1.2
-	pkgrel = 3
-	url = http://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Main_Page
+	pkgrel = 4
+	url = https://sourceforge.net/projects/dnaa/
 	arch = i686
 	arch = x86_64
 	license = GPL2
-	makedepends = gawk
 	depends = zlib
 	depends = bzip2
 	depends = r
@@ -15,9 +16,11 @@ pkgbase = dnaa
 	source = http://downloads.sourceforge.net/project/bfast/bfast/0.7.0/bfast-0.7.0a.tar.gz
 	source = http://downloads.sourceforge.net/project/samtools/samtools/0.1.18/samtools-0.1.18.tar.bz2
 	source = http://downloads.sourceforge.net/project/dnaa/dnaa/0.1.2/dnaa-0.1.2.tar.gz
-	md5sums = 9b0574dce903ab83e39e371b0a3bbbc6
-	md5sums = 71dab132e21c0766f0de84c2371a9157
-	md5sums = a11eb449af9bf14906d00fdba5150ead
+	source = ToUpper_build_fix.patch
+	sha256sums = ed8de49693165a87d5dbef352207c424b1bf6f670a83acf49a4f4f188444995e
+	sha256sums = f3faaf34430d4782956562eb72906289e8e34d44d0c4d73837bdbeead7746b16
+	sha256sums = e6549590066de19e7c5989404830fa3ea82607b864a25147ca16b20a28dd6b68
+	sha256sums = 7efc85235c49789b208b7b0b879241b608cccd16ec949fc2d7ad09800ea3ff8c
 
 pkgname = dnaa
 
diff --git a/PKGBUILD b/PKGBUILD
index a2942376547c..28d0614e629b 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -2,13 +2,12 @@
 
 pkgname=dnaa
 pkgver=0.1.2
-pkgrel=3
+pkgrel=4
 pkgdesc='An analysis package for short reads from next-generation sequencing'
 arch=('i686' 'x86_64')
-url="http://sourceforge.net/apps/mediawiki/dnaa/index.php?title=Main_Page"
+url="https://sourceforge.net/projects/dnaa/"
 license=('GPL2')
 depends=('zlib' 'bzip2' 'r' 'perl')
-makedepends=('gawk')
 conflicts=('dwgsim')
 
 # Upstream doesn't provide a way to use already-installed bfast or samtools...
@@ -16,8 +15,13 @@ source=(
 "http://downloads.sourceforge.net/project/bfast/bfast/0.7.0/bfast-0.7.0a.tar.gz"
 "http://downloads.sourceforge.net/project/samtools/samtools/0.1.18/samtools-0.1.18.tar.bz2"
 "http://downloads.sourceforge.net/project/${pkgname}/${pkgname}/${pkgver}/${pkgname}-${pkgver}.tar.gz"
+"ToUpper_build_fix.patch" # fix compile error
 )
 
+prepare() {
+  patch -p1 < ToUpper_build_fix.patch
+}
+
 build() {
   cd ${pkgname}-${pkgver}
   [[ ! -L bfast ]] && ln -s ../bfast-0.7.0a bfast
@@ -30,6 +34,8 @@ package() {
   cd ${pkgname}-${pkgver}
   make DESTDIR=${pkgdir} install
 }
-md5sums=('9b0574dce903ab83e39e371b0a3bbbc6'
-         '71dab132e21c0766f0de84c2371a9157'
-         'a11eb449af9bf14906d00fdba5150ead')
+
+sha256sums=('ed8de49693165a87d5dbef352207c424b1bf6f670a83acf49a4f4f188444995e'
+            'f3faaf34430d4782956562eb72906289e8e34d44d0c4d73837bdbeead7746b16'
+            'e6549590066de19e7c5989404830fa3ea82607b864a25147ca16b20a28dd6b68'
+            '7efc85235c49789b208b7b0b879241b608cccd16ec949fc2d7ad09800ea3ff8c')
diff --git a/ToUpper_build_fix.patch b/ToUpper_build_fix.patch
new file mode 100644
index 000000000000..650015550377
--- /dev/null
+++ b/ToUpper_build_fix.patch
@@ -0,0 +1,26 @@
+diff --git a/bfast-0.7.0a/bfast/BLib.c b/bfast-0.7.0a/bfast/BLib.c
+index 45f1488..1894a6b 100644
+--- a/bfast-0.7.0a/bfast/BLib.c
++++ b/bfast-0.7.0a/bfast/BLib.c
+@@ -90,7 +90,7 @@ void ToLowerRead(char *r, int readLength)
+ }
+ 
+ /* TODO */
+-inline char ToUpper(char a)
++char ToUpper(char a)
+ {
+   if(97 <= a && a < 122) return (char)(a - 32);
+   return a;
+diff --git a/bfast-0.7.0a/bfast/BLib.h b/bfast-0.7.0a/bfast/BLib.h
+index 6c87810..c116899 100644
+--- a/bfast-0.7.0a/bfast/BLib.h
++++ b/bfast-0.7.0a/bfast/BLib.h
+@@ -16,7 +16,7 @@ int GetFastaHeaderLine(FILE*, char*);
+ int ParseFastaHeaderLine(char*);
+ char ToLower(char);
+ void ToLowerRead(char*, int);
+-inline char ToUpper(char);
++char ToUpper(char);
+ void ToUpperRead(char*, int);
+ void ReverseRead(char*, char*, int);
+ void ReverseReadFourBit(int8_t*, int8_t*, int);