Date: Thu, 3 Oct 2019 01:36:45 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-armv6-default][biology/clustal-omega] Failed for clustal-omega-1.2.4 in configure Message-ID: <201910030136.x931ajKD079138@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: jwb@FreeBSD.org Last committer: jwb@FreeBSD.org Ident: $FreeBSD: head/biology/clustal-omega/Makefile 470582 2018-05-21 22:15:26Z jwb $ Log URL: http://beefy8.nyi.freebsd.org/data/head-armv6-default/p513638_s353025/logs/clustal-omega-1.2.4.log Build URL: http://beefy8.nyi.freebsd.org/build.html?mastername=head-armv6-default&build=p513638_s353025 Log: =>> Building biology/clustal-omega build started at Thu Oct 3 01:36:25 UTC 2019 port directory: /usr/ports/biology/clustal-omega package name: clustal-omega-1.2.4 building for: FreeBSD head-armv6-default-job-06 13.0-CURRENT FreeBSD 13.0-CURRENT 1300048 arm maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/clustal-omega/Makefile 470582 2018-05-21 22:15:26Z jwb $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300040 Jail OSVERSION: 1300048 Job Id: 06 !!! Jail is newer than host. (Jail: 1300048, Host: 1300040) !!! !!! 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=1300048 UNAME_v=FreeBSD 13.0-CURRENT 1300048 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=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-armv6-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= 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--- ---End OPTIONS List--- --MAINTAINER-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/clustal-omega/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/clustal-omega/work HOME=/wrkdirs/usr/ports/biology/clustal-omega/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/clustal-omega/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/clustal-omega/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/clustal-omega/work HOME=/wrkdirs/usr/ports/biology/clustal-omega/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/clustal-omega/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 -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " 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="in stall -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/clustal-omega" EXAMPLESDIR="share/examples/clustal-omega" DATADIR="share/clustal-omega" WWWDIR="www/clustal-omega" ETCDIR="etc/clustal-omega" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/clustal-omega DOCSDIR=/usr/local/share/doc/clustal-omega EXAMPLESDIR=/usr/local/share/examples/clustal-omega WWWDIR=/usr/local/www/clustal-omega ETCDIR=/usr/local/etc/clustal-omega --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 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) Target: armv6-unknown-freebsd13.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) 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 8.0.1 (tags/RELEASE_801/final 366581) (based on LLVM 8.0.1) 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=1300048 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 GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> clustal-omega-1.2.4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.12.0.txz [head-armv6-default-job-06] Installing pkg-1.12.0... [head-armv6-default-job-06] Extracting pkg-1.12.0: .......... done pkg-static: Cannot runscript POST-INSTALL:Operation not permitted ===> clustal-omega-1.2.4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of clustal-omega-1.2.4 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ <snip> =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for clustal-omega-1.2.4 =========================================================================== =======================<phase: build-depends >============================ =========================================================================== =======================<phase: lib-depends >============================ ===> clustal-omega-1.2.4 depends on shared library: libargtable2.so - not found ===> Installing existing package /packages/All/argtable-2.13_2.txz [head-armv6-default-job-06] Installing argtable-2.13_2... [head-armv6-default-job-06] Extracting argtable-2.13_2: .......... done pkg-static: Cannot runscript POST-INSTALL:Operation not permitted ===== Message from argtable-2.13_2: -- ===> NOTICE: The argtable port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> clustal-omega-1.2.4 depends on shared library: libargtable2.so - found (/usr/local/lib/libargtable2.so) ===> Returning to build of clustal-omega-1.2.4 =========================================================================== =======================<phase: configure >============================ ===> Configuring for clustal-omega-1.2.4 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/clustal-omega/work/clustal-omega-1.2.4/m4/libtool.m4 ===> FreeBSD 10 autotools fix applied to /wrkdirs/usr/ports/biology/clustal-omega/work/clustal-omega-1.2.4/configure configure: loading site script /usr/ports/Templates/config.site configure: Welcome to Clustal Omega - version 1.2.4 (AndreaGiacomo) +NMMMMMMMMMS= MMMMM? :MMMMM8 IMMMMS MMMMM, ~MMMMN ,MMMMM =MMMMM MMMMM ?MMMMM +MMMMM MMMMMS MMMMM MMMMM MMMMM: MMMMM MMMMM+ MMMMM MMMMM~ MMMMM MMMMM MMMMMZ MMMMM MMMMM ,MMMMZ MMMM8 MMMM+ MMMMS MMMM, MMMMO MMMM ,N SMMM MMM8 +8 ,M7 M+ M+ :M8 ,MMMMMMMMMMMMI MMMMMMMMMMMM8 ,MMMMMMMMMMMM8 MMMMMMMMMMMM8 ,MMMMMMMMMMMMN MMMMMMMMMMMM8 checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether make sets $(MAKE)... yes checking for style of include used by make... GNU checking for gcc... /nxb-bin/usr/bin/cc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether /nxb-bin/usr/bin/cc accepts -g... yes checking for /nxb-bin/usr/bin/cc option to accept ISO C89... none needed checking dependency style of /nxb-bin/usr/bin/cc... gcc3 checking how to run the C preprocessor... /nxb-bin/usr/bin/cpp checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep 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 minix/config.h... (cached) no checking whether it is safe to define __EXTENSIONS__... yes checking build system type... armv6-portbld-freebsd13.0 checking host system type... armv6-portbld-freebsd13.0 checking whether make sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by /nxb-bin/usr/bin/cc... /nxb-bin/usr/bin/ld checking if the linker (/nxb-bin/usr/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm checking the name lister (/usr/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 262144 checking whether the shell understands some XSI constructs... yes checking whether the shell understands "+="... no checking for /nxb-bin/usr/bin/ld option to reload object files... -r checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for ar... ar checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from /nxb-bin/usr/bin/cc object... ok checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if /nxb-bin/usr/bin/cc supports -fno-rtti -fno-exceptions... yes checking for /nxb-bin/usr/bin/cc option to produce PIC... -fPIC -DPIC checking if /nxb-bin/usr/bin/cc PIC flag -fPIC -DPIC works... yes checking if /nxb-bin/usr/bin/cc static flag -static works... yes checking if /nxb-bin/usr/bin/cc supports -c -o file.o... yes checking if /nxb-bin/usr/bin/cc supports -c -o file.o... (cached) yes checking whether the /nxb-bin/usr/bin/cc linker (/nxb-bin/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd13.0 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... yes checking for a BSD-compatible install... /usr/bin/install -c checking for gcc... (cached) /nxb-bin/usr/bin/cc checking whether we are using the GNU C compiler... (cached) yes checking whether /nxb-bin/usr/bin/cc accepts -g... (cached) yes checking for /nxb-bin/usr/bin/cc option to accept ISO C89... (cached) none needed checking dependency style of /nxb-bin/usr/bin/cc... (cached) gcc3 checking how to run the C preprocessor... /nxb-bin/usr/bin/cpp checking whether we are using the GNU C++ compiler... yes checking whether /nxb-bin/usr/bin/c++ accepts -g... yes checking dependency style of /nxb-bin/usr/bin/c++... gcc3 checking whether we are using the GNU C++ compiler... (cached) yes checking whether /nxb-bin/usr/bin/c++ accepts -g... (cached) yes checking dependency style of /nxb-bin/usr/bin/c++... (cached) gcc3 checking how to run the C++ preprocessor... /nxb-bin/usr/bin/c++ -E checking for ld used by /nxb-bin/usr/bin/c++... /nxb-bin/usr/bin/ld checking if the linker (/nxb-bin/usr/bin/ld) is GNU ld... yes checking whether the /nxb-bin/usr/bin/c++ linker (/nxb-bin/usr/bin/ld) supports shared libraries... yes checking for /nxb-bin/usr/bin/c++ option to produce PIC... -fPIC -DPIC checking if /nxb-bin/usr/bin/c++ PIC flag -fPIC -DPIC works... yes checking if /nxb-bin/usr/bin/c++ static flag -static works... yes checking if /nxb-bin/usr/bin/c++ supports -c -o file.o... yes checking if /nxb-bin/usr/bin/c++ supports -c -o file.o... (cached) yes checking whether the /nxb-bin/usr/bin/c++ linker (/nxb-bin/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd13.0 ld.so checking how to hardcode library paths into programs... immediate checking how to run the C++ preprocessor... /nxb-bin/usr/bin/c++ -E checking for ANSI C header files... (cached) yes checking assert.h usability... yes checking assert.h presence... yes checking for assert.h... yes checking for ctype.h... (cached) yes checking for float.h... (cached) yes checking for limits.h... (cached) yes checking for math.h... (cached) yes checking for memory.h... (cached) yes checking for stdarg.h... (cached) yes checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for time.h... (cached) yes checking for unistd.h... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes checking for inline... inline checking for log in -lm... yes checking for log2 in -lm... yes checking argtable2.h usability... yes checking argtable2.h presence... yes checking for argtable2.h... yes checking for arg_parse in -largtable2... yes checking for OpenMP flag of C compiler... unknown checking whether byte ordering is bigendian... no checking for ntohs... yes checking for ntohl... yes checking for ntons... no checking for ntonl... no checking size of unsigned short... configure: error: in `/wrkdirs/usr/ports/biology/clustal-omega/work/clustal-omega-1.2.4': configure: error: cannot compute sizeof (unsigned short) See `config.log' for more details. ===> Script "configure" failed unexpectedly. Please report the problem to jwb@FreeBSD.org [maintainer] and attach the "/wrkdirs/usr/ports/biology/clustal-omega/work/clustal-omega-1.2.4/config.log" including the output of the failure of your make command. Also, it might be a good idea to provide an overview of all packages installed on your system (e.g. a /usr/local/sbin/pkg-static info -g -Ea). *** Error code 1 Stop. make: stopped in /usr/ports/biology/clustal-omega
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