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Maintainer: po...@freebsd.org Last committer: t...@freebsd.org Ident: $FreeBSD: head/biology/primer3/Makefile 354670 2014-05-20 19:32:39Z tijl $ Log URL: http://thunderx1.nyi.freebsd.org/data/head-arm64-default/p463867_s330635/logs/primer3-2.3.6.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=head-arm64-default&build=p463867_s330635 Log: =>> Building biology/primer3 build started at Tue Mar 13 16:32:54 UTC 2018 port directory: /usr/ports/biology/primer3 package name: primer3-2.3.6 building for: FreeBSD head-arm64-default-job-03 12.0-CURRENT FreeBSD 12.0-CURRENT 1200060 arm64 maintained by: po...@freebsd.org Makefile ident: $FreeBSD: head/biology/primer3/Makefile 354670 2014-05-20 19:32:39Z tijl $ Poudriere version: 3.2.4-67-gb1dd83c4 Host OSVERSION: 1200060 Jail OSVERSION: 1200060 Job Id: 03 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1200060 UNAME_v=FreeBSD 12.0-CURRENT 1200060 UNAME_r=12.0-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 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.4-67-gb1dd83c4 MASTERMNT=/usr/local/poudriere/data/.m/head-arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-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-- po...@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 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -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 #### /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 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: aarch64-unknown-freebsd12.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: aarch64-unknown-freebsd12.0 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" OUTPUT_58173849_921dbbb2=yes OUTPUT_9bdba57c_921dbbb2=yes OUTPUT_6a4fe7f5_921dbbb2=yes OUTPUT_6bcac02b_921dbbb2=yes OUTPUT_67d20829_921dbbb2=yes OUTPUT_bfa62e83_921dbbb2=yes OUTPUT_f0b4d593_921dbbb2=yes OUTPUT_308abb44_921dbbb2=yes OUTPUT_f00456e5_921dbbb2=yes OUTPUT_65ad290d_921dbbb2=yes OUTPUT_b2657cc3_921dbbb2=yes OUTPUT_380987f7_921dbbb2=yes ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=12.0-CURRENT OSREL=12.0 OSVERSION=1200060 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### 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) 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 >============================ ===> 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-1.10.5.txz [head-arm64-default-job-03] Installing pkg-1.10.5... [head-arm64-default-job-03] Extracting pkg-1.10.5: .......... 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-arm64-default-job-03] `-- Installing gettext-runtime-0.19.8.1_1... [head-arm64-default-job-03] | `-- Installing indexinfo-0.3.1... [head-arm64-default-job-03] | `-- Extracting indexinfo-0.3.1: .... done [head-arm64-default-job-03] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [head-arm64-default-job-03] Extracting gmake-4.2.1_2: .......... 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 -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 -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 -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 -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 -fno-strict-aliasing -g -Wall -D__USE_FIXED_PROTOTYPES__ -Wno-deprecated -o libprimer3.o libprimer3.c c++ -c -O2 -pipe -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 -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 -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 _______________________________________________ freebsd-pkg-fallout@freebsd.org mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "freebsd-pkg-fallout-unsubscr...@freebsd.org"
