Date: Sat, 3 Feb 2018 05:12:11 GMT From: pkg-fallout@FreeBSD.org To: pkg-fallout@FreeBSD.org Subject: [package - head-i386-default][biology/primer3] Failed for primer3-2.3.6 in build Message-ID: <201802030512.w135CBmJ049002@beefy11.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: ports@FreeBSD.org Last committer: tijl@FreeBSD.org Ident: $FreeBSD: head/biology/primer3/Makefile 354670 2014-05-20 19:32:39Z tijl $ Log URL: http://beefy11.nyi.freebsd.org/data/head-i386-default/p460764_s328823/logs/primer3-2.3.6.log Build URL: http://beefy11.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p460764_s328823 Log: =>> Building biology/primer3 build started at Sat Feb 3 05:11:58 UTC 2018 port directory: /usr/ports/biology/primer3 package name: primer3-2.3.6 building for: FreeBSD head-i386-default-job-19 12.0-CURRENT FreeBSD 12.0-CURRENT 1200056 i386 maintained by: ports@FreeBSD.org Makefile ident: $FreeBSD: head/biology/primer3/Makefile 354670 2014-05-20 19:32:39Z tijl $ Poudriere version: 3.2.4-34-g673bd441 Host OSVERSION: 1200054 Jail OSVERSION: 1200056 Job Id: 19 !!! Jail is newer than host. (Jail: 1200056, Host: 1200054) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1200056 UNAME_v=FreeBSD 12.0-CURRENT 1200056 UNAME_r=12.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/head-i386-default/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk OLDPWD=/usr/local/poudriere/data/.m/head-i386-default/ref/.p P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS PWD=/usr/local/poudriere/data/.m/head-i386-default/ref/.p/pool MASTERNAME=head-i386-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.2.4-34-g673bd441 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local PACKAGE_BUILDING=yes 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 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 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 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 NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector -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-- PORTDOCS="" PORTEXAMPLES="" OSREL=12.0 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 MACHINE=i386 MACHINE_ARCH=i386 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 #### /usr/ports/Mk/Scripts/ports_env.sh #### ARCH=i386 CONFIGURE_MAX_CMD_LEN=262144 OPSYS=FreeBSD OSREL=12.0 OSVERSION=1200056 PYTHONBASE=/usr/local UID=0 _OSRELEASE=12.0-CURRENT #### Misc Poudriere #### GID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 524288 stack size (kbytes, -s) 65536 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> 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-1.10.4.txz [head-i386-default-job-19] Installing pkg-1.10.4... [head-i386-default-job-19] Extracting pkg-1.10.4: .......... 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port ===> 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: <snip> [head-i386-default-job-19] `-- Installing gettext-runtime-0.19.8.1_1... [head-i386-default-job-19] | `-- Installing indexinfo-0.3.1... [head-i386-default-job-19] | `-- Extracting indexinfo-0.3.1: .... done [head-i386-default-job-19] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [head-i386-default-job-19] Extracting gmake-4.2.1_1: .......... done ===> primer3-2.3.6 depends on executable: gmake - 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 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ primer3_boulder_main.c c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++ -c -O2 -pipe -fstack-protector -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] 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 ) ~~~~~~~~^~~ ~~~~ 8 warnings generated. c++ -c -O2 -pipe -fstack-protector -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] c++ -c -O2 -pipe -fstack-protector -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 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -Wno-deprecated -o libprimer3.o libprimer3.c c++ -c -O2 -pipe -fstack-protector -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] ar rv libprimer3.a libprimer3.o p3_seq_lib.o ar: warning: creating libprimer3.a a - libprimer3.o a - p3_seq_lib.o ranlib libprimer3.a c++ -c -O2 -pipe -fstack-protector -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: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k, mg, c; ^~~~~~~~~ dpal.c:368:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k, mg, c; ^~~~~~~~~ dpal.c:368:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k, mg, c; ^~~~~~~~~ dpal.c:368:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k, mg, c; ^~~~~~~~~ dpal.c:368:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k, mg, c; ^~~~~~~~~ dpal.c:369:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; ^~~~~~~~~ dpal.c:369:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; ^~~~~~~~~ dpal.c:369:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; ^~~~~~~~~ dpal.c:594:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k, mg, mgy, c; ^~~~~~~~~ dpal.c:594:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k, mg, mgy, c; ^~~~~~~~~ dpal.c:594:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k, mg, mgy, c; ^~~~~~~~~ dpal.c:594:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k, mg, mgy, c; ^~~~~~~~~ dpal.c:594:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k, mg, mgy, c; ^~~~~~~~~ dpal.c:594:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k, mg, mgy, c; ^~~~~~~~~ dpal.c:595:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; ^~~~~~~~~ dpal.c:595:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; ^~~~~~~~~ dpal.c:595:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int gap = in->gap, gapl = in->gapl, max_gap = in->max_gap; ^~~~~~~~~ dpal.c:760:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j; ^~~~~~~~~ dpal.c:760:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j; ^~~~~~~~~ dpal.c:761:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int gap = in->gap; ^~~~~~~~~ dpal.c:762:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int smax; /* The optimum score. */ ^~~~~~~~~ dpal.c:763:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int score; /* Current score. */ ^~~~~~~~~ dpal.c:764:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int a; ^~~~~~~~~ dpal.c:852:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k; ^~~~~~~~~ dpal.c:852:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k; ^~~~~~~~~ dpal.c:852:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j, k; ^~~~~~~~~ dpal.c:853:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int gap = in->gap; ^~~~~~~~~ dpal.c:854:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int smax; /* The optimum score. */ ^~~~~~~~~ dpal.c:855:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int score; /* Current score. */ ^~~~~~~~~ dpal.c:856:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int a, t; ^~~~~~~~~ dpal.c:856:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int a, t; ^~~~~~~~~ dpal.c:1049:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register const unsigned char *p; ^~~~~~~~~ dpal.c:1072:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j; ^~~~~~~~~ dpal.c:1072:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i, j; ^~~~~~~~~ dpal.c:1073:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int gap = in->gap; ^~~~~~~~~ dpal.c:1074:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int smax; /* The optimum score. */ ^~~~~~~~~ dpal.c:1075:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int score; /* Current score. */ ^~~~~~~~~ dpal.c:1076:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int a; ^~~~~~~~~ 38 warnings generated. ar rv libdpal.a dpal_primer.o ar: warning: creating libdpal.a a - dpal_primer.o ranlib libdpal.a c++ -c -O2 -pipe -fstack-protector -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -ffloat-store -o thal_primer.o thal.c c++: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated] c++: warning: optimization flag '-ffloat-store' is not supported [-Wignored-optimization-argument] thal.c:426:13: error: comparison between pointer and integer ('int' and 'const unsigned char *') if ('\0' == oligo_f) { ~~~~ ^ ~~~~~~~ thal.c:431:13: error: comparison between pointer and integer ('int' and 'const unsigned char *') if ('\0' == oligo_r) { ~~~~ ^ ~~~~~~~ thal.c:2407:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register char s; ^~~~~~~~~ thal.c:2408:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register char e; ^~~~~~~~~ 2 warnings and 2 errors generated. gmake[1]: *** [Makefile:192: thal_primer.o] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/primer3/work/primer3-2.3.6/src' *** Error code 1 Stop. make: stopped in /usr/ports/biology/primer3
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