salmon: Successful build

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: salmon: Successful build
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Fri, 14 Sep 2018 15:34:14 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Sep 14 10:34:14 2018 -0500
Changeset:	1f87e1ebec061472a2204b7312880fea418fa5dd

Modified Files:
	salmon/Makefile
	salmon/PLIST
	salmon/distinfo
	salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__flagstat.c
	salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__merge.c
	salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__test.c
	salmon/patches/patch-CMakeLists.txt
	salmon/patches/patch-scripts_fetchRapMap.sh
	salmon/patches/patch-src_CMakeLists.txt
Removed Files:
	salmon/patches/patch-work_staden-io__lib-1.14.8.1_progs_scram__merge.c

Log Message:
salmon: Successful build

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=1f87e1ebec061472a2204b7312880fea418fa5dd

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 salmon/Makefile                                    | 28 +---------------------
 salmon/PLIST                                       |  3 +++
 salmon/distinfo                                    | 13 +++++-----
 ...staden-io__lib-1.14.8.1_progs_scram__flagstat.c |  1 +
 ....._staden-io__lib-1.14.8.1_progs_scram__merge.c |  1 +
 ...-.._staden-io__lib-1.14.8.1_progs_scram__test.c |  1 +
 salmon/patches/patch-CMakeLists.txt                |  1 +
 salmon/patches/patch-scripts_fetchRapMap.sh        |  1 +
 salmon/patches/patch-src_CMakeLists.txt            |  1 +
 ...rk_staden-io__lib-1.14.8.1_progs_scram__merge.c |  2 --
 10 files changed, 16 insertions(+), 36 deletions(-)

diffs:
diff --git a/salmon/Makefile b/salmon/Makefile
index 7ffe793605..aaecb4b4a6 100644
--- a/salmon/Makefile
+++ b/salmon/Makefile
@@ -5,11 +5,6 @@
 #              Thu Sep 13 14:20:25 CDT 2018               #
 ###########################################################
 
-###########################################################
-# Unconverted and partially converted FreeBSD port syntax:
-
-#LIBS+=		-L${PREFIX}/lib -lthr
-
 DISTNAME=	salmon-${PV}
 DIST_SUBDIR=	salmon
 CATEGORIES=	biology
@@ -46,37 +41,16 @@ DEPENDS=	bash>=0:../../shells/bash \
 
 USE_LANGUAGES=	c c++
 USE_TOOLS+=	cmake gmake
-# FreeBSD's SHEBANG_FILES may include bash, perl, python, etc.
-# I don't know which is which, so you'll have to finish.
-# Add bash, etc. to USE_TOOLS if used below.
-# 
 REPLACE_BASH=	scripts/*.sh
 REPLACE_PYTHON=	scripts/*.py
 USE_CMAKE=	yes
-CMAKE_ARGS+=	-DDISTDIR:PATH=${DISTDIR} \
-		https://github.com/COMBINE-lab/libgff/archive/ \
-		https://github.com/COMBINE-lab/staden-io_lib/archive/
+CMAKE_ARGS+=	-DDISTDIR:PATH=${DISTDIR} -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON
 
 CONFIGURE_ENV+=	DISTDIR=${DISTDIR} DIST_SUBDIR=salmon
-#MAKE_ENV+=	WRKDIR=${WRKDIR} DISTDIR=${DISTDIR} DIST_SUBDIR=salmon
 LDFLAGS+=	-lz
 
 PV=		0.11.3
-DATADIR=	${PREFIX}/share/salmon
-DOCSDIR=	${PREFIX}/share/doc/salmon
-EXAMPLESDIR=	${PREFIX}/share/examples/salmon
-
-# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
-# .include "../../mk/bsd.prefs.mk"
-
-# Keep this if there are user-selectable options.
-# .include "options.mk"
-
-# Specify which directories to create before install.
-# You should only need this if using your own install target.
-INSTALLATION_DIRS=	bin include lib ${PKGMANDIR}/man1 share/doc share/examples
 
-# Convert any _DEPENDS above that have a buildlink3.mk
 .include "../../devel/libgetopt/buildlink3.mk"
 .include "../../devel/zlib/buildlink3.mk"
 .include "../../devel/boost-libs/buildlink3.mk"
diff --git a/salmon/PLIST b/salmon/PLIST
index 48d96a5493..25df36c94b 100644
--- a/salmon/PLIST
+++ b/salmon/PLIST
@@ -1 +1,4 @@
 @comment $NetBSD$
+bin/salmon
+lib/libsalmon_core.a
+@pkgdir lib/pkgconfig
diff --git a/salmon/distinfo b/salmon/distinfo
index 7538b15ee2..ea01ad2bcb 100644
--- a/salmon/distinfo
+++ b/salmon/distinfo
@@ -16,10 +16,9 @@ SHA1 (salmon/v1.14.8.1.tar.gz) = c79897aa508b0cda2d96e8d1760c74b9c4e7e94e
 RMD160 (salmon/v1.14.8.1.tar.gz) = f8cfaf1198d9ae738321dffd89752a4732898399
 SHA512 (salmon/v1.14.8.1.tar.gz) = 535c6701e61a1786ceb7b22905afe702d277e0383816fba82f69af553dd22ca497bf00766f9768fd9173621632483a02ea9919437e1786008b2236c1c2c8c69f
 Size (salmon/v1.14.8.1.tar.gz) = 2506985 bytes
-SHA1 (patch-.._staden-io__lib-1.14.8.1_progs_scram__flagstat.c) = 2ac5b7bea94d4738102da0c729c4ee75c8214300
-SHA1 (patch-.._staden-io__lib-1.14.8.1_progs_scram__merge.c) = 09ee761a3630a0c9ff8ff8d1ffa7ac0faeacd91b
-SHA1 (patch-.._staden-io__lib-1.14.8.1_progs_scram__test.c) = d707e1d76817ca92862193dea5d66ca5b8a2de89
-SHA1 (patch-CMakeLists.txt) = db36ef16c1b889091fd6231e61f5a0fe926de596
-SHA1 (patch-scripts_fetchRapMap.sh) = 616f79e16a67575f9d684ce351f7e31d002912f3
-SHA1 (patch-src_CMakeLists.txt) = 824564cd7592f02902e607206c8bbb0bd4049f04
-SHA1 (patch-work_staden-io__lib-1.14.8.1_progs_scram__merge.c) = adc83b19e793491b1c6ea0fd8b46cd9f32e592fc
+SHA1 (patch-.._staden-io__lib-1.14.8.1_progs_scram__flagstat.c) = cee5861638874d34abf63584338a8f795acf0abd
+SHA1 (patch-.._staden-io__lib-1.14.8.1_progs_scram__merge.c) = 24cbbbd497dafe44ecfb3d9487ca57607ba3e7cb
+SHA1 (patch-.._staden-io__lib-1.14.8.1_progs_scram__test.c) = 30642ccd969e7d995d2753ce4ef07dca42d728f5
+SHA1 (patch-CMakeLists.txt) = 518850e191c9c42dcddc7fab837c7547be168ffc
+SHA1 (patch-scripts_fetchRapMap.sh) = 8ead0056969ab6719cc3dd1d2130235a526f6c8d
+SHA1 (patch-src_CMakeLists.txt) = 87330faf34660a0dbb42d87f7fa71a0840ecf456
diff --git a/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__flagstat.c b/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__flagstat.c
index 58611a7a40..6e3adfe81c 100644
--- a/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__flagstat.c
+++ b/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__flagstat.c
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Needed by pkgsrc on all platforms
 --- ../staden-io_lib-1.14.8.1/progs/scram_flagstat.c.orig	2018-09-13 20:14:26.052077584 +0000
 +++ ../staden-io_lib-1.14.8.1/progs/scram_flagstat.c
 @@ -45,9 +45,7 @@
diff --git a/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__merge.c b/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__merge.c
index 9815811a84..cb8e5d7132 100644
--- a/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__merge.c
+++ b/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__merge.c
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Needed by pkgsrc on all platforms
 --- ../staden-io_lib-1.14.8.1/progs/scram_merge.c.orig	2018-09-13 20:12:38.101447761 +0000
 +++ ../staden-io_lib-1.14.8.1/progs/scram_merge.c
 @@ -45,9 +45,7 @@
diff --git a/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__test.c b/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__test.c
index 3e5bc4db8b..34cb1f67cd 100644
--- a/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__test.c
+++ b/salmon/patches/patch-.._staden-io__lib-1.14.8.1_progs_scram__test.c
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Needed by pkgsrc on all platforms
 --- ../staden-io_lib-1.14.8.1/progs/scram_test.c.orig	2018-09-13 20:14:39.851669404 +0000
 +++ ../staden-io_lib-1.14.8.1/progs/scram_test.c
 @@ -45,9 +45,7 @@
diff --git a/salmon/patches/patch-CMakeLists.txt b/salmon/patches/patch-CMakeLists.txt
index 0adbd8b02f..f50cc72409 100644
--- a/salmon/patches/patch-CMakeLists.txt
+++ b/salmon/patches/patch-CMakeLists.txt
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Unbundle deps, eliminate build phase downloads
 --- CMakeLists.txt.orig	2018-08-29 22:38:43.000000000 +0000
 +++ CMakeLists.txt
 @@ -47,7 +47,7 @@ set(CPACK_PACKAGE_NAME
diff --git a/salmon/patches/patch-scripts_fetchRapMap.sh b/salmon/patches/patch-scripts_fetchRapMap.sh
index 8f2ee529c2..9837e3c53f 100644
--- a/salmon/patches/patch-scripts_fetchRapMap.sh
+++ b/salmon/patches/patch-scripts_fetchRapMap.sh
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Eliminate build phase download
 --- scripts/fetchRapMap.sh.orig	2018-09-11 14:54:51 UTC
 +++ scripts/fetchRapMap.sh
 @@ -30,7 +30,7 @@ EXPECTED_SHA256=b863548383448c21a862cc56
diff --git a/salmon/patches/patch-src_CMakeLists.txt b/salmon/patches/patch-src_CMakeLists.txt
index 9414aef0c9..3c876b44e4 100644
--- a/salmon/patches/patch-src_CMakeLists.txt
+++ b/salmon/patches/patch-src_CMakeLists.txt
@@ -1,5 +1,6 @@
 $NetBSD$
 
+# Unbundle deps
 --- src/CMakeLists.txt.orig	2018-09-10 20:40:46 UTC
 +++ src/CMakeLists.txt
 @@ -2,7 +2,7 @@ include_directories(
diff --git a/salmon/patches/patch-work_staden-io__lib-1.14.8.1_progs_scram__merge.c b/salmon/patches/patch-work_staden-io__lib-1.14.8.1_progs_scram__merge.c
deleted file mode 100644
index afc76512f4..0000000000
--- a/salmon/patches/patch-work_staden-io__lib-1.14.8.1_progs_scram__merge.c
+++ /dev/null
@@ -1,2 +0,0 @@
-$NetBSD$
-
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