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Maintainer: j...@freebsd.org Log URL: https://pkg-status.freebsd.org/ampere2/data/main-arm64-default/p8fb94260154e_s510fd83138/logs/clustalw-2.1_2.log Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=p8fb94260154e_s510fd83138 Log: =>> Building biology/clustalw build started at Fri Jul 14 11:15:19 UTC 2023 port directory: /usr/ports/biology/clustalw package name: clustalw-2.1_2 building for: FreeBSD main-arm64-default-job-13 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 arm64 maintained by: j...@freebsd.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400089 Jail OSVERSION: 1400093 Job Id: 13 !!! Jail is newer than host. (Jail: 1400093, Host: 1400089) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400093 UNAME_v=FreeBSD 14.0-CURRENT 1400093 UNAME_r=14.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-arm64-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-- j...@freebsd.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/clustalw/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/clustalw/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/clustalw/work/.cache HOME=/wrkdirs/usr/ports/biology/clustalw/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/clustalw/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/clustalw/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/clustalw/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/clustalw/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/clustalw/work/.cache HOME=/wrkdirs/usr/ports/biology/clustalw/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/clustalw/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/clustalw/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INS TALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/clustalw" EXAMPLESDIR="share/examples/clustalw" DATADIR="share/clustalw" WWWDIR="www/clustalw" ETCDIR="etc/clustalw" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/clustalw DOCSDIR=/usr/local/share/doc/clustalw EXAMPLESDIR=/usr/local/share/examples/clustalw WWWDIR=/usr/local/www/clustalw ETCDIR=/usr/local/etc/clustalw --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400093 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License LGPL3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> clustalw-2.1_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.4.pkg [main-arm64-default-job-13] Installing pkg-1.20.4... [main-arm64-default-job-13] Extracting pkg-1.20.4: .......... done ===> clustalw-2.1_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of clustalw-2.1_2 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by clustalw-2.1_2 for building =========================================================================== =======================<phase: checksum >============================ ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by clustalw-2.1_2 for building => SHA256 Checksum OK for clustalw-2.1.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License LGPL3 accepted by the user ===> Fetching all distfiles required by clustalw-2.1_2 for building ===> Extracting for clustalw-2.1_2 => SHA256 Checksum OK for clustalw-2.1.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for clustalw-2.1_2 ===> Applying FreeBSD patches for clustalw-2.1_2 from /usr/ports/biology/clustalw/files =========================================================================== =======================<phase: build-depends >============================ =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for clustalw-2.1_2 configure: loading site script /usr/ports/Templates/config.site checking build system type... aarch64-portbld-freebsd14.0 checking host system type... aarch64-portbld-freebsd14.0 checking target system type... aarch64-portbld-freebsd14.0 building for freebsd14.0 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 whether make sets $(MAKE)... (cached) yes checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether cc accepts -g... yes checking for cc option to accept ISO C89... none needed checking for style of include used by make... GNU checking dependency style of cc... gcc3 checking whether we are using the GNU C++ compiler... yes checking whether c++ accepts -g... yes checking dependency style of c++... gcc3 checking for ranlib... ranlib checking how to run the C++ preprocessor... c++ -E 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 stdbool.h that conforms to C99... (cached) yes checking for _Bool... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes configure: creating ./config.status config.status: creating Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/clustalw_version.h config.status: creating src/config.h config.status: executing depfiles commands =========================================================================== =======================<phase: build >============================ ===> Building for clustalw-2.1_2 --- all-recursive --- Making all in m4 Making all in src --- all --- /usr/bin/make all-recursive --- all-recursive --- --- FullPairwiseAlign.o --- --- FastPairwiseAlign.o --- --- FullPairwiseAlign.o --- c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT FullPairwiseAlign.o -MD -MP -MF .deps/FullPairwiseAlign.Tpo -c -o FullPairwiseAlign.o `test -f './pairwise/FullPairwiseAlign.cpp' || echo './'`./pairwise/FullPairwiseAlign.cpp --- FastPairwiseAlign.o --- c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT FastPairwiseAlign.o -MD -MP -MF .deps/FastPairwiseAlign.Tpo -c -o FastPairwiseAlign.o `test -f './pairwise/FastPairwiseAlign.cpp' || echo './'`./pairwise/FastPairwiseAlign.cpp In file included from ./pairwise/FastPairwiseAlign.cpp:10: In file included from ./pairwise/FastPairwiseAlign.h:9: In file included from ./pairwise/PairwiseAlignBase.h:10: In file included from ./pairwise/../alignment/Alignment.h:42: In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] void printInFormat(vector<short>& temp, char* name = "tempfile.out"); ^ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] void printVectorToFile(vector<short>& temp, char* name = "tempfile.out"); ^ --- FullPairwiseAlign.o --- In file included from ./pairwise/FullPairwiseAlign.cpp:9: In file included from ./pairwise/FullPairwiseAlign.h:9: In file included from ./pairwise/PairwiseAlignBase.h:10: In file included from ./pairwise/../alignment/Alignment.h:42: In file included from ./pairwise/../alignment/../substitutionMatrix/globalmatrix.h:8: ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] void printInFormat(vector<short>& temp, char* name = "tempfile.out"); ^ ./pairwise/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] void printVectorToFile(vector<short>& temp, char* name = "tempfile.out"); ^ 2 warnings generated. mv -f .deps/FullPairwiseAlign.Tpo .deps/FullPairwiseAlign.Po --- MSFFileParser.o --- c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT MSFFileParser.o -MD -MP -MF .deps/MSFFileParser.Tpo -c -o MSFFileParser.o `test -f './fileInput/MSFFileParser.cpp' || echo './'`./fileInput/MSFFileParser.cpp --- FastPairwiseAlign.o --- 2 warnings generated. mv -f .deps/FastPairwiseAlign.Tpo .deps/FastPairwiseAlign.Po --- FileReader.o --- c++ -DHAVE_CONFIG_H -I. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -MT FileReader.o -MD -MP -MF .deps/FileReader.Tpo -c -o FileReader.o `test -f './fileInput/FileReader.cpp' || echo './'`./fileInput/FileReader.cpp In file included from ./fileInput/FileReader.cpp:29: In file included from ./fileInput/FileReader.h:12: In file included from ./fileInput/../alignment/Alignment.h:42: In file included from ./fileInput/../alignment/../substitutionMatrix/globalmatrix.h:8: ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:96:62: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] void printInFormat(vector<short>& temp, char* name = "tempfile.out"); ^ ./fileInput/../alignment/../substitutionMatrix/SubMatrix.h:97:66: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings] void printVectorToFile(vector<short>& temp, char* name = "tempfile.out"); ^ In file included from ./fileInput/FileReader.cpp:29: ./fileInput/FileReader.h:42:38: error: no template named 'auto_ptr' void checkInfile(int* nseqs, auto_ptr<FileParser>& fileParser); ^ ./fileInput/FileReader.cpp:155:5: error: no template named 'auto_ptr' auto_ptr<FileParser> fileParser; // Means we dont need to delete it! ^ ./fileInput/FileReader.cpp:426:42: error: no template named 'auto_ptr' void FileReader::checkInfile(int *nseqs, auto_ptr<FileParser>& fileParser) ^ 2 warnings and 3 errors generated. *** [FileReader.o] Error code 1 make[4]: stopped in /wrkdirs/usr/ports/biology/clustalw/work/clustalw-2.1/src --- MSFFileParser.o --- mv -f .deps/MSFFileParser.Tpo .deps/MSFFileParser.Po 1 error make[4]: stopped in /wrkdirs/usr/ports/biology/clustalw/work/clustalw-2.1/src make[3]: stopped in /wrkdirs/usr/ports/biology/clustalw/work/clustalw-2.1/src make[2]: stopped in /wrkdirs/usr/ports/biology/clustalw/work/clustalw-2.1/src make[1]: stopped in /wrkdirs/usr/ports/biology/clustalw/work/clustalw-2.1 ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/clustalw
