fix build

2 files changed, 23 insertions, 8 deletions

diff --git a/.SRCINFO b/.SRCINFO
index f1817fbfe338..4d19f36e4b52 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,7 +1,7 @@
 pkgbase = kallisto
 	pkgdesc = Quantify abundances of transcripts from RNA-Seq data
 	pkgver = 0.46.2
-	pkgrel = 1
+	pkgrel = 2
 	url = http://pachterlab.github.io/kallisto/
 	arch = i686
 	arch = x86_64
diff --git a/PKGBUILD b/PKGBUILD
index 6e3290837789..49a05b749bf0 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,6 +1,6 @@
 pkgname=kallisto
 pkgver=0.46.2
-pkgrel=1
+pkgrel=2
 pkgdesc='Quantify abundances of transcripts from RNA-Seq data'
 url="http://pachterlab.github.io/$pkgname/"
 license=(BSD)
@@ -10,19 +10,34 @@ makedepends=(cmake autoconf automake)
 source=("https://github.com/pachterlab/$pkgname/archive/v$pkgver.tar.gz")
 sha256sums=('c447ca8ddc40fcbd7d877d7c868bc8b72807aa8823a8a8d659e19bdd515baaf2')
 
+prepare() {
+	cd "$srcdir/$pkgname-$pkgver"
+
+	# https://github.com/pachterlab/kallisto/issues/303#issuecomment-884612169
+	pushd ext/htslib
+	sed -i '/AC_PROG_CC/a \
+AC_CANONICAL_HOST \
+AC_PROG_INSTALL \
+' configure.ac
+	autoreconf -i
+	autoheader
+	autoconf
+	popd
+
+	# add missing header
+	sed -i '/#include <algorithm>/a #include <limits>' src/MinCollector.cpp
+}
+
 build() {
-	(
-		cd "$srcdir/$pkgname-$pkgver/ext/htslib"
-		autoreconf
-	)
+	cd "$srcdir/$pkgname-$pkgver"
 	rm -rf build
 	mkdir -p build
 	cd build
-	cmake -DCMAKE_INSTALL_PREFIX:PATH="$pkgdir/usr" "$srcdir/$pkgname-$pkgver"
+	cmake -DCMAKE_INSTALL_PREFIX:PATH="$pkgdir/usr" ..
 	make
 }
 
 package() {
-	cd build
+	cd "$srcdir/$pkgname-$pkgver/build"
 	make install
 }