[package - 112arm64-quarterly][biology/mummer] Failed for mummer-4.0.0.b2.2_2 in build
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu Oct 31 11:23:43 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/2019Q4/biology/mummer/Makefile 507372 2019-07-26 20:46:53Z gerald $
Log URL: http://thunderx1.nyi.freebsd.org/data/112arm64-quarterly/515940/logs/mummer-4.0.0.b2.2_2.log
Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=112arm64-quarterly&build=515940
Log:
=>> Building biology/mummer
build started at Thu Oct 31 11:21:13 UTC 2019
port directory: /usr/ports/biology/mummer
package name: mummer-4.0.0.b2.2_2
building for: FreeBSD 112arm64-quarterly-job-19 11.2-RELEASE-p15 FreeBSD 11.2-RELEASE-p15 1102000 arm64
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: branches/2019Q4/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-1.12.0.txz
[112arm64-quarterly-job-19] Installing pkg-1.12.0...
[112arm64-quarterly-job-19] Extracting pkg-1.12.0: .......... 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 >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for mummer-4.0.0.b2.2_2
===> Applying FreeBSD patches for mummer-4.0.0.b2.2_2
===========================================================================
=======================<phase: build-depends >============================
===> mummer-4.0.0.b2.2_2 depends on executable: yaggo - not found
===> Installing existing package /packages/All/yaggo-1.5.9.txz
[112arm64-quarterly-job-19] Installing yaggo-1.5.9...
[112arm64-quarterly-job-19] `-- Installing ruby-2.6.5,1...
[112arm64-quarterly-job-19] | `-- Installing libedit-3.1.20190324,1...
[112arm64-quarterly-job-19] | `-- Extracting libedit-3.1.20190324,1: .......... done
[112arm64-quarterly-job-19] | `-- Installing libffi-3.2.1_3...
[112arm64-quarterly-job-19] | | `-- Installing indexinfo-0.3.1...
[112arm64-quarterly-job-19] | | `-- Extracting indexinfo-0.3.1: .... done
[112arm64-quarterly-job-19] | `-- Extracting libffi-3.2.1_3: .......... done
[112arm64-quarterly-job-19] | `-- Installing libyaml-0.2.2...
[112arm64-quarterly-job-19] | `-- Extracting libyaml-0.2.2: ......... done
[112arm64-quarterly-job-19] `-- Extracting ruby-2.6.5,1: .......... done
[112arm64-quarterly-job-19] Extracting yaggo-1.5.9: ...... done
=====
Message from ruby-2.6.5,1:
--
Some of the standard commands are provided as separate ports for ease
of upgrading:
<snip>
[112arm64-quarterly-job-19] Extracting automake-1.16.1_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
[112arm64-quarterly-job-19] Installing libtool-2.4.6_1...
[112arm64-quarterly-job-19] 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... aarch64-portbld-freebsd11.2
checking host system type... aarch64-portbld-freebsd11.2
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... cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking whether cc understands -c and -o together... yes
checking dependency style of cc... gcc3
checking for a sed that does not truncate output... (cached) /usr/bin/sed
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
checking for fgrep... (cached) /usr/bin/fgrep
checking for ld used by cc... /usr/bin/ld
checking if the linker (/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 aarch64-portbld-freebsd11.2 file names to aarch64-portbld-freebsd11.2 format... func_convert_file_noop
checking how to convert aarch64-portbld-freebsd11.2 file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... no
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... no
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm output from 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... cpp
checking for ANSI C header files... (cached) yes
checking for sys/types.h... (cached) yes
checking for sys/stat.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for dlfcn.h... (cached) yes
checking for objdir... .libs
checking if cc supports -fno-rtti -fno-exceptions... yes
checking for cc option to produce PIC... -fPIC -DPIC
checking if cc PIC flag -fPIC -DPIC works... yes
checking if cc static flag -static works... yes
checking if cc supports -c -o file.o... yes
checking if cc supports -c -o file.o... (cached) yes
checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... freebsd11.2 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 c++ accepts -g... yes
checking dependency style of c++... gcc3
checking how to run the C++ preprocessor... c++ -E
checking for ld used by c++... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes
checking for c++ option to produce PIC... -fPIC -DPIC
checking if c++ PIC flag -fPIC -DPIC works... yes
checking if c++ static flag -static works... yes
checking if c++ supports -c -o file.o... yes
checking if c++ supports -c -o file.o... (cached) yes
checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... freebsd11.2 ld.so
checking how to hardcode library paths into programs... immediate
checking for gcc... (cached) cc
checking whether we are using the GNU C compiler... (cached) yes
checking whether cc accepts -g... (cached) yes
checking for cc option to accept ISO C89... (cached) none needed
checking whether cc understands -c and -o together... (cached) yes
checking dependency style of 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... yes
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$||'`;\
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$||'`;\
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 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 $depbase.Plo
libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/essaMEM/sparseSA.lo -MD -MP -MF src/essaMEM/.deps/sparseSA.Tpo -c src/essaMEM/sparseSA.cpp -fPIC -DPIC -o src/essaMEM/.libs/sparseSA.o
depbase=`echo src/essaMEM/sssort_compact.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ./libtool --tag=CXX --mode=compile 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 $depbase.Plo
libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/essaMEM/sssort_compact.lo -MD -MP -MF src/essaMEM/.deps/sssort_compact.Tpo -c src/essaMEM/sssort_compact.cc -fPIC -DPIC -o src/essaMEM/.libs/sssort_compact.o
depbase=`echo src/tigr/mgaps.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ./libtool --tag=CXX --mode=compile 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 $depbase.Plo
libtool: compile: c++ -DHAVE_CONFIG_H -I. -Wall -I./include -std=c++11 -std=c++0x -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT src/tigr/mgaps.lo -MD -MP -MF src/tigr/.deps/mgaps.Tpo -c src/tigr/mgaps.cc -fPIC -DPIC -o src/tigr/.libs/mgaps.o
depbase=`echo src/tigr/postnuc.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/sh ./libtool --tag=CXX --mode=compile 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: 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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