!25 [sync] PR-24: Resolving ncbi-blast conflicts with bzip2 and proj

From: @openeuler-sync-bot 
Reviewed-by: @shinwell_hu 
Signed-off-by: @shinwell_hu

add-riscv-support.patch

@@ -0,0 +1,19 @@
+Author: misaka00251 <liuxin@iscas.ac.cn>
+Date:   Wed Sep 21 11:15:51 2022 +0800
+
+	Fix support for RISC-V.
+
+diff --git a/c++/src/build-system/config.guess b/c++/src/build-system/config.guess
+index f475ceb..57481db 100755
+--- a/c++/src/build-system/config.guess
++++ b/c++/src/build-system/config.guess
+@@ -979,6 +979,9 @@ EOF
+     ppc:Linux:*:*)
+ 	echo powerpc-unknown-linux-gnu
+ 	exit ;;
++	riscv32:Linux:*:* | riscv32be:Linux:*:* | riscv64:Linux:*:* | riscv64be:Linux:*:*)
++	echo ${UNAME_MACHINE}-unknown-linux-gnu
++	exit ;;
+     s390:Linux:*:* | s390x:Linux:*:*)
+ 	echo ${UNAME_MACHINE}-ibm-linux
+ 	exit ;;

disable-a-dependency-module-that-is-not-actually-use.patch

@@ -0,0 +1,53 @@
+From b84f84f9bd7b418dff6e47bdf6b3008a5ab74cf0 Mon Sep 17 00:00:00 2001
+From: herengui <herengui@kylinsec.com.cn>
+Date: Tue, 3 Dec 2024 15:16:53 +0000
+Subject: [PATCH] disable a dependency module that is not actually used
+
+Signed-off-by: herengui <herengui@kylinsec.com.cn>
+---
+ c++/src/objects/CMakeLists.txt   | 1 -
+ c++/src/objects/Makefile.in      | 2 +-
+ c++/src/objects/Makefile.sources | 2 +-
+ 3 files changed, 2 insertions(+), 3 deletions(-)
+
+diff --git a/c++/src/objects/CMakeLists.txt b/c++/src/objects/CMakeLists.txt
+index 42c240b..b37ec99 100644
+--- a/c++/src/objects/CMakeLists.txt
++++ b/c++/src/objects/CMakeLists.txt
+@@ -37,7 +37,6 @@ NCBI_add_subdirectory(
+   pcassay
+   pcassay2
+   pcsubstance
+-  proj
+   pub
+   pubmed
+   remap
+diff --git a/c++/src/objects/Makefile.in b/c++/src/objects/Makefile.in
+index 6f4ea42..c9c507b 100644
+--- a/c++/src/objects/Makefile.in
++++ b/c++/src/objects/Makefile.in
+@@ -6,7 +6,7 @@
+ USR_PROJ = sources
+ 
+ SUB_PROJ = general biblio medline pub seqcode seq seqset submit \
+-           seqedit seqsplit id1 id2 entrez2 pubmed medlars mla proj \
++           seqedit seqsplit id1 id2 entrez2 pubmed medlars mla \
+            scoremat blast blastdb blastxml blastxml2 mmdb cn3d cdd ncbimime \
+            pcsubstance pcassay pcassay2 gbseq insdseq tinyseq biotree entrezgene \
+            omssa remap seqtest taxon1 taxon3 gbproj trackmgr valerr valid \
+diff --git a/c++/src/objects/Makefile.sources b/c++/src/objects/Makefile.sources
+index cad3b3b..8c53cfe 100644
+--- a/c++/src/objects/Makefile.sources
++++ b/c++/src/objects/Makefile.sources
+@@ -13,7 +13,7 @@ include $(builddir)/Makefile.mk
+ MODULES = omssa access biblio blast blastdb blastxml blastxml2 cdd cn3d docsum biotree \
+           entrez2 entrezgene featdef gbseq general id1 id2 insdseq \
+           macro medlars medline mim mla mmdb1 mmdb2 mmdb3 ncbimime objprt \
+-          proj pub pubmed scoremat seq seqalign seqblock seqcode \
++          pub pubmed scoremat seq seqalign seqblock seqcode \
+           seqfeat seqloc seqsplit seqres seqset submit taxon1 taxon3 tinyseq \
+           pcsubstance pcassay remap homologene seqedit seqtable seqtest \
+           trackmgr gbproj valerr valid genesbyloc
+-- 
+2.43.0
+

ncbi-blast.spec

@@ -1,11 +1,15 @@
 Name:                ncbi-blast
-Version:             2.12.0
+Version:             2.14.0
-Release:             2
+Release:             3
 Summary:             NCBI BLAST finds regions of similarity between biological sequences.
 License:             Public Domain
 URL:                 https://blast.ncbi.nlm.nih.gov/Blast.cgi
-Source0:             https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-src.tar.gz
+Source0:             https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-%{version}+-src.tar.gz
-BuildRequires:       lmdb lmdb-devel gcc-c++ make
+%ifarch riscv64
+Patch0:              add-riscv-support.patch
+%endif
+Patch1:              disable-a-dependency-module-that-is-not-actually-use.patch
+BuildRequires:       gcc-c++ make cpio zlib-devel lmdb-devel bzip2-devel
 %description
 The NCBI Basic Local Alignment Search Tool (BLAST) finds regions of
 local similarity between sequences. The program compares nucleotide or
@@ -16,33 +20,53 @@ members of gene families.
 
 %prep
 %autosetup -n %{name}-%{version}+-src -p1
+%ifarch loongarch64
+%_update_config_guess
+%_update_config_sub
+%endif
 
 %build
 cd c++
 export CFLAGS="%{build_cflags}"
 export CXXFLAGS="%{build_cxxflags}"
 export LDFLAGS="%{build_ldflags}"
-./configure
+./configure  --prefix=/usr --with-dll --with-mt --with-bz2
 cd ReleaseMT/build
 sed -i "s/-fPIC/-fPIC -g/g" Makefile.mk
 %make_build all_r
 
 %install
-install -d %{buildroot}%{_bindir}
+cd c++
-install -d %{buildroot}%{_includedir}/ncbi-blast
+install -d -m 0755 %{buildroot}%{_bindir}
-install -d %{buildroot}%{_libdir}/ncbi-blast
+install -d -m 0755 %{buildroot}%{_includedir}/ncbi-tools++
-rm -rf c++/ReleaseMT/bin/windowmasker_2.2.22_adapter.py
+install -d -m 0755 %{buildroot}%{_libdir}/
-install -m 0755 c++/ReleaseMT/bin/* %{buildroot}%{_bindir}/
+rm -rf ReleaseMT/bin/windowmasker_2.2.22_adapter.py
-cp -r c++/ReleaseMT/inc/* %{buildroot}%{_includedir}/ncbi-blast
+install -m 0755 ReleaseMT/bin/* %{buildroot}%{_bindir}/
-cp c++/ReleaseMT/lib/* %{buildroot}%{_libdir}/ncbi-blast/
+cp -r ReleaseMT/inc/* %{buildroot}%{_includedir}/ncbi-tools++
+cp -r ReleaseMT/lib/* %{buildroot}%{_libdir}/
 
 %files
 %defattr(-,root,root)
 %_bindir/*
-%{_includedir}/ncbi-blast/*
+%{_includedir}/ncbi-tools++/*
-%{_libdir}/ncbi-blast/*
+%{_libdir}/*
 
 %changelog
+* Tue Dec 03 2024 herengui <herengui@kylinsec.com.cn> - 2.14.0-3
+- Resolving ncbi-blast conflicts with bzip2 and proj
+
+* Tue Apr 2 2024 zhangxianting <zhangxianting@uniontech.com> - 2.14.0-2
+- not need requires package
+
+* Fri Jul 2 2023 guoyizhang <kuoi@bioarchlinux.org> - 2.14.0-1
+- update to 2.14.0
+
+* Wed May 31 2023 huajingyun <huajingyun@loongson.cn> - 2.12.0-4
+- update config.guess and config.sub for loongarch64
+
+* Thu Nov 24 2022 misaka00251 <liuxin@iscas.ac.cn> - 2.12.0-3
+- Add riscv support
+
 * Tue Feb 15 2022 herengui <herengui@uniontech.com> - 2.12.0-2
 - add missing buildrquires.
 

ncbi-blast.yaml

@@ -0,0 +1,4 @@
+version_control: github
+src_repo: ncbi-blast/ncbi-blast
+tag_prefix: ^
+separator: .