Index: devel/protobuf/Makefile =================================================================== RCS file: /public/netbsd-rsync/pkgsrc/devel/protobuf/Makefile,v retrieving revision 1.9 diff -u -r1.9 Makefile --- devel/protobuf/Makefile 10 Jun 2015 01:31:51 -0000 1.9 +++ devel/protobuf/Makefile 4 Aug 2016 01:41:12 -0000 @@ -14,6 +14,11 @@ USE_LIBTOOL= yes USE_LANGUAGES= c++ c +# Remove conflicts with protbuf3 +CONFIGURE_ARGS+= --program-suffix=2 +GNU_CONFIGURE_LIBDIR= ${PREFIX}/lib/protobuf2 +CONFIGURE_ARGS+= --includedir=${PREFIX}/include/protobuf2 + SET_LIBDIR= yes PKGCONFIG_OVERRIDE+= protobuf-lite.pc.in @@ -21,6 +26,11 @@ TEST_TARGET= check +# Remove conflicts with protbuf3 +post-install: + ${MV} ${DESTDIR}${PREFIX}/lib/protobuf2/pkgconfig \ + ${DESTDIR}${PREFIX}/lib + BUILDLINK_API_DEPENDS.zlib+= zlib>=1.2.0.4 .include "../../devel/zlib/buildlink3.mk" .include "../../mk/pthread.buildlink3.mk" Index: devel/protobuf/PLIST =================================================================== RCS file: /public/netbsd-rsync/pkgsrc/devel/protobuf/PLIST,v retrieving revision 1.3 diff -u -r1.3 PLIST --- devel/protobuf/PLIST 10 Jun 2015 01:31:51 -0000 1.3 +++ devel/protobuf/PLIST 4 Aug 2016 01:44:03 -0000 @@ -1,63 +1,63 @@ -@comment $NetBSD: PLIST,v 1.3 2015/06/10 01:31:51 wiedi Exp $ -bin/protoc -include/google/protobuf/compiler/code_generator.h -include/google/protobuf/compiler/command_line_interface.h -include/google/protobuf/compiler/cpp/cpp_generator.h -include/google/protobuf/compiler/importer.h -include/google/protobuf/compiler/java/java_generator.h -include/google/protobuf/compiler/parser.h -include/google/protobuf/compiler/plugin.h -include/google/protobuf/compiler/plugin.pb.h -include/google/protobuf/compiler/plugin.proto -include/google/protobuf/compiler/python/python_generator.h -include/google/protobuf/descriptor.h -include/google/protobuf/descriptor.pb.h -include/google/protobuf/descriptor.proto -include/google/protobuf/descriptor_database.h -include/google/protobuf/dynamic_message.h -include/google/protobuf/extension_set.h -include/google/protobuf/generated_enum_reflection.h -include/google/protobuf/generated_message_reflection.h -include/google/protobuf/generated_message_util.h -include/google/protobuf/io/coded_stream.h -include/google/protobuf/io/gzip_stream.h -include/google/protobuf/io/printer.h -include/google/protobuf/io/strtod.h -include/google/protobuf/io/tokenizer.h -include/google/protobuf/io/zero_copy_stream.h -include/google/protobuf/io/zero_copy_stream_impl.h -include/google/protobuf/io/zero_copy_stream_impl_lite.h -include/google/protobuf/message.h -include/google/protobuf/message_lite.h -include/google/protobuf/reflection_ops.h -include/google/protobuf/repeated_field.h -include/google/protobuf/service.h -include/google/protobuf/stubs/atomicops.h -include/google/protobuf/stubs/atomicops_internals_arm64_gcc.h -include/google/protobuf/stubs/atomicops_internals_arm_gcc.h -include/google/protobuf/stubs/atomicops_internals_arm_qnx.h -include/google/protobuf/stubs/atomicops_internals_atomicword_compat.h -include/google/protobuf/stubs/atomicops_internals_generic_gcc.h -include/google/protobuf/stubs/atomicops_internals_macosx.h -include/google/protobuf/stubs/atomicops_internals_mips_gcc.h -include/google/protobuf/stubs/atomicops_internals_pnacl.h -include/google/protobuf/stubs/atomicops_internals_solaris.h -include/google/protobuf/stubs/atomicops_internals_tsan.h -include/google/protobuf/stubs/atomicops_internals_x86_gcc.h -include/google/protobuf/stubs/atomicops_internals_x86_msvc.h -include/google/protobuf/stubs/common.h -include/google/protobuf/stubs/once.h -include/google/protobuf/stubs/platform_macros.h -include/google/protobuf/stubs/stl_util.h -include/google/protobuf/stubs/template_util.h -include/google/protobuf/stubs/type_traits.h -include/google/protobuf/text_format.h -include/google/protobuf/unknown_field_set.h -include/google/protobuf/wire_format.h -include/google/protobuf/wire_format_lite.h -include/google/protobuf/wire_format_lite_inl.h -lib/libprotobuf-lite.la -lib/libprotobuf.la -lib/libprotoc.la +@comment $NetBSD$ +bin/protoc2 +include/protobuf2/google/protobuf/compiler/code_generator.h +include/protobuf2/google/protobuf/compiler/command_line_interface.h +include/protobuf2/google/protobuf/compiler/cpp/cpp_generator.h +include/protobuf2/google/protobuf/compiler/importer.h +include/protobuf2/google/protobuf/compiler/java/java_generator.h +include/protobuf2/google/protobuf/compiler/parser.h +include/protobuf2/google/protobuf/compiler/plugin.h +include/protobuf2/google/protobuf/compiler/plugin.pb.h +include/protobuf2/google/protobuf/compiler/plugin.proto +include/protobuf2/google/protobuf/compiler/python/python_generator.h +include/protobuf2/google/protobuf/descriptor.h +include/protobuf2/google/protobuf/descriptor.pb.h +include/protobuf2/google/protobuf/descriptor.proto +include/protobuf2/google/protobuf/descriptor_database.h +include/protobuf2/google/protobuf/dynamic_message.h +include/protobuf2/google/protobuf/extension_set.h +include/protobuf2/google/protobuf/generated_enum_reflection.h +include/protobuf2/google/protobuf/generated_message_reflection.h +include/protobuf2/google/protobuf/generated_message_util.h +include/protobuf2/google/protobuf/io/coded_stream.h +include/protobuf2/google/protobuf/io/gzip_stream.h +include/protobuf2/google/protobuf/io/printer.h +include/protobuf2/google/protobuf/io/strtod.h +include/protobuf2/google/protobuf/io/tokenizer.h +include/protobuf2/google/protobuf/io/zero_copy_stream.h +include/protobuf2/google/protobuf/io/zero_copy_stream_impl.h +include/protobuf2/google/protobuf/io/zero_copy_stream_impl_lite.h +include/protobuf2/google/protobuf/message.h +include/protobuf2/google/protobuf/message_lite.h +include/protobuf2/google/protobuf/reflection_ops.h +include/protobuf2/google/protobuf/repeated_field.h +include/protobuf2/google/protobuf/service.h +include/protobuf2/google/protobuf/stubs/atomicops.h +include/protobuf2/google/protobuf/stubs/atomicops_internals_arm64_gcc.h +include/protobuf2/google/protobuf/stubs/atomicops_internals_arm_gcc.h +include/protobuf2/google/protobuf/stubs/atomicops_internals_arm_qnx.h +include/protobuf2/google/protobuf/stubs/atomicops_internals_atomicword_compat.h +include/protobuf2/google/protobuf/stubs/atomicops_internals_generic_gcc.h +include/protobuf2/google/protobuf/stubs/atomicops_internals_macosx.h +include/protobuf2/google/protobuf/stubs/atomicops_internals_mips_gcc.h +include/protobuf2/google/protobuf/stubs/atomicops_internals_pnacl.h +include/protobuf2/google/protobuf/stubs/atomicops_internals_solaris.h +include/protobuf2/google/protobuf/stubs/atomicops_internals_tsan.h +include/protobuf2/google/protobuf/stubs/atomicops_internals_x86_gcc.h +include/protobuf2/google/protobuf/stubs/atomicops_internals_x86_msvc.h +include/protobuf2/google/protobuf/stubs/common.h +include/protobuf2/google/protobuf/stubs/once.h +include/protobuf2/google/protobuf/stubs/platform_macros.h +include/protobuf2/google/protobuf/stubs/stl_util.h +include/protobuf2/google/protobuf/stubs/template_util.h +include/protobuf2/google/protobuf/stubs/type_traits.h +include/protobuf2/google/protobuf/text_format.h +include/protobuf2/google/protobuf/unknown_field_set.h +include/protobuf2/google/protobuf/wire_format.h +include/protobuf2/google/protobuf/wire_format_lite.h +include/protobuf2/google/protobuf/wire_format_lite_inl.h lib/pkgconfig/protobuf-lite.pc lib/pkgconfig/protobuf.pc +lib/protobuf2/libprotobuf-lite.la +lib/protobuf2/libprotobuf.la +lib/protobuf2/libprotoc.la Index: devel/protobuf-c/Makefile =================================================================== RCS file: /public/netbsd-rsync/pkgsrc/devel/protobuf-c/Makefile,v retrieving revision 1.2 diff -u -r1.2 Makefile --- devel/protobuf-c/Makefile 21 Feb 2016 16:04:20 -0000 1.2 +++ devel/protobuf-c/Makefile 4 Aug 2016 01:51:45 -0000 @@ -15,6 +15,8 @@ USE_TOOLS+= pkg-config aclocal autoconf automake gmake USE_LANGUAGES= c99 c++ +CONFIGURE_ENV+= PROTOC=${PREFIX}/bin/protoc2 + PKGCONFIG_OVERRIDE+= protobuf-c/libprotobuf-c.pc.in pre-configure: Index: biology/plinkseq/Makefile =================================================================== RCS file: /public/netbsd-rsync/pkgsrc/biology/plinkseq/Makefile,v retrieving revision 1.3 diff -u -r1.3 Makefile --- biology/plinkseq/Makefile 8 Feb 2014 12:27:14 -0000 1.3 +++ biology/plinkseq/Makefile 4 Aug 2016 08:25:53 -0000 @@ -13,9 +13,12 @@ GNU_CONFIGURE= yes USE_LIBTOOL= yes USE_LANGUAGES= c c++ -USE_TOOLS= bash:run +USE_TOOLS= bash:run autoconf automake autoreconf REPLACE_BASH= browser/pbrowse.in index/index.in +CONFIGURE_ARGS+= --with-protobuf-libdir=${PREFIX}/lib/protobuf2 +CONFIGURE_ARGS+= --with-protobuf-includedir=${PREFIX}/include/protobuf2 + LDFLAGS.SunOS+= -lsocket -lnsl .include "../../mk/bsd.prefs.mk" @@ -29,10 +32,13 @@ $(CP) $(FILESDIR)/pp.proto $(WRKSRC)/lib/ $(CP) $(FILESDIR)/variant.proto $(WRKSRC)/lib/ +pre-configure: + ${RUN} cd ${WRKSRC} && autoreconf -fiv + # Regenerate: pre-build: - cd $(WRKSRC)/lib && protoc --cpp_out=. pp.proto && mv pp.pb.cc pp.pb.cpp - cd $(WRKSRC)/lib && protoc --cpp_out=. variant.proto && mv variant.pb.cc variant.pb.cpp + cd $(WRKSRC)/lib && protoc2 --cpp_out=. pp.proto && mv pp.pb.cc pp.pb.cpp + cd $(WRKSRC)/lib && protoc2 --cpp_out=. variant.proto && mv variant.pb.cc variant.pb.cpp .include "../../devel/protobuf/buildlink3.mk" .include "../../mk/bsd.pkg.mk" Index: biology/plinkseq/distinfo =================================================================== RCS file: /public/netbsd-rsync/pkgsrc/biology/plinkseq/distinfo,v retrieving revision 1.4 diff -u -r1.4 distinfo --- biology/plinkseq/distinfo 2 Nov 2015 18:42:22 -0000 1.4 +++ biology/plinkseq/distinfo 4 Aug 2016 02:37:34 -0000 @@ -4,8 +4,13 @@ RMD160 (plinkseq-0.08.tar.gz) = bce0966ea5f25d8c1091157561aaf533a98595ec SHA512 (plinkseq-0.08.tar.gz) = c82db774df26988f9af377d5493cf579bbf1a219b43987f74381f795ade2340dd486c8d7d629612fd6068a023ea605540f2c972bf7fb71d665730262ef94cb80 Size (plinkseq-0.08.tar.gz) = 2991871 bytes +SHA1 (patch-browser_Makefile.am) = d8af1bb40d9694c67bdf1781a3535606ce8da2ac SHA1 (patch-browser_main.c) = 2bbeed764180b0a0e30f134b40c650cfa20bdcec SHA1 (patch-browser_mongoose.c) = 02233e0dd1f4c7923ffabf1a16b30c374253d87e +SHA1 (patch-client_Makefile.am) = acc38ca4ea15718a84e6966c4b1cb4a6d203097b +SHA1 (patch-configure.ac) = f6e1b6aa56f5c034351dcb98025521db58e1fe03 +SHA1 (patch-index_Makefile.am) = ab456acaeb109ea4bec06017465daa08e6db6b35 +SHA1 (patch-lib_Makefile.am) = a826ed1c7b638d53226202ecf0cd5e83544015ca SHA1 (patch-lib_annot.cpp) = b405bca26186ea08241ad5936c2a1b43212d8dec SHA1 (patch-lib_annot.h) = 5efccddf878b4628ae7186d59a726a157d356196 SHA1 (patch-lib_token.cpp) = 848e7b790db6a4784697482ea330b4d474731368 Index: biology/plinkseq/patches/patch-browser_Makefile.am =================================================================== RCS file: biology/plinkseq/patches/patch-browser_Makefile.am diff -N biology/plinkseq/patches/patch-browser_Makefile.am --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ biology/plinkseq/patches/patch-browser_Makefile.am 4 Aug 2016 02:37:33 -0000 @@ -0,0 +1,15 @@ +$NetBSD$ + +--- browser/Makefile.am.orig 2011-11-17 17:17:36.000000000 +0000 ++++ browser/Makefile.am +@@ -15,8 +15,8 @@ pbrowse_cgi_LDADD = ../lib/libplinkseq.l + + pbrowse_cgi_CPPFLAGS = -I../lib + +-if WITH_PROTOBUF +-pbrowse_cgi_CPPFLAGS += -I $(PROTOBUF_PREFIX)/include ++if WITH_PROTOBUF_INCLUDEDIR ++pbrowse_cgi_CPPFLAGS += -I $(PROTOBUF_INCLUDEDIR) + endif + + Index: biology/plinkseq/patches/patch-client_Makefile.am =================================================================== RCS file: biology/plinkseq/patches/patch-client_Makefile.am diff -N biology/plinkseq/patches/patch-client_Makefile.am --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ biology/plinkseq/patches/patch-client_Makefile.am 4 Aug 2016 02:37:33 -0000 @@ -0,0 +1,15 @@ +$NetBSD$ + +--- client/Makefile.am.orig 2012-01-04 04:02:24.000000000 +0000 ++++ client/Makefile.am +@@ -42,8 +42,8 @@ pseq_LDADD = ../lib/libplinkseq.la + pseq_CPPFLAGS = -I../lib + pseq_LDFLAGS = -lz -ldl + +-if WITH_PROTOBUF +-pseq_CPPFLAGS += -I $(PROTOBUF_PREFIX)/include ++if WITH_PROTOBUF_INCLUDEDIR ++pseq_CPPFLAGS += -I $(PROTOBUF_INCLUDEDIR) + endif + + if DEBUG Index: biology/plinkseq/patches/patch-configure.ac =================================================================== RCS file: biology/plinkseq/patches/patch-configure.ac diff -N biology/plinkseq/patches/patch-configure.ac --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ biology/plinkseq/patches/patch-configure.ac 4 Aug 2016 02:37:33 -0000 @@ -0,0 +1,70 @@ +$NetBSD$ + +--- configure.ac.orig 2012-02-15 20:54:35.000000000 +0000 ++++ configure.ac +@@ -11,6 +11,8 @@ AC_INIT([plinkseq], [0.08], [bthomas@atg + # foreign allows automake to run without the AUTHORS, COPYING, etc. files + AM_INIT_AUTOMAKE([-Wall -Werror foreign]) + ++AM_PROG_AR ++ + LT_PREREQ([2.2]) + LT_INIT([pic-only disable-static]) + +@@ -40,37 +42,32 @@ AM_CONDITIONAL([STATIC], [test x$static + # Protobuf dependency + # + +-# did user specify --with-protobuf? propagate to automake if she did. +-AC_ARG_WITH([protobuf], ++# did user specify --with-protobuf-libdir? propagate to automake if she did. ++AC_ARG_WITH([protobuf-libdir], + [AS_HELP_STRING( +- [--with-protobuf=/path/to/protobuf], +- [Specify path to protobuf] ++ [--with-protobuf-libdir=/path/to/protobuf/libdir], ++ [Specify path to protobuf libdir] + )], +- [AC_SUBST([PROTOBUF_PREFIX], [${withval}])], +- [protobuf=false] ++ [AC_SUBST([PROTOBUF_LIBDIR], [${withval}])], ++ [protobuf-libdir=false] + ) + +-# set WITH_PROTOBUF variable so the Makefile knows whether protobuf was specified on command line +-AM_CONDITIONAL([WITH_PROTOBUF], [test "x$protobuf" != xfalse]) +- +-# if --with-protobuf wasn't given, try to build with machine installation of protobuf +-AS_IF( +-[test "x$protobuf" = "xfalse"], +-AC_CHECK_LIB(protobuf, main, +-[AC_SUBST([HAVE_LIBPROTOBUF], [1])], +-[AC_MSG_ERROR([[ +- +-Cannot find protobuf, which is required to build PLINK/SEQ. +-Please install protobuf (2.4.1) on your system. +-If you do not have root access, you can install protobuf to +-a local directory and link to it with: ++# set WITH_PROTOBUF_LIBDIR variable so the Makefile knows whether protobuf was specified on command line ++AM_CONDITIONAL([WITH_PROTOBUF_LIBDIR], [test "x$protobuf-libdir" != xfalse]) + +- ./configure --with-protobuf=/path/to/protobuf/prefix +- +-]]) +-]) ++# did user specify --with-protobuf-includedir? propagate to automake if she did. ++AC_ARG_WITH([protobuf-includedir], ++ [AS_HELP_STRING( ++ [--with-protobuf-includedir=/path/to/protobuf/includedir], ++ [Specify path to protobuf includedir] ++ )], ++ [AC_SUBST([PROTOBUF_INCLUDEDIR], [${withval}])], ++ [protobuf-includedir=false] + ) + ++# set WITH_PROTOBUF_INCLUDEDIR variable so the Makefile knows whether protobuf was specified on command line ++AM_CONDITIONAL([WITH_PROTOBUF_INCLUDEDIR], [test "x$protobuf-includedir" != xfalse]) ++ + AC_CONFIG_FILES([ + Makefile + lib/Makefile Index: biology/plinkseq/patches/patch-index_Makefile.am =================================================================== RCS file: biology/plinkseq/patches/patch-index_Makefile.am diff -N biology/plinkseq/patches/patch-index_Makefile.am --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ biology/plinkseq/patches/patch-index_Makefile.am 4 Aug 2016 02:37:33 -0000 @@ -0,0 +1,15 @@ +$NetBSD$ + +--- index/Makefile.am.orig 2012-02-16 20:42:42.000000000 +0000 ++++ index/Makefile.am +@@ -11,8 +11,8 @@ index_cgi_LDADD = ../lib/libplinkseq.la + + index_cgi_CPPFLAGS = -I../lib + +-if WITH_PROTOBUF +-index_cgi_CPPFLAGS += -I $(PROTOBUF_PREFIX)/include ++if WITH_PROTOBUF_INCLUDEDIR ++index_cgi_CPPFLAGS += -I $(PROTOBUF_INCLUDEDIR) + endif + + Index: biology/plinkseq/patches/patch-lib_Makefile.am =================================================================== RCS file: biology/plinkseq/patches/patch-lib_Makefile.am diff -N biology/plinkseq/patches/patch-lib_Makefile.am --- /dev/null 1 Jan 1970 00:00:00 -0000 +++ biology/plinkseq/patches/patch-lib_Makefile.am 4 Aug 2016 02:37:33 -0000 @@ -0,0 +1,22 @@ +$NetBSD$ + +--- lib/Makefile.am.orig 2012-01-04 04:02:24.000000000 +0000 ++++ lib/Makefile.am +@@ -112,12 +112,13 @@ sqlite3.c + libplinkseq_la_CPPFLAGS = + libplinkseq_la_LIBADD = -lz + +-if WITH_PROTOBUF +-libplinkseq_la_CPPFLAGS += -I $(PROTOBUF_PREFIX)/include +-libplinkseq_la_LIBADD += -L$(PROTOBUF_PREFIX)/lib ++if WITH_PROTOBUF_INCLUDEDIR ++libplinkseq_la_CPPFLAGS += -I $(PROTOBUF_INCLUDEDIR) ++endif ++if WITH_PROTOBUF_LIBDIR ++libplinkseq_la_LIBADD += -L$(PROTOBUF_LIBDIR) + endif + + libplinkseq_la_LIBADD += -lprotobuf + + ACLOCAL_AMFLAGS = -I m4 +- Index: net/mosh/Makefile =================================================================== RCS file: /public/netbsd-rsync/pkgsrc/net/mosh/Makefile,v retrieving revision 1.14 diff -u -r1.14 Makefile --- net/mosh/Makefile 5 Mar 2016 11:29:08 -0000 1.14 +++ net/mosh/Makefile 4 Aug 2016 01:48:08 -0000 @@ -16,6 +16,8 @@ USE_TOOLS+= pkg-config USE_LANGUAGES+= c c++ +CONFIGURE_ENV+= PROTOC=${PREFIX}/bin/protoc2 + REPLACE_PERL+= scripts/mosh.pl .include "../../devel/ncurses/buildlink3.mk"