Date: Mon, 14 Jan 2019 08:37:09 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 120armv7-quarterly][biology/unanimity] Failed for unanimity-3.1.0_2 in build Message-ID: <201901140837.x0E8b9wb006863@beefy13.nyi.freebsd.org>
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Maintainer: jwb@FreeBSD.org Last committer: tcberner@FreeBSD.org Ident: $FreeBSD: branches/2019Q1/biology/unanimity/Makefile 488341 2018-12-25 20:25:39Z tcberner $ Log URL: http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/489961/logs/unanimity-3.1.0_2.log Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=489961 Log: =>> Building biology/unanimity build started at Mon Jan 14 08:35:06 UTC 2019 port directory: /usr/ports/biology/unanimity package name: unanimity-3.1.0_2 building for: FreeBSD 120armv7-quarterly-job-21 12.0-RELEASE-p2 FreeBSD 12.0-RELEASE-p2 1200086 arm maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: branches/2019Q1/biology/unanimity/Makefile 488341 2018-12-25 20:25:39Z tcberner $ Poudriere version: 3.2.8 Host OSVERSION: 1300002 Jail OSVERSION: 1200086 Job Id: 21 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RELEASE-p2 1200086 UNAME_r=12.0-RELEASE-p2 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 QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8 MASTERMNT=/usr/local/poudriere/data/.m/120armv7-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/120armv7-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=120armv7-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/120armv7-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-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- PKG_CONFIG=pkgconf PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/unanimity/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/unanimity/work HOME=/wrkdirs/usr/ports/biology/unanimity/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/unanimity/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/unanimity/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/unanimity/work HOME=/wrkdirs/usr/ports/biology/unanimity/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/unanimity/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 DESTDIR=/wrkdirs/usr/ports/biology/unanimity/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -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-- CMAKE_BUILD_TYPE="release" PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd12 PYTHON_PYOEXTENSION=pyo PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/unanimity" EXAMPLESDIR="share/examples/unanimity" DATADIR="share/unanimity" WWWDIR="www/unanimity" ETCDIR="etc/unanimity" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/unanimity DOCSDIR=/usr/local/share/doc/unanimity EXAMPLESDIR=/usr/local/share/examples/unanimity WWWDIR=/usr/local/www/unanimity ETCDIR=/usr/local/etc/unanimity --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=arm MACHINE_ARCH=armv7 ARCH=${MACHINE_ARCH} #### /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. 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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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--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_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 6.0.1 (tags/RELEASE_601/final 335540) (based on LLVM 6.0.1) Target: armv7-unknown-freebsd12.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv7 OPSYS=FreeBSD _OSRELEASE=12.0-RELEASE-p2 OSREL=12.0 OSVERSION=1200086 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 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 BSD3CLAUSE accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> unanimity-3.1.0_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [120armv7-quarterly-job-21] Installing pkg-1.10.5_5... [120armv7-quarterly-job-21] Extracting pkg-1.10.5_5: .......... done ===> unanimity-3.1.0_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of unanimity-3.1.0_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by unanimity-3.1.0_2 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by unanimity-3.1.0_2 for building => SHA256 Checksum OK for PacificBiosciences-unanimity-v3.1.0_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ <snip> *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** ===> unanimity-3.1.0_2 depends on package: pbbam>=g20180416 - found ===> Returning to build of unanimity-3.1.0_2 ===> unanimity-3.1.0_2 depends on package: pbcopper>=g20180413 - not found ===> Installing existing package /packages/All/pbcopper-g20180413_3.txz [120armv7-quarterly-job-21] Installing pbcopper-g20180413_3... [120armv7-quarterly-job-21] Extracting pbcopper-g20180413_3: .......... done ===> unanimity-3.1.0_2 depends on package: pbcopper>=g20180413 - found ===> Returning to build of unanimity-3.1.0_2 ===> unanimity-3.1.0_2 depends on file: /usr/local/bin/cmake - not found ===> Installing existing package /packages/All/cmake-3.13.2.txz [120armv7-quarterly-job-21] Installing cmake-3.13.2... [120armv7-quarterly-job-21] `-- Installing expat-2.2.6_1... [120armv7-quarterly-job-21] `-- Extracting expat-2.2.6_1: .......... done [120armv7-quarterly-job-21] `-- Installing jsoncpp-1.8.1_5... [120armv7-quarterly-job-21] `-- Extracting jsoncpp-1.8.1_5: .......... done [120armv7-quarterly-job-21] `-- Installing libarchive-3.3.3,1... [120armv7-quarterly-job-21] | `-- Installing liblz4-1.8.3,1... [120armv7-quarterly-job-21] | `-- Extracting liblz4-1.8.3,1: .......... done [120armv7-quarterly-job-21] | `-- Installing lzo2-2.10_1... [120armv7-quarterly-job-21] | `-- Extracting lzo2-2.10_1: .......... done [120armv7-quarterly-job-21] `-- Extracting libarchive-3.3.3,1: .......... done [120armv7-quarterly-job-21] `-- Installing libuv-1.24.1... [120armv7-quarterly-job-21] `-- Extracting libuv-1.24.1: .......... done [120armv7-quarterly-job-21] `-- Installing rhash-1.3.5... [120armv7-quarterly-job-21] `-- Extracting rhash-1.3.5: .......... done [120armv7-quarterly-job-21] Extracting cmake-3.13.2: .......... done ===> unanimity-3.1.0_2 depends on file: /usr/local/bin/cmake - found ===> Returning to build of unanimity-3.1.0_2 ===> unanimity-3.1.0_2 depends on executable: ninja - not found ===> Installing existing package /packages/All/ninja-1.8.2_1,2.txz [120armv7-quarterly-job-21] Installing ninja-1.8.2_1,2... [120armv7-quarterly-job-21] `-- Installing python27-2.7.15... [120armv7-quarterly-job-21] | `-- Installing gettext-runtime-0.19.8.1_2... [120armv7-quarterly-job-21] | | `-- Installing indexinfo-0.3.1... [120armv7-quarterly-job-21] | | `-- Extracting indexinfo-0.3.1: .... done [120armv7-quarterly-job-21] | `-- Extracting gettext-runtime-0.19.8.1_2: .......... done [120armv7-quarterly-job-21] | `-- Installing libffi-3.2.1_3... [120armv7-quarterly-job-21] | `-- Extracting libffi-3.2.1_3: .......... done [120armv7-quarterly-job-21] | `-- Installing readline-7.0.5... [120armv7-quarterly-job-21] | `-- Extracting readline-7.0.5: .......... done [120armv7-quarterly-job-21] `-- Extracting python27-2.7.15: .......... done [120armv7-quarterly-job-21] Extracting ninja-1.8.2_1,2: ......... done Message from python27-2.7.15: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== ===> unanimity-3.1.0_2 depends on executable: ninja - found ===> Returning to build of unanimity-3.1.0_2 ===> unanimity-3.1.0_2 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-1.5.4,1.txz [120armv7-quarterly-job-21] Installing pkgconf-1.5.4,1... [120armv7-quarterly-job-21] Extracting pkgconf-1.5.4,1: .......... done ===> unanimity-3.1.0_2 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of unanimity-3.1.0_2 ===> unanimity-3.1.0_2 depends on file: /usr/local/bin/python2.7 - found =========================================================================== =======================<phase: lib-depends >============================ ===> unanimity-3.1.0_2 depends on shared library: libhts.so - found (/usr/local/lib/libhts.so) ===> unanimity-3.1.0_2 depends on shared library: libboost_regex.so - found (/usr/local/lib/libboost_regex.so) =========================================================================== =======================<phase: configure >============================ ===> Configuring for unanimity-3.1.0_2 ===> Performing in-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/unanimity/work/unanimity-3.1.0 -- The CXX compiler identification is Clang 6.0.1 -- The C compiler identification is Clang 6.0.1 -- Check for working CXX compiler: /nxb-bin/usr/bin/c++ -- Check for working CXX compiler: /nxb-bin/usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working C compiler: /nxb-bin/usr/bin/cc -- Check for working C compiler: /nxb-bin/usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Detecting C compile features -- Detecting C compile features - done -- Boost version: 1.69.0 -- Looking for pthread.h -- Looking for pthread.h - found -- Found Threads: TRUE -- Found PkgConfig: pkgconf (found version "1.5.4") -- Checking for module 'zlib' -- Found zlib, version 1.2.10 -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS -- Performing Test HAS_NO_UNUSED_LOCAL_TYPEDEFS - Success -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: BOOST_PYTHON_SUFFIX CMAKE_COLOR_MAKEFILE CMAKE_C_FLAGS_DEBUG CMAKE_MODULE_LINKER_FLAGS CMAKE_SHARED_LINKER_FLAGS CMAKE_VERBOSE_MAKEFILE Python_ADDITIONAL_VERSIONS -- Build files have been written to: /wrkdirs/usr/ports/biology/unanimity/work/unanimity-3.1.0 =========================================================================== =======================<phase: build >============================ ===> Building for unanimity-3.1.0_2 [1/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/ccs.dir/main/ccs.cpp.o -MF src/CMakeFiles/ccs.dir/main/ccs.cpp.o.d -o src/CMakeFiles/ccs.dir/main/ccs.cpp.o -c src/main/ccs.cpp [2/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude 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-I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/IPoaModel.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/IPoaModel.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/IPoaModel.cpp.o -c src/genomicconsensus/experimental/IPoaModel.cpp [9/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Input.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Input.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Input.cpp.o -c src/genomicconsensus/experimental/Input.cpp src/genomicconsensus/experimental/Input.cpp:72:21: warning: lambda capture 'window' is not used [-Wunused-lambda-capture] [&window, &partialHitLength](const BamRecord& lhs, const BamRecord& rhs) { ^ 1 warning generated. [10/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Intervals.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Intervals.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Intervals.cpp.o -c src/genomicconsensus/experimental/Intervals.cpp [11/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Output.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Output.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Output.cpp.o -c src/genomicconsensus/experimental/Output.cpp [12/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Settings.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Settings.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Settings.cpp.o -c src/genomicconsensus/experimental/Settings.cpp [13/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Sorting.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Sorting.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Sorting.cpp.o -c src/genomicconsensus/experimental/Sorting.cpp src/genomicconsensus/experimental/Sorting.cpp:40:32: warning: lambda capture 'window' is not used [-Wunused-lambda-capture] [&window, lengthInWindow](const BamRecord& lhs, const BamRecord& rhs) { ^ src/genomicconsensus/experimental/Sorting.cpp:49:32: warning: lambda capture 'window' is not used [-Wunused-lambda-capture] [&window, lengthInWindow](const PacBio::BAM::BamRecord& lhs, ^ 2 warnings generated. [14/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Workflow.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Workflow.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/Workflow.cpp.o -c src/genomicconsensus/experimental/Workflow.cpp [15/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/arrow/ArrowModel.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/arrow/ArrowModel.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/arrow/ArrowModel.cpp.o -c src/genomicconsensus/experimental/arrow/ArrowModel.cpp [16/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastaWriter.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastaWriter.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastaWriter.cpp.o -c src/genomicconsensus/experimental/io/FastaWriter.cpp [17/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastqWriter.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastqWriter.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/FastqWriter.cpp.o -c src/genomicconsensus/experimental/io/FastqWriter.cpp [18/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/GffWriter.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/GffWriter.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/GffWriter.cpp.o -c src/genomicconsensus/experimental/io/GffWriter.cpp [19/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/VcfWriter.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/VcfWriter.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/io/VcfWriter.cpp.o -c src/genomicconsensus/experimental/io/VcfWriter.cpp [20/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/plurality/PluralityModel.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/plurality/PluralityModel.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/plurality/PluralityModel.cpp.o -c src/genomicconsensus/experimental/plurality/PluralityModel.cpp In file included from src/genomicconsensus/experimental/plurality/PluralityModel.cpp:9: include/pacbio/genomicconsensus/experimental/plurality/Plurality.h:129:31: warning: field 'bases' is uninitialized when used here [-Wuninitialized] : bases{std::move(bases)}, frequency{frequency_} ^ 1 warning generated. [21/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/poa/PoaModel.cpp.o -MF src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/poa/PoaModel.cpp.o.d -o src/CMakeFiles/unanimity.dir/genomicconsensus/experimental/poa/PoaModel.cpp.o -c src/genomicconsensus/experimental/poa/PoaModel.cpp [22/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/ChemistryMapping.cpp.o -MF src/CMakeFiles/unanimity.dir/ChemistryMapping.cpp.o.d -o src/CMakeFiles/unanimity.dir/ChemistryMapping.cpp.o -c src/ChemistryMapping.cpp [23/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/ChemistryTriple.cpp.o -MF src/CMakeFiles/unanimity.dir/ChemistryTriple.cpp.o.d -o src/CMakeFiles/unanimity.dir/ChemistryTriple.cpp.o -c src/ChemistryTriple.cpp [24/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/Interval.cpp.o -MF src/CMakeFiles/unanimity.dir/Interval.cpp.o.d -o src/CMakeFiles/unanimity.dir/Interval.cpp.o -c src/Interval.cpp [25/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/ReadId.cpp.o -MF src/CMakeFiles/unanimity.dir/ReadId.cpp.o.d -o src/CMakeFiles/unanimity.dir/ReadId.cpp.o -c src/ReadId.cpp [26/82] /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o -MF src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o.d -o src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o -c src/SparsePoa.cpp FAILED: src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o /nxb-bin/usr/bin/c++ -I/usr/local/include/PacBio -Iinclude -Igenerated -I/usr/local/include -I/usr/local/include/htslib -Ithird-party/cpp-optparse -I/usr/local/include/pbbam -Ithird-party/cssw -Isrc -O2 -pipe -fno-strict-aliasing -Wall -Wextra -Wno-unused-parameter -Wno-unused-variable -Wno-unused-local-typedefs -O2 -pipe -fno-strict-aliasing -std=c++14 -MD -MT src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o -MF src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o.d -o src/CMakeFiles/unanimity.dir/SparsePoa.cpp.o -c src/SparsePoa.cpp In file included from src/SparsePoa.cpp:14: In file included from include/pacbio/ccs/SparseAlignment.h:18: In file included from include/pacbio/align/SparseAlignment.h:16: In file included from include/pacbio/align/FindSeeds.h:11: In file included from /usr/local/include/pbcopper/qgram/Index.h:76: /usr/local/include/pbcopper/qgram/internal/Index-inl.h:120:37: error: non-constant-expression cannot be narrowed from type 'unsigned long long' to 'size_t' (aka 'unsigned int') in initializer list [-Wc++11-narrowing] return IndexHits{&suffixArray_, iter, end, queryPos}; ^~~~ /usr/local/include/pbcopper/qgram/internal/Index-inl.h:120:37: note: insert an explicit cast to silence this issue return IndexHits{&suffixArray_, iter, end, queryPos}; ^~~~ static_cast<size_t>( ) /usr/local/include/pbcopper/qgram/internal/Index-inl.h:120:43: error: non-constant-expression cannot be narrowed from type 'unsigned long long' to 'size_t' (aka 'unsigned int') in initializer list [-Wc++11-narrowing] return IndexHits{&suffixArray_, iter, end, queryPos}; ^~~ /usr/local/include/pbcopper/qgram/internal/Index-inl.h:120:43: note: insert an explicit cast to silence this issue return IndexHits{&suffixArray_, iter, end, queryPos}; ^~~ static_cast<size_t>( ) 2 errors generated. ninja: build stopped: subcommand failed. *** Error code 1 Stop. make: stopped in /usr/ports/biology/unanimity
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