[package - 113armv6-quarterly][biology/mummer] Failed for mummer-4.0.0.b2.2_2 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sat Sep 26 02:38:51 UTC 2020
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri at FreeBSD.org
Last committer: gerald at FreeBSD.org
Ident: $FreeBSD: branches/2020Q3/biology/mummer/Makefile 507372 2019-07-26 20:46:53Z gerald $
Log URL: http://beefy15.nyi.freebsd.org/data/113armv6-quarterly/550049/logs/mummer-4.0.0.b2.2_2.log
Build URL: http://beefy15.nyi.freebsd.org/build.html?mastername=113armv6-quarterly&build=550049
Log:
=>> Building biology/mummer
build started at Sat Sep 26 02:36:59 UTC 2020
port directory: /usr/ports/biology/mummer
package name: mummer-4.0.0.b2.2_2
building for: FreeBSD 113armv6-quarterly-job-12 11.3-RELEASE-p5 FreeBSD 11.3-RELEASE-p5 1103000 arm
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: branches/2020Q3/biology/mummer/Makefile 507372 2019-07-26 20:46:53Z gerald $
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=======================<phase: check-sanity >============================
===> License ART10 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> mummer-4.0.0.b2.2_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.14.6.txz
[113armv6-quarterly-job-12] Installing pkg-1.14.6...
[113armv6-quarterly-job-12] Extracting pkg-1.14.6: .......... done
===> mummer-4.0.0.b2.2_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of mummer-4.0.0.b2.2_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License ART10 accepted by the user
===> Fetching all distfiles required by mummer-4.0.0.b2.2_2 for building
===========================================================================
=======================<phase: checksum >============================
===> License ART10 accepted by the user
===> Fetching all distfiles required by mummer-4.0.0.b2.2_2 for building
=> SHA256 Checksum OK for mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License ART10 accepted by the user
===> Fetching all distfiles required by mummer-4.0.0.b2.2_2 for building
===> Extracting for mummer-4.0.0.b2.2_2
=> SHA256 Checksum OK for mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
<snip>
[113armv6-quarterly-job-12] Extracting automake-1.16.2: .......... done
===> mummer-4.0.0.b2.2_2 depends on package: automake>=1.16.1 - found
===> Returning to build of mummer-4.0.0.b2.2_2
===> mummer-4.0.0.b2.2_2 depends on executable: libtoolize - not found
===> Installing existing package /packages/All/libtool-2.4.6_1.txz
[113armv6-quarterly-job-12] Installing libtool-2.4.6_1...
[113armv6-quarterly-job-12] Extracting libtool-2.4.6_1: .......... done
===> mummer-4.0.0.b2.2_2 depends on executable: libtoolize - found
===> Returning to build of mummer-4.0.0.b2.2_2
===> mummer-4.0.0.b2.2_2 depends on package: perl5>=5.30.r1<5.31 - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for mummer-4.0.0.b2.2_2
libtoolize: putting auxiliary files in '.'.
libtoolize: copying file './ltmain.sh'
libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'.
libtoolize: copying file 'm4/libtool.m4'
libtoolize: copying file 'm4/ltoptions.m4'
libtoolize: copying file 'm4/ltsugar.m4'
libtoolize: copying file 'm4/ltversion.m4'
libtoolize: copying file 'm4/lt~obsolete.m4'
configure.ac:8: installing './compile'
configure.ac:2: installing './config.guess'
configure.ac:2: installing './config.sub'
configure.ac:4: installing './install-sh'
configure.ac:4: installing './missing'
Makefile.am: installing './depcomp'
parallel-tests: installing './test-driver'
configure: loading site script /usr/ports/Templates/config.site
checking build system type... armv6-portbld-freebsd11.3
checking host system type... armv6-portbld-freebsd11.3
checking for a BSD-compatible install... /usr/bin/install -c
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checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p
checking for gawk... (cached) /usr/bin/awk
checking whether gmake sets $(MAKE)... yes
checking whether gmake supports nested variables... yes
checking whether gmake supports nested variables... (cached) yes
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checking how to associate runtime and link libraries... printf %s\n
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checking command to parse /usr/bin/nm output from /nxb-bin/usr/bin/cc object... ok
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checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
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checking if mt is a manifest tool... no
checking how to run the C preprocessor... /nxb-bin/usr/bin/cpp
checking for ANSI C header files... (cached) yes
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checking for objdir... .libs
checking if /nxb-bin/usr/bin/cc supports -fno-rtti -fno-exceptions... yes
checking for /nxb-bin/usr/bin/cc option to produce PIC... -fPIC -DPIC
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checking dynamic linker characteristics... freebsd11.3 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
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checking whether /nxb-bin/usr/bin/c++ accepts -g... yes
checking dependency style of /nxb-bin/usr/bin/c++... gcc3
checking how to run the C++ preprocessor... /nxb-bin/usr/bin/c++ -E
checking for ld used by /nxb-bin/usr/bin/c++... /nxb-bin/usr/bin/ld
checking if the linker (/nxb-bin/usr/bin/ld) is GNU ld... yes
checking whether the /nxb-bin/usr/bin/c++ linker (/nxb-bin/usr/bin/ld) supports shared libraries... yes
checking for /nxb-bin/usr/bin/c++ option to produce PIC... -fPIC -DPIC
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checking dynamic linker characteristics... freebsd11.3 ld.so
checking how to hardcode library paths into programs... immediate
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checking whether we are using the GNU C compiler... (cached) yes
checking whether /nxb-bin/usr/bin/cc accepts -g... (cached) yes
checking for /nxb-bin/usr/bin/cc option to accept ISO C89... (cached) none needed
checking whether /nxb-bin/usr/bin/cc understands -c and -o together... (cached) yes
checking dependency style of /nxb-bin/usr/bin/cc... (cached) gcc3
checking for env... /usr/bin/env
checking for OpenMP flag of C++ compiler... unknown
checking for yaggo... /usr/local/bin/yaggo
checking for gnuplot... no
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checking for __int128... no
checking if std::thread::sleep_for is supported... yes
checking for perl... (cached) /usr/local/bin/perl
checking for Perl prefix... /usr/local
checking for Perl extension include path... /usr/local/lib/perl5/5.30/mach/CORE
checking for Perl extension target directory... /usr/local/lib/perl5/site_perl/mach/5.30
checking for Perl extensions C preprocessor flags... -DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include
checking for Perl extensions linker flags... -shared -L/usr/local/lib/perl5/5.30/mach/CORE -lperl -L/usr/local/lib -fstack-protector-strong
configure: compiling with flags: CXXFLAGS=-std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating mummer.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
===========================================================================
=======================<phase: build >============================
===> Building for mummer-4.0.0.b2.2_2
gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5'
/usr/local/bin/yaggo -o src/umd/nucmer_cmdline.hpp src/umd/nucmer_cmdline.yaggo
/usr/local/bin/yaggo -o tests/generate_sequences_cmdline.hpp tests/generate_sequences_cmdline.yaggo
/usr/local/bin/yaggo -o tests/ufasta_src/dsort_cmdline.hpp tests/ufasta_src/dsort_cmdline.yaggo
/usr/local/bin/yaggo -o tests/ufasta_src/sort_cmdline.hpp tests/ufasta_src/sort_cmdline.yaggo
/usr/local/bin/yaggo -o tests/check_cigar_cmdline.hpp tests/check_cigar_cmdline.yaggo
/usr/local/bin/yaggo -o tests/check_LCP_cmdline.hpp tests/check_LCP_cmdline.yaggo
gmake all-am
gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5'
depbase=`echo src/essaMEM/fasta.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/essaMEM/fasta.o -MD -MP -MF $depbase.Tpo -c -o src/essaMEM/fasta.o src/essaMEM/fasta.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/essaMEM/mummer.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
/nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/essaMEM/mummer.o -MD -MP -MF $depbase.Tpo -c -o src/essaMEM/mummer.o src/essaMEM/mummer.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo src/essaMEM/sparseSA.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ./libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/essaMEM/sparseSA.lo -MD -MP -MF $depbase.Tpo -c -o src/essaMEM/sparseSA.lo src/essaMEM/sparseSA.cpp &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/essaMEM/sparseSA.lo -MD -MP -MF src/essaMEM/.deps/sparseSA.Tpo -c src/essaMEM/sparseSA.cpp -fPIC -DPIC -o src/essaMEM/.libs/sparseSA.o
depbase=`echo src/essaMEM/sssort_compact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ./libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/essaMEM/sssort_compact.lo -MD -MP -MF $depbase.Tpo -c -o src/essaMEM/sssort_compact.lo src/essaMEM/sssort_compact.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/essaMEM/sssort_compact.lo -MD -MP -MF src/essaMEM/.deps/sssort_compact.Tpo -c src/essaMEM/sssort_compact.cc -fPIC -DPIC -o src/essaMEM/.libs/sssort_compact.o
depbase=`echo src/tigr/mgaps.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ./libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/tigr/mgaps.lo -MD -MP -MF $depbase.Tpo -c -o src/tigr/mgaps.lo src/tigr/mgaps.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/tigr/mgaps.lo -MD -MP -MF src/tigr/.deps/mgaps.Tpo -c src/tigr/mgaps.cc -fPIC -DPIC -o src/tigr/.libs/mgaps.o
depbase=`echo src/tigr/postnuc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ./libtool --tag=CXX --mode=compile /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/tigr/postnuc.lo -MD -MP -MF $depbase.Tpo -c -o src/tigr/postnuc.lo src/tigr/postnuc.cc &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile: /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/tigr/postnuc.lo -MD -MP -MF src/tigr/.deps/postnuc.Tpo -c src/tigr/postnuc.cc -fPIC -DPIC -o src/tigr/.libs/postnuc.o
src/tigr/postnuc.cc:174:37: error: non-constant-expression cannot be narrowed from type 'signed char' to 'char' in initializer list [-Wc++11-narrowing]
Alignments.push_back({ *Mp, CurrCp->dirB } );
^~~~~~~~~~~~
src/tigr/postnuc.cc:174:37: note: insert an explicit cast to silence this issue
Alignments.push_back({ *Mp, CurrCp->dirB } );
^~~~~~~~~~~~
static_cast<char>( )
1 error generated.
gmake[2]: *** [Makefile:1903: src/tigr/postnuc.lo] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5'
gmake[1]: *** [Makefile:1110: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5'
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/mummer
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