[package - 120armv7-quarterly][biology/mummer] Failed for mummer-4.0.0.b2.2_1 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sat May 18 08:04:32 UTC 2019
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/2019Q2/biology/mummer/Makefile 487272 2018-12-12 01:35:33Z gerald $
Log URL: http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/501700/logs/mummer-4.0.0.b2.2_1.log
Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=501700
Log:
=>> Building biology/mummer
build started at Sat May 18 08:03:11 UTC 2019
port directory: /usr/ports/biology/mummer
package name: mummer-4.0.0.b2.2_1
building for: FreeBSD 120armv7-quarterly-job-15 12.0-RELEASE-p5 FreeBSD 12.0-RELEASE-p5 1200086 arm
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: branches/2019Q2/biology/mummer/Makefile 487272 2018-12-12 01:35:33Z gerald $
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=======================<phase: check-sanity >============================
===> License ART10 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> mummer-4.0.0.b2.2_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.10.5_5.txz
[120armv7-quarterly-job-15] Installing pkg-1.10.5_5...
[120armv7-quarterly-job-15] Extracting pkg-1.10.5_5: .......... done
===> mummer-4.0.0.b2.2_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of mummer-4.0.0.b2.2_1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License ART10 accepted by the user
===> Fetching all distfiles required by mummer-4.0.0.b2.2_1 for building
===========================================================================
=======================<phase: checksum >============================
===> License ART10 accepted by the user
===> Fetching all distfiles required by mummer-4.0.0.b2.2_1 for building
=> SHA256 Checksum OK for mummer4-mummer-v4.0.0beta2-2-g277dac5_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
<snip>
===> Returning to build of mummer-4.0.0.b2.2_1
===> mummer-4.0.0.b2.2_1 depends on executable: gmake - not found
===> Installing existing package /packages/All/gmake-4.2.1_3.txz
[120armv7-quarterly-job-15] Installing gmake-4.2.1_3...
[120armv7-quarterly-job-15] `-- Installing gettext-runtime-0.19.8.1_2...
[120armv7-quarterly-job-15] `-- Extracting gettext-runtime-0.19.8.1_2: .......... done
[120armv7-quarterly-job-15] Extracting gmake-4.2.1_3: .......... done
===> mummer-4.0.0.b2.2_1 depends on executable: gmake - found
===> Returning to build of mummer-4.0.0.b2.2_1
===> mummer-4.0.0.b2.2_1 depends on package: perl5>=5.28.r1<5.29 - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for mummer-4.0.0.b2.2_1
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... armv7-portbld-freebsd12.0
checking host system type... armv7-portbld-freebsd12.0
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
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
checking how to print strings... printf
checking whether gmake supports the include directive... yes (GNU style)
checking for gcc... /nxb-bin/usr/bin/cc
checking whether the C compiler works... yes
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checking for suffix of executables...
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checking whether /nxb-bin/usr/bin/cc accepts -g... yes
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checking dependency style of /nxb-bin/usr/bin/cc... gcc3
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checking for ld used by /nxb-bin/usr/bin/cc... /nxb-bin/usr/bin/ld
checking if the linker (/nxb-bin/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
checking the name lister (/usr/bin/nm) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... (cached) 262144
checking how to convert armv7-portbld-freebsd12.0 file names to armv7-portbld-freebsd12.0 format... func_convert_file_noop
checking how to convert armv7-portbld-freebsd12.0 file names to toolchain format... func_convert_file_noop
checking for /nxb-bin/usr/bin/ld option to reload object files... -r
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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
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
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 unistd.h... (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
checking if /nxb-bin/usr/bin/cc PIC flag -fPIC -DPIC works... yes
checking if /nxb-bin/usr/bin/cc static flag -static works... yes
checking if /nxb-bin/usr/bin/cc supports -c -o file.o... yes
checking if /nxb-bin/usr/bin/cc supports -c -o file.o... (cached) yes
checking whether the /nxb-bin/usr/bin/cc linker (/nxb-bin/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... freebsd12.0 ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking whether we are using the GNU C++ compiler... yes
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
checking if /nxb-bin/usr/bin/c++ PIC flag -fPIC -DPIC works... yes
checking if /nxb-bin/usr/bin/c++ static flag -static works... yes
checking if /nxb-bin/usr/bin/c++ supports -c -o file.o... yes
checking if /nxb-bin/usr/bin/c++ supports -c -o file.o... (cached) yes
checking whether the /nxb-bin/usr/bin/c++ linker (/nxb-bin/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... freebsd12.0 ld.so
checking how to hardcode library paths into programs... immediate
checking for gcc... (cached) /nxb-bin/usr/bin/cc
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
checking for gnuplot5... no
checking for gnuplot4... no
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/perl5/5.28/mach/CORE
checking for Perl extension target directory... /usr/local/lib/perl5/site_perl/mach/5.28
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/perl5/5.28/mach/CORE -lperl -L/usr/local/lib -fstack-protector-strong
configure: compiling with flags: CXXFLAGS=-std=c++0x -O2 -pipe -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_1
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 -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 -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 -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 $depbase.Plo
libtool: compile: /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fno-strict-aliasing -MT src/essaMEM/sparseSA.lo -MD -MP -MF src/essaMEM/.deps/sparseSA.Tpo -c src/essaMEM/sparseSA.cpp -fPIC -DPIC -o src/essaMEM/.libs/sparseSA.o
depbase=`echo src/essaMEM/sssort_compact.lo | sed 's|[^/]*$|.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 -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 $depbase.Plo
libtool: compile: /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fno-strict-aliasing -MT src/essaMEM/sssort_compact.lo -MD -MP -MF src/essaMEM/.deps/sssort_compact.Tpo -c src/essaMEM/sssort_compact.cc -fPIC -DPIC -o src/essaMEM/.libs/sssort_compact.o
depbase=`echo src/tigr/mgaps.lo | sed 's|[^/]*$|.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 -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 $depbase.Plo
libtool: compile: /nxb-bin/usr/bin/c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fno-strict-aliasing -MT src/tigr/mgaps.lo -MD -MP -MF src/tigr/.deps/mgaps.Tpo -c src/tigr/mgaps.cc -fPIC -DPIC -o src/tigr/.libs/mgaps.o
depbase=`echo src/tigr/postnuc.lo | sed 's|[^/]*$|.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 -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 -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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