Date: Mon, 3 Dec 2018 14:36:02 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - 120armv7-quarterly][biology/ngs-sdk] Failed for ngs-sdk-2.9.2 in build Message-ID: <201812031436.wB3Ea2H8049553@beefy13.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: yuri@FreeBSD.org Ident: $FreeBSD: branches/2018Q4/biology/ngs-sdk/Makefile 480103 2018-09-19 18:09:37Z yuri $ Log URL: http://beefy13.nyi.freebsd.org/data/120armv7-quarterly/486311/logs/ngs-sdk-2.9.2.log Build URL: http://beefy13.nyi.freebsd.org/build.html?mastername=120armv7-quarterly&build=486311 Log: =>> Building biology/ngs-sdk build started at Mon Dec 3 14:35:47 UTC 2018 port directory: /usr/ports/biology/ngs-sdk package name: ngs-sdk-2.9.2 building for: FreeBSD 120armv7-quarterly-job-19 12.0-RC3 FreeBSD 12.0-RC3 1200086 arm maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: branches/2018Q4/biology/ngs-sdk/Makefile 480103 2018-09-19 18:09:37Z yuri $ Poudriere version: 3.2.8 Host OSVERSION: 1300002 Jail OSVERSION: 1200086 Job Id: 19 ---Begin Environment--- SHELL=/bin/csh UNAME_p=armv7 UNAME_m=arm ABI_FILE=/usr/lib/crt1.o OSVERSION=1200086 UNAME_v=FreeBSD 12.0-RC3 1200086 UNAME_r=12.0-RC3 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-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --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/ngs-sdk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ngs-sdk/work HOME=/wrkdirs/usr/ports/biology/ngs-sdk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ngs-sdk/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=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ngs-sdk/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ngs-sdk/work HOME=/wrkdirs/usr/ports/biology/ngs-sdk/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ngs-sdk/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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-2.9.2/ngs-sdk/ngs/unix/armv7/ -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -I/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-2.9.2/ngs-sdk/ngs/unix/armv7/ -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=12.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.26.2 PERL_VER=5.26 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/5.26 DOCSDIR="share/doc/ngs" EXAMPLESDIR="share/examples/ngs" DATADIR="share/ngs" WWWDIR="www/ngs" ETCDIR="etc/ngs" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ngs DOCSDIR=/usr/local/share/doc/ngs EXAMPLESDIR=/usr/local/share/examples/ngs WWWDIR=/usr/local/www/ngs ETCDIR=/usr/local/etc/ngs --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. 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 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-RC3 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 PD accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> ngs-sdk-2.9.2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [120armv7-quarterly-job-19] Installing pkg-1.10.5_5... [120armv7-quarterly-job-19] Extracting pkg-1.10.5_5: .......... done ===> ngs-sdk-2.9.2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ngs-sdk-2.9.2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License PD accepted by the user ===> Fetching all distfiles required by ngs-sdk-2.9.2 for building =========================================================================== =======================<phase: checksum >============================ ===> License PD accepted by the user ===> Fetching all distfiles required by ngs-sdk-2.9.2 for building => SHA256 Checksum OK for ncbi-ngs-2.9.2_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License PD accepted by the user ===> Fetching all distfiles required by ngs-sdk-2.9.2 for building ===> Extracting for ngs-sdk-2.9.2 => SHA256 Checksum OK for ncbi-ngs-2.9.2_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for ngs-sdk-2.9.2 ===> Applying FreeBSD patches for ngs-sdk-2.9.2 =========================================================================== =======================<phase: build-depends >============================ ===> ngs-sdk-2.9.2 depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz [120armv7-quarterly-job-19] Installing gmake-4.2.1_2... [120armv7-quarterly-job-19] `-- Installing gettext-runtime-0.19.8.1_1... [120armv7-quarterly-job-19] | `-- Installing indexinfo-0.3.1... [120armv7-quarterly-job-19] | `-- Extracting indexinfo-0.3.1: .... done [120armv7-quarterly-job-19] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [120armv7-quarterly-job-19] Extracting gmake-4.2.1_2: .......... done ===> ngs-sdk-2.9.2 depends on executable: gmake - found ===> Returning to build of ngs-sdk-2.9.2 ===> ngs-sdk-2.9.2 depends on package: perl5>=5.26<5.27 - not found ===> Installing existing package /packages/All/perl5-5.26.2.txz [120armv7-quarterly-job-19] Installing perl5-5.26.2... [120armv7-quarterly-job-19] Extracting perl5-5.26.2: .......... done Message from perl5-5.26.2: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. ===> ngs-sdk-2.9.2 depends on package: perl5>=5.26<5.27 - found ===> Returning to build of ngs-sdk-2.9.2 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for ngs-sdk-2.9.2 CONFIGURING ngs-sdk Configuring NGS-SDK package checking system type... FreeBSD checking machine architecture... arm configure: error: unsupported architecture 'FreeBSD' =========================================================================== =======================<phase: build >============================ ===> Building for ngs-sdk-2.9.2 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-2.9.2' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-2.9.2/ngs-sdk' *** File 'Makefile.config.FreeBSD.arm' is missing. Please run ./configure gmake[2]: *** [/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-2.9.2/ngs-sdk/Makefile.rules:72: Makefile.config.FreeBSD.arm] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-2.9.2/ngs-sdk' gmake[1]: *** [Makefile:52: ngs-sdk] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ngs-sdk/work/ngs-2.9.2' *** Error code 1 Stop. make: stopped in /usr/ports/biology/ngs-sdk
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