Sun Jul 9 08:39:03 2023 UTC ()
ncbi-blast+: Require at least gcc7.


(nia)
diff -r1.35 -r1.36 pkgsrc/biology/ncbi-blast+/Makefile
cvs diff -r1.35 -r1.36 pkgsrc/biology/ncbi-blast+/Makefile (switch to unified diff)

--- pkgsrc/biology/ncbi-blast+/Makefile 2023/05/28 22:48:27 1.35
+++ pkgsrc/biology/ncbi-blast+/Makefile 2023/07/09 08:39:03 1.36
@@ -1,87 +1,91 @@ @@ -1,87 +1,91 @@
1# $NetBSD: Makefile,v 1.35 2023/05/28 22:48:27 bacon Exp $ 1# $NetBSD: Makefile,v 1.36 2023/07/09 08:39:03 nia Exp $
2 2
3DISTNAME= ncbi-blast-2.14.0+-src 3DISTNAME= ncbi-blast-2.14.0+-src
4PKGNAME= ${DISTNAME:S/+-src//:S/blast/blast+/} 4PKGNAME= ${DISTNAME:S/+-src//:S/blast/blast+/}
5CATEGORIES= biology 5CATEGORIES= biology
6MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \ 6MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
7 https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/ 7 https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/
8 8
9MAINTAINER= bacon@NetBSD.org 9MAINTAINER= bacon@NetBSD.org
10HOMEPAGE= http://blast.ncbi.nlm.nih.gov/ 10HOMEPAGE= http://blast.ncbi.nlm.nih.gov/
11COMMENT= NCBI implementation of Basic Local Alignment Search Tool 11COMMENT= NCBI implementation of Basic Local Alignment Search Tool
12LICENSE= public-domain 12LICENSE= public-domain
13 13
 14# configure: error:
 15# Please upgrade to a compiler supporting C++ '17, such as GCC 7.1 or newer.
 16GCC_REQD+= 7
 17
14# Nobody does bioinformatics on 32-bit processors anymore 18# Nobody does bioinformatics on 32-bit processors anymore
15ONLY_FOR_PLATFORM= ${LP64PLATFORMS} 19ONLY_FOR_PLATFORM= ${LP64PLATFORMS}
16 20
17# Fix "undefined _ThreadRuneLocale" error on FreeBSD 10.0 21# Fix "undefined _ThreadRuneLocale" error on FreeBSD 10.0
18# Fix "unknown options" in configure 22# Fix "unknown options" in configure
19SUBST_CLASSES+= configure 23SUBST_CLASSES+= configure
20SUBST_STAGE.configure= pre-configure 24SUBST_STAGE.configure= pre-configure
21SUBST_SED.configure+= -e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|' 25SUBST_SED.configure+= -e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|'
22SUBST_SED.configure+= -e '/--infodir=DIR/d' 26SUBST_SED.configure+= -e '/--infodir=DIR/d'
23SUBST_SED.configure+= -e '/--mandir=DIR/d' 27SUBST_SED.configure+= -e '/--mandir=DIR/d'
24SUBST_FILES.configure+= src/build-system/configure 28SUBST_FILES.configure+= src/build-system/configure
25 29
26USE_TOOLS+= bash gmake perl 30USE_TOOLS+= bash gmake perl
27USE_LANGUAGES= c c++ 31USE_LANGUAGES= c c++
28GNU_CONFIGURE= yes 32GNU_CONFIGURE= yes
29GNU_CONFIGURE_STRICT= no # doesn't know --enable-option-checking 33GNU_CONFIGURE_STRICT= no # doesn't know --enable-option-checking
30REPLACE_BASH= scripts/common/impl/define_random_macros.sh 34REPLACE_BASH= scripts/common/impl/define_random_macros.sh
31REPLACE_BASH+= src/app/blast/get_species_taxids.sh 35REPLACE_BASH+= src/app/blast/get_species_taxids.sh
32REPLACE_PERL= src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl 36REPLACE_PERL= src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl
33REPLACE_PYTHON= src/app/winmasker/windowmasker_2.2.22_adapter.py 37REPLACE_PYTHON= src/app/winmasker/windowmasker_2.2.22_adapter.py
34REPLACE_PYTHON+= src/app/blast/cleanup-blastdb-volumes.py 38REPLACE_PYTHON+= src/app/blast/cleanup-blastdb-volumes.py
35MKPIE_SUPPORTED= no # Temporary fix 39MKPIE_SUPPORTED= no # Temporary fix
36 40
37# The test for amq can hang, but amq is not needed so just avoid the test 41# The test for amq can hang, but amq is not needed so just avoid the test
38# configure chooses /usr/local/bin/ar with no flags 42# configure chooses /usr/local/bin/ar with no flags
39# Resolve a conflict with libproj by moving libs to a subdir 43# Resolve a conflict with libproj by moving libs to a subdir
40CONFIGURE_ENV= ncbi_cv_prog_amq_w=no 44CONFIGURE_ENV= ncbi_cv_prog_amq_w=no
41CONFIGURE_ARGS+= AR="ar cr" --without-boost 45CONFIGURE_ARGS+= AR="ar cr" --without-boost
42CONFIGURE_ARGS+= --libdir=${PREFIX}/lib/ncbi-tools++ 46CONFIGURE_ARGS+= --libdir=${PREFIX}/lib/ncbi-tools++
43WRKSRC= ${WRKDIR}/${DISTNAME}/c++ 47WRKSRC= ${WRKDIR}/${DISTNAME}/c++
44 48
45.include "../../mk/bsd.prefs.mk" 49.include "../../mk/bsd.prefs.mk"
46 50
47.if ${OPSYS} == NetBSD 51.if ${OPSYS} == NetBSD
48# statfs is deprecated on NetBSD, but still exists in libc 52# statfs is deprecated on NetBSD, but still exists in libc
49# configure checks only for undefined reference, not for usability 53# configure checks only for undefined reference, not for usability
50CONFIGURE_ENV+= ac_cv_func_statfs=no 54CONFIGURE_ENV+= ac_cv_func_statfs=no
51.endif 55.endif
52 56
53.if ${OPSYS} == Darwin 57.if ${OPSYS} == Darwin
54CONFIGURE_ARGS+= --without-openmp 58CONFIGURE_ARGS+= --without-openmp
55.endif 59.endif
56 60
57# c++/src/objtools/edit/seq_entry_edit.cpp: In member function 'void ncbi::objects::edit::{anonymous}::CSeqdescSortMap::Init()': 61# c++/src/objtools/edit/seq_entry_edit.cpp: In member function 'void ncbi::objects::edit::{anonymous}::CSeqdescSortMap::Init()':
58# c++/src/objtools/edit/seq_entry_edit.cpp:172:44: error: array subscript has type 'char' [-Werror=char-subscripts] 62# c++/src/objtools/edit/seq_entry_edit.cpp:172:44: error: array subscript has type 'char' [-Werror=char-subscripts]
59# while (descr_insert_order[index] != 0) 63# while (descr_insert_order[index] != 0)
60# Maybe fix this later. 64# Maybe fix this later.
61BUILDLINK_TRANSFORM+= rm:-Werror=char-subscripts 65BUILDLINK_TRANSFORM+= rm:-Werror=char-subscripts
62 66
63post-install: 67post-install:
64 ${FIND} ${DESTDIR}${PREFIX} -name '\.cvs*' -exec rm -rf '{}' \; 68 ${FIND} ${DESTDIR}${PREFIX} -name '\.cvs*' -exec rm -rf '{}' \;
65 ${FIND} ${DESTDIR}${PREFIX} -name '\.subversion*' -exec rm -rf '{}' \; 69 ${FIND} ${DESTDIR}${PREFIX} -name '\.subversion*' -exec rm -rf '{}' \;
66 ${FIND} ${DESTDIR}${PREFIX} -name '\.git*' -exec rm -rf '{}' \; 70 ${FIND} ${DESTDIR}${PREFIX} -name '\.git*' -exec rm -rf '{}' \;
67.if ${OPSYS} != Darwin 71.if ${OPSYS} != Darwin
68 ${STRIP} ${DESTDIR}${PREFIX}/lib/ncbi-tools++/*.so 72 ${STRIP} ${DESTDIR}${PREFIX}/lib/ncbi-tools++/*.so
69.endif 73.endif
70 74
71.include "../../devel/zlib/buildlink3.mk" 75.include "../../devel/zlib/buildlink3.mk"
72.include "../../archivers/lzo/buildlink3.mk" 76.include "../../archivers/lzo/buildlink3.mk"
73.include "../../archivers/bzip2/buildlink3.mk" 77.include "../../archivers/bzip2/buildlink3.mk"
74.include "../../archivers/zstd/buildlink3.mk" 78.include "../../archivers/zstd/buildlink3.mk"
75.include "../../devel/pcre/buildlink3.mk" 79.include "../../devel/pcre/buildlink3.mk"
76.include "../../databases/lmdb/buildlink3.mk" 80.include "../../databases/lmdb/buildlink3.mk"
77.include "../../security/gnutls/buildlink3.mk" 81.include "../../security/gnutls/buildlink3.mk"
78.include "../../devel/gmp/buildlink3.mk" 82.include "../../devel/gmp/buildlink3.mk"
79.include "../../devel/libidn2/buildlink3.mk" 83.include "../../devel/libidn2/buildlink3.mk"
80.include "../../security/nettle/buildlink3.mk" 84.include "../../security/nettle/buildlink3.mk"
81.include "../../security/libtasn1/buildlink3.mk" 85.include "../../security/libtasn1/buildlink3.mk"
82.include "../../security/p11-kit/buildlink3.mk" 86.include "../../security/p11-kit/buildlink3.mk"
83.include "../../security/libgcrypt/buildlink3.mk" 87.include "../../security/libgcrypt/buildlink3.mk"
84.include "../../databases/sqlite3/buildlink3.mk" 88.include "../../databases/sqlite3/buildlink3.mk"
85.include "../../security/libgpg-error/buildlink3.mk" 89.include "../../security/libgpg-error/buildlink3.mk"
86.include "../../lang/python/application.mk" 90.include "../../lang/python/application.mk"
87.include "../../mk/bsd.pkg.mk" 91.include "../../mk/bsd.pkg.mk"