Date: Sat, 19 Dec 2020 01:34:51 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 121arm64-quarterly][biology/mummer] Failed for mummer-4.0.0.b2.2_2 in build Message-ID: <202012190134.0BJ1Yp1b019118@ampere1.nyi.freebsd.org>
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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@FreeBSD.org Last committer: gerald@FreeBSD.org Ident: $FreeBSD: branches/2020Q4/biology/mummer/Makefile 507372 2019-07-26 20:46:53Z gerald $ Log URL: http://ampere1.nyi.freebsd.org/data/121arm64-quarterly/558367/logs/mummer-4.0.0.b2.2_2.log Build URL: http://ampere1.nyi.freebsd.org/build.html?mastername=121arm64-quarterly&build=558367 Log: =>> Building biology/mummer build started at Sat Dec 19 01:33:37 UTC 2020 port directory: /usr/ports/biology/mummer package name: mummer-4.0.0.b2.2_2 building for: FreeBSD 121arm64-quarterly-job-03 12.1-RELEASE FreeBSD 12.1-RELEASE arm64 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: branches/2020Q4/biology/mummer/Makefile 507372 2019-07-26 20:46:53Z gerald $ Poudriere version: 3.2.8-8-gaf08dbda Host OSVERSION: 1300121 Jail OSVERSION: 1201000 Job Id: 03 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1201000 UNAME_v=FreeBSD 12.1-RELEASE UNAME_r=12.1-RELEASE BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-8-gaf08dbda MASTERMNT=/usr/local/poudriere/data/.m/121arm64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/121arm64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=121arm64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/121arm64-quarterly/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --disable-static --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mummer/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mummer/work HOME=/wrkdirs/usr/ports/biology/mummer/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mummer/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/mummer/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/mummer/work HOME=/wrkdirs/usr/ports/biology/mummer/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/mummer/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=12.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.0 PERL_VER=5.32 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.32 DOCSDIR="share/doc/mummer" EXAMPLESDIR="share/examples/mummer" DATADIR="share/mummer" WWWDIR="www/mummer" ETCDIR="etc/mummer" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/mummer DOCSDIR=/usr/local/share/doc/mummer EXAMPLESDIR=/usr/local/share/examples/mummer WWWDIR=/usr/local/www/mummer ETCDIR=/usr/local/etc/mummer --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: aarch64-unknown-freebsd12.1 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=12.1-RELEASE OSREL=12.1 OSVERSION=1201000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<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-1.15.10.txz [121arm64-quarterly-job-03] Installing pkg-1.15.10... [121arm64-quarterly-job-03] Extracting pkg-1.15.10: .......... 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 from /usr/ports/biology/mummer/files =========================================================================== =======================<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 [121arm64-quarterly-job-03] Installing yaggo-1.5.9... [121arm64-quarterly-job-03] `-- Installing ruby-2.6.6_1,1... [121arm64-quarterly-job-03] | `-- Installing libedit-3.1.20191231,1... [121arm64-quarterly-job-03] | `-- Extracting libedit-3.1.20191231,1: .......... done [121arm64-quarterly-job-03] | `-- Installing libffi-3.3_1... [121arm64-quarterly-job-03] | | `-- Installing indexinfo-0.3.1... [121arm64-quarterly-job-03] | | `-- Extracting indexinfo-0.3.1: .... done [121arm64-quarterly-job-03] | `-- Extracting libffi-3.3_1: .......... done [121arm64-quarterly-job-03] | `-- Installing libyaml-0.2.5... [121arm64-quarterly-job-03] | `-- Extracting libyaml-0.2.5: ......... done [121arm64-quarterly-job-03] `-- Extracting ruby-2.6.6_1,1: .......... done [121arm64-quarterly-job-03] Extracting yaggo-1.5.9: ...... done ===== Message from ruby-2.6.6_1,1: -- Some of the standard commands are provided as separate ports for ease of upgrading: <snip> 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) 524288 checking how to convert aarch64-portbld-freebsd12.1 file names to aarch64-portbld-freebsd12.1 format... func_convert_file_noop checking how to convert aarch64-portbld-freebsd12.1 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... freebsd12.1 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... freebsd12.1 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/perl5/5.32/mach/CORE checking for Perl extension target directory... /usr/local/lib/perl5/site_perl/mach/5.32 checking for Perl extensions C preprocessor flags... -DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -DUSE_THREAD_SAFE_LOCALE -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include checking for Perl extensions linker flags... -shared -L/usr/local/lib/perl5/5.32/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/tigr/show-coords.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/tigr/show-coords.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/show-coords.o src/tigr/show-coords.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/delta.o | sed 's|[^/]*$|.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/tigr/delta.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/delta.o src/tigr/delta.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/show-aligns.o | sed 's|[^/]*$|.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/tigr/show-aligns.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/show-aligns.o src/tigr/show-aligns.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/translate.o | sed 's|[^/]*$|.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/tigr/translate.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/translate.o src/tigr/translate.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/show-snps.o | sed 's|[^/]*$|.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/tigr/show-snps.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/show-snps.o src/tigr/show-snps.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/show-tiling.o | sed 's|[^/]*$|.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/tigr/show-tiling.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/show-tiling.o src/tigr/show-tiling.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/show-diff.o | sed 's|[^/]*$|.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/tigr/show-diff.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/show-diff.o src/tigr/show-diff.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/repeat-match.o | sed 's|[^/]*$|.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/tigr/repeat-match.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/repeat-match.o src/tigr/repeat-match.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/annotate.o | sed 's|[^/]*$|.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/tigr/annotate.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/annotate.o src/tigr/annotate.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/combineMUMs.o | sed 's|[^/]*$|.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/tigr/combineMUMs.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/combineMUMs.o src/tigr/combineMUMs.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/delta-filter.o | sed 's|[^/]*$|.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/tigr/delta-filter.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/delta-filter.o src/tigr/delta-filter.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/umd/nucmer_main.o | sed 's|[^/]*$|.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/umd/nucmer_main.o -MD -MP -MF $depbase.Tpo -c -o src/umd/nucmer_main.o src/umd/nucmer_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/mgaps_main.o | sed 's|[^/]*$|.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/tigr/mgaps_main.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/mgaps_main.o src/tigr/mgaps_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/postnuc_main.o | sed 's|[^/]*$|.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/tigr/postnuc_main.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/postnuc_main.o src/tigr/postnuc_main.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/prepro.o | sed 's|[^/]*$|.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/tigr/prepro.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/prepro.o src/tigr/prepro.cc &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo src/tigr/postpro.o | sed 's|[^/]*$|.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/tigr/postpro.o -MD -MP -MF $depbase.Tpo -c -o src/tigr/postpro.o src/tigr/postpro.cc &&\ mv -f $depbase.Tpo $depbase.Po sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]GNUPLOT_EXE[@],false,g' < scripts/mummerplot.pl > mummerplot && chmod a+x mummerplot sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]GNUPLOT_EXE[@],false,g' < scripts/dnadiff.pl > dnadiff && chmod a+x dnadiff sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]GNUPLOT_EXE[@],false,g' < scripts/promer.pl > promer && chmod a+x promer sed -e 's,[@]PERL[@],/usr/local/bin/perl,g' -e 's,[@]BIN_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]LIB_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5/scripts,g' -e 's,[@]LIBEXEC_DIR[@],/wrkdirs/usr/ports/biology/mummer/work/mummer-4.0.0beta2-2-g277dac5,g' -e 's,[@]GNUPLOT_EXE[@],false,g' < scripts/exact-tandems.sh > exact-tandems && chmod a+x exact-tandems depbase=`echo src/essaMEM/fasta.o | sed 's|[^/]*$|.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]: *** Waiting for unfinished jobs.... 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' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/mummer
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