Date: Mon, 12 Apr 2021 08:51:05 GMT From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: dd048035a8f5 - main - biology/ngs-sdk: Improve the 'install' target and other parts of Makefile, report issues to upstream. Message-ID: <202104120851.13C8p5ow052990@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=dd048035a8f50b282d6dc310f19587007eda8fc2 commit dd048035a8f50b282d6dc310f19587007eda8fc2 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2021-04-12 08:47:34 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2021-04-12 08:51:03 +0000 biology/ngs-sdk: Improve the 'install' target and other parts of Makefile, report issues to upstream. --- biology/ngs-sdk/Makefile | 35 +++++----- biology/ngs-sdk/files/patch-Makefile | 13 ---- biology/ngs-sdk/files/patch-configure | 11 ---- .../ngs-sdk/files/patch-ngs-sdk_Makefile.install | 11 ++++ .../ngs-sdk/files/patch-ngs-sdk_setup_install.perl | 13 ---- .../files/patch-ngs-sdk_setup_konfigure.perl | 75 +++++++++------------- biology/ngs-sdk/pkg-plist | 6 +- 7 files changed, 62 insertions(+), 102 deletions(-) diff --git a/biology/ngs-sdk/Makefile b/biology/ngs-sdk/Makefile index efd286d1a0d4..ca7321dc39fc 100644 --- a/biology/ngs-sdk/Makefile +++ b/biology/ngs-sdk/Makefile @@ -1,5 +1,6 @@ PORTNAME= ngs DISTVERSION= 2.11.0 +PORTREVISION= 1 CATEGORIES= biology PKGNAMESUFFIX= -sdk @@ -14,26 +15,30 @@ BROKEN_riscv64= fails to configure: unsupported architecture 'FreeBSD' NOT_FOR_ARCHS= powerpc64 NOT_FOR_ARCHS_REASON= os-arch.prl needs to be taught about powerpc64 -USES= gmake perl5 -GNU_CONFIGURE= yes +USES= compiler:c++11-lang gmake perl5 +USE_PERL5= build +USE_LDCONFIG= yes + USE_GITHUB= yes GH_ACCOUNT= ncbi -ALL_TARGET= default -USE_LDCONFIG= yes -CFLAGS+= -I${WRKSRC}/ngs-sdk/ngs/unix/${ARCH}/ +HAS_CONFIGURE= yes +CONFIGURE_ARGS= --prefix="${STAGEDIR}${PREFIX}" --build-prefix="${WRKSRC}/build" + +ALL_TARGET= ngs-sdk -post-patch: +post-extract: @cd ${WRKSRC}/ngs-sdk/ngs/unix && ${LN} -s x86_64 amd64 -do-install: - cd ${WRKSRC}/ngs-sdk && ${COPYTREE_SHARE} ngs ${STAGEDIR}/${PREFIX}/include - ${INSTALL_PROGRAM} ${WRKSRC}/ngs-sdk/${ARCH}-portbld-*/ngs-sdk/FreeBSD/clang/${ARCH}/rel/lib/libngs-sdk.so.${DISTVERSION} ${STAGEDIR}${PREFIX}/lib/ - cd ${STAGEDIR}${PREFIX}/lib/ && \ - ${LN} -s libngs-sdk.so.${DISTVERSION} libngs-sdk.so.${DISTVERSION:R:R} && \ - ${LN} -s libngs-sdk.so.${DISTVERSION:R:R} libngs-sdk.so -.for l in libngs-c++.a libngs-adapt-c++.a - ${INSTALL_LIB} ${WRKSRC}/ngs-sdk/${ARCH}-portbld-*/ngs-sdk/FreeBSD/clang/${ARCH}/rel/lib/${l}.${PORTVERSION} ${STAGEDIR}${PREFIX}/lib/${l} -.endfor +do-install: # install target from the project breaks: https://github.com/ncbi/ngs/issues/34 + # install headers + cd ${WRKSRC}/ngs-sdk && ${COPYTREE_SHARE} ngs ${STAGEDIR}${PREFIX}/include + ${RM} -r ${STAGEDIR}${PREFIX}/include/ngs/win + # install libraries + cd ${WRKSRC}/build/ngs-sdk/FreeBSD/clang/amd64/rel/lib && ${COPYTREE_SHARE} . ${STAGEDIR}${PREFIX}/lib + # remove static libs built instead of shared libs, see https://github.com/ncbi/ngs/issues/33 + cd ${STAGEDIR}${PREFIX}/lib && ${RM} libngs-c++.a* libngs-adapt-c++.a* + # strip + ${STRIP_CMD} ${STAGEDIR}${PREFIX}/lib/libngs-sdk.so.2.11.0 .include <bsd.port.mk> diff --git a/biology/ngs-sdk/files/patch-Makefile b/biology/ngs-sdk/files/patch-Makefile deleted file mode 100644 index 963de357e518..000000000000 --- a/biology/ngs-sdk/files/patch-Makefile +++ /dev/null @@ -1,13 +0,0 @@ ---- Makefile.orig 2018-06-10 19:59:04 UTC -+++ Makefile -@@ -27,9 +27,7 @@ default: subdirs - - # the sub-directories - SUBDIRS = \ -- ngs-sdk \ -- ngs-java \ -- ngs-python \ -+ ngs-sdk - - SUBDIRS_CLN = \ - $(addsuffix _cln,$(SUBDIRS)) diff --git a/biology/ngs-sdk/files/patch-configure b/biology/ngs-sdk/files/patch-configure deleted file mode 100644 index f83ac70d996a..000000000000 --- a/biology/ngs-sdk/files/patch-configure +++ /dev/null @@ -1,11 +0,0 @@ ---- configure.orig 2018-06-10 19:58:29 UTC -+++ configure -@@ -41,7 +41,7 @@ if [ "$FILENAME" != configure -a ! -s co - echo configure: error: configure should be run as ./configure - else - cd $CURDIR -- for D in ngs-sdk ngs-java ngs-python -+ for D in ngs-sdk - do - if [ -d $D ] - then echo "CONFIGURING $D" diff --git a/biology/ngs-sdk/files/patch-ngs-sdk_Makefile.install b/biology/ngs-sdk/files/patch-ngs-sdk_Makefile.install new file mode 100644 index 000000000000..b9cf320d1f6d --- /dev/null +++ b/biology/ngs-sdk/files/patch-ngs-sdk_Makefile.install @@ -0,0 +1,11 @@ +--- ngs-sdk/Makefile.install.orig 2021-04-12 08:00:01 UTC ++++ ngs-sdk/Makefile.install +@@ -37,7 +37,7 @@ LIBRARIES_TO_INSTALL = \ + ngs-c++.$(VERSION_LIBX) \ + ngs-adapt-c++.$(VERSION_LIBX) \ + +-LIB_TARGET = $(INST_LIBDIR)$(BITS) ++LIB_TARGET = $(INST_LIBDIR) + + LIBRARIES_WITH_PREFIX = \ + $(addprefix $(LIB_TARGET)/$(LPFX),$(LIBRARIES_TO_INSTALL)) diff --git a/biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl b/biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl deleted file mode 100644 index 640e227e429e..000000000000 --- a/biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl +++ /dev/null @@ -1,13 +0,0 @@ ---- ngs-sdk/setup/install.perl.orig 2018-06-10 20:03:25 UTC -+++ ngs-sdk/setup/install.perl -@@ -1283,8 +1283,8 @@ sub prepare { - ' $_{INST_JARDIR } = "$_{PREFIX}/jar"; ' . - ' $_{INST_SHAREDIR} = "$_{PREFIX}/share"; ' . - ' $_{INCDIR } = "$Bin/../include"; ' . -- ' $_{LIBDIR64 } = "$Bin/../lib64"; ' . -- ' $_{LIBDIR32 } = "$Bin/../lib32"; '; -+ ' $_{LIBDIR64 } = "$Bin/../lib"; ' . -+ ' $_{LIBDIR32 } = "$Bin/../lib"; '; - if ($HAVE{TWO_LIBS}) { - $code .= - '$_{INST_NGSLIBDIR} = "' . "$root/usr/local/ngs/ngs-sdk/lib\";" diff --git a/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl b/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl index 5a199c8ad1dd..ef1f8a936a62 100644 --- a/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl +++ b/biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl @@ -1,26 +1,33 @@ ---- ngs-sdk/setup/konfigure.perl.orig 2020-04-01 16:34:36 UTC +--- ngs-sdk/setup/konfigure.perl.orig 2021-03-15 18:08:20 UTC +++ ngs-sdk/setup/konfigure.perl -@@ -202,7 +202,7 @@ print "checking system type... " unless ($AUTORUN); +@@ -204,7 +204,7 @@ print "checking system type... " unless ($AUTORUN); my ($OS, $ARCH, $OSTYPE, $MARCH, @ARCHITECTURES) = OsArch(); println $OSTYPE unless ($AUTORUN); -unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') { -+unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win' || $OSTYPE eq 'FreeBSD') { ++unless ($OSTYPE =~ /linux/i || $OSTYPE =~ /freebsd/i || $OSTYPE =~ /darwin/i || $OSTYPE eq 'win') { println "configure: error: unsupported system '$OSTYPE'"; exit 1; } -@@ -221,6 +221,10 @@ if ($OS eq 'linux') { - println $OS_DISTRIBUTOR unless ($AUTORUN); - } +@@ -225,7 +225,7 @@ if ($OS eq 'linux') { -+if ($MARCH eq 'amd64') { -+ $MARCH = 'x86_64'; -+} -+ print "checking machine architecture... " unless ($AUTORUN); println $MARCH unless ($AUTORUN); - unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i) { -@@ -333,6 +337,16 @@ if ($OSTYPE =~ /linux/i) { +-unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) { ++unless ($MARCH =~ /x86_64/i || $MARCH =~ /amd64/i || $MARCH =~ /i?86/i || $MARCH =~ /aarch64/) { + println "configure: error: unsupported architecture '$OSTYPE':'$MARCH'"; + exit 1; + } +@@ -312,6 +312,8 @@ my $BITS; + + if ($MARCH =~ /x86_64/i) { + $BITS = 64; ++} elsif ($MARCH =~ /amd64/i) { ++ $BITS = 64; + } elsif ($MARCH eq 'fat86') { + $BITS = '32_64'; + } elsif ($MARCH =~ /i?86/i) { +@@ -337,6 +339,25 @@ if ($OSTYPE =~ /linux/i) { $OSINC = 'unix'; $TOOLS = 'gcc' unless ($TOOLS); $PYTHON = 'python'; @@ -33,40 +40,16 @@ + $EXEX = ''; + $OSINC = 'unix'; + $TOOLS = 'clang' unless ($TOOLS); -+ $PYTHON = 'python'; ++ $PYTHON = $ENV{FREEBSD_PYTHON_CMD}; ++} elsif ($OSTYPE =~ /darwin/i) { ++ $LPFX = 'lib'; ++ $OBJX = 'o'; ++ $LOBX = 'pic.o'; ++ $LIBX = 'a'; ++ $SHLX = 'dylib'; ++ $EXEX = ''; ++ $OSINC = 'unix'; ++ $TOOLS = 'clang' unless ($TOOLS); } elsif ($OSTYPE =~ /darwin/i) { $LPFX = 'lib'; $OBJX = 'o'; -@@ -379,11 +393,11 @@ if ($TOOLS =~ /gcc$/) { - } elsif ($TOOLS eq 'clang') { - $CPP = 'clang++' unless ($CPP); - $CC = 'clang -c'; -- my $versionMin = '-mmacosx-version-min=10.10'; -+ my $versionMin = ''; - $CP = "$CPP -c $versionMin"; - if ($BITS ne '32_64') { - $ARCH_FL = '-arch i386' if ($BITS == 32); -- $OPT = '-O3'; -+ $OPT = $ENV{'CXXFLAGS'}; - $AR = 'ar rc'; - $LD = "clang $ARCH_FL"; - $LP = "$CPP $versionMin $ARCH_FL"; -@@ -508,7 +522,7 @@ foreach my $href (DEPENDS()) { - $I = $t if (-e $t); - } - push ( @L, File::Spec->catdir($OPT{$o}, 'lib') ); -- push ( @L, File::Spec->catdir($OPT{$o}, 'lib64') ); -+ #push ( @L, File::Spec->catdir($OPT{$o}, 'lib64') ); - } - my ($i, $l) = find_lib($_, $I, @L); - if (defined $i || $l) { -@@ -929,8 +943,7 @@ EndText - L($F, "PIC = $PIC") if ($PIC); - if ($PKG{LNG} eq 'C') { - if ($TOOLS =~ /clang/i) { -- L($F, 'SONAME = -install_name ' . -- '$(INST_LIBDIR)$(BITS)/$(subst $(VERSION),$(MAJVERS),$(@F)) \\'); -+ L($F, 'SONAME = -Wl,-soname=$(subst $(VERSION),$(MAJVERS),$(@F)) \\'); - L($F, ' -compatibility_version $(MAJMIN) -current_version $(VERSION) \\'); - L($F, ' -flat_namespace -undefined suppress'); - } else { diff --git a/biology/ngs-sdk/pkg-plist b/biology/ngs-sdk/pkg-plist index 422d5540493d..5b9c929a1a46 100644 --- a/biology/ngs-sdk/pkg-plist +++ b/biology/ngs-sdk/pkg-plist @@ -87,10 +87,8 @@ include/ngs/unix/arm64/atomic32.h include/ngs/unix/fat86/atomic32.h include/ngs/unix/i386/atomic32.h include/ngs/unix/x86_64/atomic32.h -include/ngs/win/atomic32.h -include/ngs/win/stdbool.h -lib/libngs-adapt-c++.a -lib/libngs-c++.a +lib/libngs-adapt-c++-static.a +lib/libngs-c++-static.a lib/libngs-sdk.so lib/libngs-sdk.so.2 lib/libngs-sdk.so.2.11.0
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