necat: fix build and clean-up

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: necat: fix build and clean-up
From: Brook Milligan <brook%nmsu.edu@localhost>
Date: Tue, 6 Aug 2024 23:17:10 +0000
Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Tue Aug 6 17:15:05 2024 -0600
Changeset:	fe00f07927d9155aa0c54c8d1a48699da17b556d

Modified Files:
	necat/Makefile
	necat/distinfo
Added Files:
	necat/patches/patch-src_Makefile
	necat/patches/patch-src_fsa_logger.hpp
	necat/patches/patch-src_main.mk
	necat/patches/patch-src_pipeline_main.mk
Removed Files:
	necat/patches/patch-Makefile
	necat/patches/patch-pipeline_main.mk

Log Message:
necat: fix build and clean-up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=fe00f07927d9155aa0c54c8d1a48699da17b556d

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

diffstat:
 necat/Makefile                           | 16 +++++++++-------
 necat/distinfo                           |  6 ++++--
 necat/patches/patch-Makefile             | 18 ------------------
 necat/patches/patch-pipeline_main.mk     | 14 --------------
 necat/patches/patch-src_Makefile         | 18 ++++++++++++++++++
 necat/patches/patch-src_fsa_logger.hpp   | 14 ++++++++++++++
 necat/patches/patch-src_main.mk          | 15 +++++++++++++++
 necat/patches/patch-src_pipeline_main.mk | 14 ++++++++++++++
 8 files changed, 74 insertions(+), 41 deletions(-)

diffs:
diff --git a/necat/Makefile b/necat/Makefile
index 9e4afeb60b..d052afdbe9 100644
--- a/necat/Makefile
+++ b/necat/Makefile
@@ -1,11 +1,11 @@
 # $NetBSD$
 
-GITHUB_PROJECT=	NECAT
-GITHUB_TAG=	refs/tags/v0.0.1_update20200803
 DISTNAME=	v0.0.1_update20200803
 PKGNAME=	${GITHUB_PROJECT:tl}-${DISTNAME:S,^v,,:S,_update,.,}
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=xiaochuanle/}
+GITHUB_PROJECT=	NECAT
+GITHUB_TAG=	refs/tags/v0.0.1_update20200803
 DIST_SUBDIR=	${GITHUB_PROJECT}
 
 MAINTAINER=	pkgsrc-users%NetBSD.org@localhost
@@ -13,11 +13,13 @@ HOMEPAGE=	https://github.com/xiaochuanle/NECAT/
 COMMENT=	Error correction and de-novo assembler Nanopore reads
 #LICENSE=	# TODO: (see mk/license.mk)
 
-WRKSRC=		${WRKDIR}/NECAT-0.0.1_update20200803/src
-USE_LANGUAGES=	c c++
-USE_TOOLS+=	gmake pax perl:run
+WRKSRC=			${WRKDIR}/NECAT-0.0.1_update20200803
+BUILD_DIRS=		src
+USE_LANGUAGES=		c c++
+USE_TOOLS+=		gmake pax perl:run
+CHECK_RELRO_SUPPORTED=	no
 
-REPLACE_PERL=	pipeline/necat.pl
+REPLACE_PERL=	src/pipeline/necat.pl
 
 REPLACE_SH+=	scripts/oc2asmpm.sh
 REPLACE_SH+=	scripts/oc2cmd.sh
@@ -31,7 +33,7 @@ REPLACE_SH+=	scripts/ontsa.sh
 INSTALLATION_DIRS+=	bin
 
 do-install:
-	cd ${WRKSRC}/../${OPSYS}-${MACHINE_ARCH}/bin && ${PAX} -rw . ${DESTDIR}${PREFIX}/bin
+	cd ${WRKSRC}/bin && ${PAX} -rw . ${DESTDIR}${PREFIX}/bin
 	${CHMOD} a-x ${DESTDIR}${PREFIX}/bin/refmap.sh
 	${CHMOD} a-x ${DESTDIR}${PREFIX}/bin/run_ctgpm.sh
 	# ${RM} -r ${DESTDIR}${PREFIX}/bin/Plgd
diff --git a/necat/distinfo b/necat/distinfo
index 53988e2453..9df8c13b61 100644
--- a/necat/distinfo
+++ b/necat/distinfo
@@ -3,5 +3,7 @@ $NetBSD$
 RMD160 (NECAT/v0.0.1_update20200803.tar.gz) = 0d52e27e37ee309ddbd1434a1d245b089dfd7d24
 SHA512 (NECAT/v0.0.1_update20200803.tar.gz) = 77b5256deb480711132adfdb8763bc1247046592e2bbecacc59934a1188f49af6d8ee678e8278606aa859417fbe5c76364c627dacbdf3e3ec0bdb8a052469690
 Size (NECAT/v0.0.1_update20200803.tar.gz) = 500777 bytes
-SHA1 (patch-Makefile) = f6c03c52eaf50ba0ab8ddea39691a64805c6bb8f
-SHA1 (patch-pipeline_main.mk) = 31568393708ea14a8346f5874ef3fdb9f2f24c93
+SHA1 (patch-src_Makefile) = 56d9f7ee4a006710cee5d9d71d318e216b9f2105
+SHA1 (patch-src_fsa_logger.hpp) = d9fd5e008d4673d66fb0a26b5665e833f5a198ee
+SHA1 (patch-src_main.mk) = eba3ec54061fec4fa3c5ff2f127144851807a155
+SHA1 (patch-src_pipeline_main.mk) = f1d5fd06eaac08f2b196559d49085535a4ffffce
diff --git a/necat/patches/patch-Makefile b/necat/patches/patch-Makefile
deleted file mode 100644
index 2b42509862..0000000000
--- a/necat/patches/patch-Makefile
+++ /dev/null
@@ -1,18 +0,0 @@
-$NetBSD$
-
-Do not change MACHINETYPE needlessly.  Doing so prevents easy
-discovery of the build directory.
-
---- Makefile.orig	2020-08-03 07:31:39.000000000 +0000
-+++ Makefile
-@@ -344,10 +344,6 @@ OSTYPE      := $(shell echo `uname`)
- OSVERSION   := $(shell echo `uname -r`)
- MACHINETYPE := $(shell echo `uname -m`)
- 
--ifeq (${MACHINETYPE}, x86_64)
--  MACHINETYPE = amd64
--endif
--
- ifeq (${MACHINETYPE}, Power Macintosh)
-   MACHINETYPE = ppc
- endif
diff --git a/necat/patches/patch-pipeline_main.mk b/necat/patches/patch-pipeline_main.mk
deleted file mode 100644
index 9e42ee2392..0000000000
--- a/necat/patches/patch-pipeline_main.mk
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD$
-
-Do not set execute permissions on a non-executable file.
-
---- pipeline/main.mk.orig	2020-08-03 07:31:39.000000000 +0000
-+++ pipeline/main.mk
-@@ -23,7 +23,6 @@ ${TARGET_DIR}/Necat.pm: pipeline/Necat.p
- ${TARGET_DIR}/necat.sh: pipeline/necat.sh
- 	@if [ ! -e ${TARGET_DIR} ] ; then mkdir -p ${TARGET_DIR} ; fi
- 	cp -pf pipeline/necat.sh ${TARGET_DIR}/necat.sh
--	chmod +x ${TARGET_DIR}/necat.sh
- 
- ${TARGET_DIR}/renecat.sh: pipeline/renecat.sh
- 	@if [ ! -e ${TARGET_DIR} ] ; then mkdir -p ${TARGET_DIR} ; fi
diff --git a/necat/patches/patch-src_Makefile b/necat/patches/patch-src_Makefile
new file mode 100644
index 0000000000..5a7e4624be
--- /dev/null
+++ b/necat/patches/patch-src_Makefile
@@ -0,0 +1,18 @@
+$NetBSD$
+
+Do not change MACHINETYPE needlessly.  Doing so prevents easy
+discovery of the build directory.
+
+--- src/Makefile.orig	2020-08-03 07:31:39.000000000 +0000
++++ src/Makefile
+@@ -344,10 +344,6 @@ OSTYPE      := $(shell echo `uname`)
+ OSVERSION   := $(shell echo `uname -r`)
+ MACHINETYPE := $(shell echo `uname -m`)
+ 
+-ifeq (${MACHINETYPE}, x86_64)
+-  MACHINETYPE = amd64
+-endif
+-
+ ifeq (${MACHINETYPE}, Power Macintosh)
+   MACHINETYPE = ppc
+ endif
diff --git a/necat/patches/patch-src_fsa_logger.hpp b/necat/patches/patch-src_fsa_logger.hpp
new file mode 100644
index 0000000000..3f9895b29e
--- /dev/null
+++ b/necat/patches/patch-src_fsa_logger.hpp
@@ -0,0 +1,14 @@
+$NetBSD$
+
+Include <stdarg.h> for va_list.
+
+--- src/fsa/logger.hpp.orig	2024-08-06 21:51:50.094015916 +0000
++++ src/fsa/logger.hpp
+@@ -2,6 +2,7 @@
+ #define FSA_LOGGER_HPP
+ 
+ 
++#include <stdarg.h>  
+ #include <stdio.h>
+ #include <map>
+ #include <string>
diff --git a/necat/patches/patch-src_main.mk b/necat/patches/patch-src_main.mk
new file mode 100644
index 0000000000..57f0917713
--- /dev/null
+++ b/necat/patches/patch-src_main.mk
@@ -0,0 +1,15 @@
+$NetBSD$
+
+--- src/main.mk.orig	2020-08-03 07:31:39.000000000 +0000
++++ src/main.mk
+@@ -1,8 +1,8 @@
+ ifeq "$(strip ${BUILD_DIR})" ""
+-  BUILD_DIR    := ../$(OSTYPE)-$(MACHINETYPE)/obj
++  BUILD_DIR    := ../obj
+ endif
+ ifeq "$(strip ${TARGET_DIR})" ""
+-  TARGET_DIR   := ../$(OSTYPE)-$(MACHINETYPE)/bin
++  TARGET_DIR   := ../bin
+ endif
+ 
+ TARGET       := libontcns.a
diff --git a/necat/patches/patch-src_pipeline_main.mk b/necat/patches/patch-src_pipeline_main.mk
new file mode 100644
index 0000000000..fcca5e37ee
--- /dev/null
+++ b/necat/patches/patch-src_pipeline_main.mk
@@ -0,0 +1,14 @@
+$NetBSD$
+
+Do not set execute permissions on a non-executable file.
+
+--- src/pipeline/main.mk.orig	2020-08-03 07:31:39.000000000 +0000
++++ src/pipeline/main.mk
+@@ -23,7 +23,6 @@ ${TARGET_DIR}/Necat.pm: pipeline/Necat.p
+ ${TARGET_DIR}/necat.sh: pipeline/necat.sh
+ 	@if [ ! -e ${TARGET_DIR} ] ; then mkdir -p ${TARGET_DIR} ; fi
+ 	cp -pf pipeline/necat.sh ${TARGET_DIR}/necat.sh
+-	chmod +x ${TARGET_DIR}/necat.sh
+ 
+ ${TARGET_DIR}/renecat.sh: pipeline/renecat.sh
+ 	@if [ ! -e ${TARGET_DIR} ] ; then mkdir -p ${TARGET_DIR} ; fi
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