necat: fix build and clean-up

diff --git a/necat/Makefile b/necat/Makefile
index 9e4afeb60b60220c84268aea55a65302491e9940..d052afdbe9aa2cd297932ee71fd879cd1a450067 100644 (file)
--- 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
@@ -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 53988e2453e6a53facfb4778434d1e47764f7f7a..9df8c13b61295422df84e6e2f7403ecd1e067b43 100644 (file)
--- 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-src_Makefile
similarity index 83%
rename from necat/patches/patch-Makefile
rename to necat/patches/patch-src_Makefile
index 2b425098629673ed87227a0600020c0ee788ef30..5a7e4624bedd6bd3a0c029082f150cf8104b5163 100644 (file)
--- a/necat/patches/patch-Makefile
+++ b/necat/patches/patch-src_Makefile
@@ -3,8 +3,8 @@ $NetBSD$
 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
+--- 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`)

diff --git a/necat/patches/patch-src_fsa_logger.hpp b/necat/patches/patch-src_fsa_logger.hpp
new file mode 100644 (file)
index 0000000..3f9895b
--- /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 (file)
index 0000000..57f0917
--- /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-pipeline_main.mk b/necat/patches/patch-src_pipeline_main.mk
similarity index 82%
rename from necat/patches/patch-pipeline_main.mk
rename to necat/patches/patch-src_pipeline_main.mk
index 9e42ee23921ab72d634cb23f86eda3e1841e0210..fcca5e37ee2ab3e559329e5dd624987b40d7ee3d 100644 (file)
--- a/necat/patches/patch-pipeline_main.mk
+++ b/necat/patches/patch-src_pipeline_main.mk
@@ -2,8 +2,8 @@ $NetBSD$
 
 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
+--- 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