Date: Mon, 27 May 2019 11:15:15 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-armv6-default][biology/seqan-apps] Failed for seqan-apps-2.4.0_6 in package Message-ID: <201905271115.x4RBFFHf048153@beefy8.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: h2+fbsdports@fsfe.org Last committer: jbeich@FreeBSD.org Ident: $FreeBSD: head/biology/seqan-apps/Makefile 498698 2019-04-12 06:36:31Z jbeich $ Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p502330_s348151/logs/seqan-apps-2.4.0_6.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p502330_s348151 Log: =>> Building biology/seqan-apps build started at Sun May 26 23:31:25 UTC 2019 port directory: /usr/ports/biology/seqan-apps package name: seqan-apps-2.4.0_6 building for: FreeBSD head-armv6-default-job-14 13.0-CURRENT FreeBSD 13.0-CURRENT 1300029 arm maintained by: h2+fbsdports@fsfe.org Makefile ident: $FreeBSD: head/biology/seqan-apps/Makefile 498698 2019-04-12 06:36:31Z jbeich $ Poudriere version: 3.2.8-4-g701d8fe1 Host OSVERSION: 1300018 Jail OSVERSION: 1300029 Job Id: 14 !!! Jail is newer than host. (Jail: 1300029, Host: 1300018) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv6 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1300029 UNAME_v=FreeBSD 13.0-CURRENT 1300029 UNAME_r=13.0-CURRENT 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=3.2.8-4-g701d8fe1 MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen PWD=/usr/local/poudriere/data/.m/head-armv6-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-armv6-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-armv6-default/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--- ===> The following configuration options are available for seqan-apps-2.4.0_6: ====> Options available for the radio ARCH: you can only select none or one of them SSE4=off: Use SSE4 and POPCNT instructions AVX2=off: Use SSE4, AVX2 and POPCNT instructions NATIVE=off: Use all available instruction sets (-march=native) ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- h2+fbsdports@fsfe.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqan-apps/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/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqan-apps/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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" DESTDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc8" CFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -fno-strict-aliasing " CPP="cpp8" CPPFLAGS="" LDFLAG S=" -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 " LIBS="" CXX="g++8" CXXFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 " 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" RM_I386="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/seqan-apps" EXAMPLESDIR="share/examples/seqan-apps" DATADIR="share/seqan-apps" WWWDIR="www/seqan-apps" ETCDIR="etc/seqan-apps" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqan-apps DOCSDIR=/usr/local/share/doc/seqan-apps EXAMPLESDIR=/usr/local/share/examples/seqan-apps WWWDIR=/usr/local/www/seqan-apps ETCDIR=/usr/local/etc/seqan-apps --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=armv6 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. 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 # 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 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: armv6-unknown-freebsd13.0-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 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=armv6 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300029 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 LGPL3 GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> seqan-apps-2.4.0_6 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [head-armv6-default-job-14] Installing pkg-1.10.5_5... [head-armv6-default-job-14] Extracting pkg-1.10.5_5: .......... done ===> seqan-apps-2.4.0_6 depends on file: /usr/local/sbin/pkg - found <snip> /usr/local/lib/gcc8/include/c++/bits/vector.tcc:413:7: note: parameter passing for argument of type 'std::vector<long long int>::iterator' {aka '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >'} changed in GCC 7.1 vector<_Tp, _Alloc>:: ^~~~~~~~~~~~~~~~~~~ /usr/local/lib/gcc8/include/c++/bits/vector.tcc: In member function 'void MasonSimulatorApp::_initContigPicker()': /usr/local/lib/gcc8/include/c++/bits/vector.tcc:109:4: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int> >' changed in GCC 7.1 _M_realloc_insert(end(), std::forward<_Args>(__args)...); ^~~~~~~~~~~~~~~~~ [123/133] : && /usr/local/bin/g++8 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/mason2/CMakeFiles/mason_simulator.dir/mason_simulator.cpp.o -o bin/mason_simulator -lexecinfo -lelf -lz apps/mason2/libmason_sim.a -lexecinfo -lelf -lz && : [124/133] /usr/local/bin/g++8 -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -MF apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o.d -o apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_frag_sequencing.cpp [125/133] : && /usr/local/bin/g++8 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/mason2/CMakeFiles/mason_frag_sequencing.dir/mason_frag_sequencing.cpp.o -o bin/mason_frag_sequencing -lexecinfo -lelf -lz apps/mason2/libmason_sim.a -lexecinfo -lelf -lz && : [126/133] /usr/local/bin/g++8 -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -MF apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o.d -o apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_methylation.cpp [127/133] : && /usr/local/bin/g++8 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/mason2/CMakeFiles/mason_methylation.dir/mason_methylation.cpp.o -o bin/mason_methylation -lexecinfo -lelf -lz apps/mason2/libmason_sim.a -lexecinfo -lelf -lz && : [128/133] /usr/local/bin/g++8 -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o -MF apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o.d -o apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_variator.cpp [129/133] : && /usr/local/bin/g++8 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/mason2/CMakeFiles/mason_variator.dir/mason_variator.cpp.o -o bin/mason_variator -lexecinfo -lelf -lz apps/mason2/libmason_sim.a -lexecinfo -lelf -lz && : [130/133] /usr/local/bin/g++8 -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o -MF apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o.d -o apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_genome.cpp [131/133] : && /usr/local/bin/g++8 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/mason2/CMakeFiles/mason_genome.dir/mason_genome.cpp.o -o bin/mason_genome -lexecinfo -lelf -lz apps/mason2/libmason_sim.a -lexecinfo -lelf -lz && : [132/133] /usr/local/bin/g++8 -DSEQAN_APP_VERSION=\"2.0.9\" -DSEQAN_DATE=\"\" -DSEQAN_HAS_EXECINFO=1 -DSEQAN_HAS_OPENMP=1 -DSEQAN_HAS_ZLIB=1 -DSEQAN_REVISION=\"tarball\" -D_FILE_OFFSET_BITS=64 -D_GLIBCXX_USE_C99=1 -D_LARGEFILE_SOURCE -I/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -DSEQAN_GLOBAL_EXCEPTION_HANDLER=1 -MD -MT apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -MF apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o.d -o apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -c /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/mason2/mason_materializer.cpp [133/133] : && /usr/local/bin/g++8 -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -W -Wall -pedantic -fopenmp -O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -Wl,-rpath=/usr/local/lib/gcc8 -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc8 -L/usr/local/lib/gcc8 -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/mason2/CMakeFiles/mason_materializer.dir/mason_materializer.cpp.o -o bin/mason_materializer -lexecinfo -lelf -lz apps/mason2/libmason_sim.a -lexecinfo -lelf -lz && : =========================================================================== =======================<phase: run-depends >============================ ===> seqan-apps-2.4.0_6 depends on executable: gcc8 - found =========================================================================== =======================<phase: stage >============================ ===> Staging for seqan-apps-2.4.0_6 ===> Generating temporary packing list [0/1] cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/alf -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/alf/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/alf/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/alf/example/small.fasta -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/bisar -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/casbar -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/four2three -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/bs_tools/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/bs_tools/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/dfi -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/example/fasta1.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/example/fasta2.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/fx_bam_coverage -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fx_tools/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fx_tools/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/gustaf -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/gustaf_mate_joining -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/adeno.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/adeno_modified.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/adeno_modified_reads.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/stellar.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/insegt -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/annoOutput.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/annotations.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/readOutput.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/tupleOutput.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_frag_sequencing -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_genome -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_materializer -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_methylation -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_simulator -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_splicing -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_variator -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_frag_sequencing -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_genome -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_materializer -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_methylation -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_simulator -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_splicing -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_variator -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/example/adeno_virus.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/micro_razers -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/example/genome.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/example/reads.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/example/reads.fa.result -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/bam2roi -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_feature_projection -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_plot_thumbnails -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/bed_sort.sh -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/gff_sort.sh -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_sort.sh -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_plot_9.sh -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/plot.awk -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/ps2pswLinks.gawk -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/example/dmel.bed -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/example/dmel.gtf -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/example/example.bam -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/R/ngsroi_0.1.tar.gz -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/R/ngsroi_0.1.zip -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/pair_align -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/pair_align/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/pair_align/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/param_chooser -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/param_chooser/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/param_chooser/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_prepare_sam -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_build_gold_standard -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_evaluate -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_prepare_sam -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_build_gold_standard -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_evaluate -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rabema/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rabema/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/razers -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/example/genome.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/example/reads.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/example/reads2.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/razers3 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/example/genome.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/example/reads.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/example/reads2.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rep_sep -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rep_sep/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rep_sep/README [1/2] cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak && /wrkdirs/usr/ports/biology/seqan-apps/work/.build/bin/sak --export-help=man > sak.1 [2/2] cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak && /wrkdirs/usr/ports/biology/seqan-apps/work/.build/bin/sak --export-help=txt > README.sak.txt -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/sak -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sak/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sak/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sak/README.sak.txt -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/man/man1/sak.1 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/sam2matrix -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sam2matrix/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sam2matrix/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/samcat -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/samcat/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/samcat/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/s4_search -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/s4_join -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/searchjoin/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/searchjoin/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/seqan_tcoffee -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/seqan_tcoffee/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/seqan_tcoffee/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/seqan_tcoffee/example/seq.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/seqcons2 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/seqcons2/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/seqcons2/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/sgip -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/iso_m2D_m196.A01 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/iso_r01_m200.A00 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/iso_r01_m200.A01 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/iso_r01_m200.B00 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/iso_r01_m200.B01 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/latin-4 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/lattice-4 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sgip/example/sts-7 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/snp_store -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/snp_store/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/snp_store/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/snp_store/example/exampleGenome.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/snp_store/example/exampleReads.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/stellar -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/stellar/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/stellar/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/stellar/example/NC_001474.fasta -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/stellar/example/NC_001477.fasta -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/stellar/example/reads.fasta -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/tree_recon -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/tree_recon/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/tree_recon/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/tree_recon/example/example.dist -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/yara_indexer -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/yara_mapper -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/yara/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/yara/README.rst ====> Compressing man pages (compress-man) =========================================================================== =======================<phase: package >============================ ===> Building package for seqan-apps-2.4.0_6 pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/compute_gain:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/fiona:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/splazers:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fiona/LICENSE:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fiona/README:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fiona/example/reads.fa:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/splazers/LICENSE:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/splazers/README:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/splazers/example/genome.fa:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/splazers/example/reads.fa:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/splazers/example/reads.fa.result:No such file or directory *** Error code 1 Stop. make: stopped in /usr/ports/biology/seqan-apps
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