[package - main-amd64-default][biology/primer3] Failed for primer3-2.3.6 in build
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Date: Tue, 25 Jul 2023 01:49:31 UTC
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: ports@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p629834653cee_s789df254cc/logs/primer3-2.3.6.log Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p629834653cee_s789df254cc Log: =>> Building biology/primer3 build started at Tue Jul 25 01:49:21 UTC 2023 port directory: /usr/ports/biology/primer3 package name: primer3-2.3.6 building for: FreeBSD main-amd64-default-job-10 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 amd64 maintained by: ports@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400089 Jail OSVERSION: 1400093 Job Id: 10 !!! 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-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-amd64-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-- ports@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/primer3/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/primer3/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/primer3/work/.cache HOME=/wrkdirs/usr/ports/biology/primer3/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/primer3/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/primer3/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/primer3/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/primer3/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/primer3/work/.cache HOME=/wrkdirs/usr/ports/biology/primer3/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/primer3/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/primer3/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_INSTALL_D ATA="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/primer3" EXAMPLESDIR="share/examples/primer3" DATADIR="share/primer3" WWWDIR="www/primer3" ETCDIR="etc/primer3" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/primer3 DOCSDIR=/usr/local/share/doc/primer3 EXAMPLESDIR=/usr/local/share/examples/primer3 WWWDIR=/usr/local/www/primer3 ETCDIR=/usr/local/etc/primer3 --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: x86_64-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: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/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_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: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400093 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES 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) 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 >============================ ===> NOTICE: The primer3 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> License GPLv2 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> primer3-2.3.6 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.4.pkg [main-amd64-default-job-10] Installing pkg-1.20.4... [main-amd64-default-job-10] Extracting pkg-1.20.4: .......... done ===> primer3-2.3.6 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of primer3-2.3.6 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> NOTICE: The primer3 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by primer3-2.3.6 for building =========================================================================== =======================<phase: checksum >============================ ===> NOTICE: The primer3 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by primer3-2.3.6 for building => SHA256 Checksum OK for primer3-src-2.3.6.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> NOTICE: The primer3 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://docs.freebsd.org/en/articles/contributing/#ports-contributing ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by primer3-2.3.6 for building ===> Extracting for primer3-2.3.6 => SHA256 Checksum OK for primer3-src-2.3.6.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for primer3-2.3.6 ===> Applying FreeBSD patches for primer3-2.3.6 from /usr/ports/biology/primer3/files =========================================================================== =======================<phase: build-depends >============================ ===> primer3-2.3.6 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [main-amd64-default-job-10] Installing gmake-4.3_2... [main-amd64-default-job-10] `-- Installing gettext-runtime-0.22_1... [main-amd64-default-job-10] | `-- Installing indexinfo-0.3.1... [main-amd64-default-job-10] | `-- Extracting indexinfo-0.3.1: .... done [main-amd64-default-job-10] `-- Extracting gettext-runtime-0.22_1: .......... done [main-amd64-default-job-10] Extracting gmake-4.3_2: .......... done ===> primer3-2.3.6 depends on package: gmake>=4.3 - found ===> Returning to build of primer3-2.3.6 =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for primer3-2.3.6 =========================================================================== =======================<phase: build >============================ ===> Building for primer3-2.3.6 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/primer3/work/primer3-2.3.6/src' c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ primer3_boulder_main.c c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o format_output.o format_output.c c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] format_output.c:418:48: warning: comparison of address of 'retval->rev' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (pa->pick_right_primer && &retval->rev != NULL ~~~~~~~~^~~ ~~~~ format_output.c:429:47: warning: comparison of address of 'retval->fwd' not equal to a null pointer is always true [-Wtautological-pointer-compare] if (pa->pick_left_primer && &retval->fwd != NULL ~~~~~~~~^~~ ~~~~ format_output.c:851:45: warning: comparison of address of 'retval->fwd' not equal to a null pointer is always true [-Wtautological-pointer-compare] if ((pa->pick_left_primer) && (&retval->fwd != NULL ) ~~~~~~~~^~~ ~~~~ format_output.c:858:48: warning: comparison of address of 'retval->intl' not equal to a null pointer is always true [-Wtautological-pointer-compare] if ((pa->pick_internal_oligo) && (&retval->intl != NULL ) ~~~~~~~~^~~~ ~~~~ format_output.c:865:46: warning: comparison of address of 'retval->rev' not equal to a null pointer is always true [-Wtautological-pointer-compare] if ((pa->pick_right_primer) && (&retval->rev != NULL ) ~~~~~~~~^~~ ~~~~ format_output.c:888:43: warning: comparison of address of 'retval->fwd' not equal to a null pointer is always true [-Wtautological-pointer-compare] if ((pa->pick_left_primer) && (&retval->fwd != NULL ) ~~~~~~~~^~~ ~~~~ format_output.c:907:46: warning: comparison of address of 'retval->intl' not equal to a null pointer is always true [-Wtautological-pointer-compare] if ((pa->pick_internal_oligo) && (&retval->intl != NULL ) ~~~~~~~~^~~~ ~~~~ format_output.c:926:44: warning: comparison of address of 'retval->rev' not equal to a null pointer is always true [-Wtautological-pointer-compare] if ((pa->pick_right_primer) && (&retval->rev != NULL ) ~~~~~~~~^~~ ~~~~ c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o read_boulder.o read_boulder.c c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] 8 warnings generated. c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o print_boulder.o print_boulder.c c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -Wno-deprecated -o libprimer3.o libprimer3.c c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o p3_seq_lib.o p3_seq_lib.c c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -o dpal_primer.o dpal.c c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i, j, k, mg, c; ^~~~~~~~~ dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i, j, k, mg, c; ^~~~~~~~~ dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i, j, k, mg, c; ^~~~~~~~~ dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i, j, k, mg, c; ^~~~~~~~~ dpal.c:368:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i, j, k, mg, c; ^~~~~~~~~ dpal.c:369:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; ^~~~~~~~~ dpal.c:369:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; ^~~~~~~~~ dpal.c:369:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; ^~~~~~~~~ dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i, j, k, mg, mgy, c; ^~~~~~~~~ dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i, j, k, mg, mgy, c; ^~~~~~~~~ dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i, j, k, mg, mgy, c; ^~~~~~~~~ dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i, j, k, mg, mgy, c; ^~~~~~~~~ dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i, j, k, mg, mgy, c; ^~~~~~~~~ dpal.c:594:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i, j, k, mg, mgy, c; ^~~~~~~~~ dpal.c:595:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; ^~~~~~~~~ dpal.c:595:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; ^~~~~~~~~ dpal.c:595:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; ^~~~~~~~~ dpal.c:760:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i, j; ^~~~~~~~~ dpal.c:760:5: error: ISO C++17 does not allow 'register' storage class specifier [-Wregister] register int i, j; ^~~~~~~~~ fatal error: too many errors emitted, stopping now [-ferror-limit=] 20 errors generated. gmake[1]: *** [Makefile:189: dpal_primer.o] Error 1 gmake[1]: *** Waiting for unfinished jobs.... gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/primer3/work/primer3-2.3.6/src' ===> 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/primer3