4 files changed, 29 insertions, 26 deletions

diff --git a/biology/htslib/files/patch-Makefile b/biology/htslib/files/patch-Makefile
index 83da01f7e5e7..cb35c2f0f055 100644
--- a/biology/htslib/files/patch-Makefile
+++ b/biology/htslib/files/patch-Makefile
@@ -1,6 +1,6 @@
---- Makefile.orig	2015-02-03 16:22:23 UTC
+--- Makefile.orig	2015-12-15 16:34:33 UTC
 +++ Makefile
-@@ -22,16 +22,9 @@
+@@ -22,16 +22,7 @@
  # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  # DEALINGS IN THE SOFTWARE.
  
@@ -8,19 +8,18 @@
 -AR     = ar
 -RANLIB = ranlib
 -
--CPPFLAGS = -I.
-+CPPFLAGS += -I.
- # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
+-CPPFLAGS =
+-# TODO: probably update cram code to make it compile cleanly with -Wc++-compat
 -CFLAGS   = -g -Wall -O2
  EXTRA_CFLAGS_PIC = -fpic
 -LDFLAGS  =
--LDLIBS   =
+-LIBS     =
  
  # For now these don't work too well as samtools also needs to know to
  # add -lbz2 and -llzma if linking against the static libhts.a library.
-@@ -57,16 +50,10 @@ bindir      = $(exec_prefix)/bin
- includedir  = $(prefix)/include
+@@ -58,16 +49,10 @@ includedir  = $(prefix)/include
  libdir      = $(exec_prefix)/lib
+ libexecdir  = $(exec_prefix)/libexec
  datarootdir = $(prefix)/share
 -mandir      = $(datarootdir)/man
 +mandir      = $(prefix)/man
@@ -35,18 +34,18 @@
 -INSTALL_DIR     = $(MKDIR_P) -m 755
 +pkgconfigdir= $(exec_prefix)/libdata/pkgconfig
  
- BUILT_PROGRAMS = \
- 	bgzip \
-@@ -82,7 +69,7 @@ BUILT_TEST_PROGRAMS = \
+ # Set by config.mk if plugins are enabled
+ plugindir =
+@@ -86,7 +71,7 @@ BUILT_TEST_PROGRAMS = \
  	test/test-vcf-api \
  	test/test-vcf-sweep
  
--all: lib-static lib-shared $(BUILT_PROGRAMS) $(BUILT_TEST_PROGRAMS)
-+all: lib-static lib-shared $(BUILT_PROGRAMS)
+-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS)
++all: lib-static lib-shared $(BUILT_PROGRAMS) plugins
  
  HTSPREFIX =
  include htslib_vars.mk
-@@ -332,7 +319,7 @@ installdirs:
+@@ -361,7 +346,7 @@ installdirs:
  # and libhts.so.NN (used by client executables at runtime).
  
  install-so: libhts.so installdirs
diff --git a/biology/htslib/files/patch-configure.ac b/biology/htslib/files/patch-configure.ac
index 7e5a1a6363bc..8e1d8bc9ea64 100644
--- a/biology/htslib/files/patch-configure.ac
+++ b/biology/htslib/files/patch-configure.ac
@@ -1,11 +1,11 @@
---- configure.ac.orig	2015-02-03 16:22:23 UTC
+--- configure.ac.orig	2015-12-15 16:34:33 UTC
 +++ configure.ac
 @@ -23,7 +23,7 @@
  # DEALINGS IN THE SOFTWARE.
  
  dnl Process this file with autoconf to produce a configure script
 -AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
-+AC_INIT([HTSlib], [@PORTVERSION@],
++AC_INIT([HTSlib], [1.3],
          [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
  AC_PREREQ(2.63)  dnl This version introduced 4-argument AC_CHECK_HEADER
  AC_CONFIG_SRCDIR(hts.c)
diff --git a/biology/htslib/files/patch-cram_cram__io.c b/biology/htslib/files/patch-cram_cram__io.c
deleted file mode 100644
index 68121b22c41b..000000000000
--- a/biology/htslib/files/patch-cram_cram__io.c
+++ /dev/null
@@ -1,10 +0,0 @@
---- cram/cram_io.c.orig	2015-02-03 16:22:23 UTC
-+++ cram/cram_io.c
-@@ -53,6 +53,7 @@ OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- #include <assert.h>
- #include <stdlib.h>
- #include <string.h>
-+#include <unistd.h>
- #include <zlib.h>
- #ifdef HAVE_LIBBZ2
- #include <bzlib.h>
diff --git a/biology/htslib/files/patch-hfile__libcurl.c b/biology/htslib/files/patch-hfile__libcurl.c
new file mode 100644
index 000000000000..449debeade28
--- /dev/null
+++ b/biology/htslib/files/patch-hfile__libcurl.c
@@ -0,0 +1,14 @@
+--- hfile_libcurl.c.orig	2015-12-22 22:35:42 UTC
++++ hfile_libcurl.c
+@@ -39,6 +39,11 @@ DEALINGS IN THE SOFTWARE.  */
+ 
+ #include <curl/curl.h>
+ 
++#include <sys/param.h>
++#if defined(__FreeBSD__) && (__FreeBSD_version < 1000033) && !defined(ENOTRECOVERABLE)
++#	define ENOTRECOVERABLE EIO
++#endif
++
+ typedef struct {
+     hFILE base;
+     CURL *easy;