From nobody Mon Jun 26 04:23:26 2023 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4QqF8G51Ndz4j4cY for ; Mon, 26 Jun 2023 04:23:26 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4QqF8G2Xksz3n2N for ; Mon, 26 Jun 2023 04:23:26 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1687753406; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=Oy+9l6ZJEVQHExW9wC+6G1tcc0b08ujK6y4MixMUWIg=; b=eqCwfoHZ078c14uFtBic1TRy83KUAkiK+W6rvhdrN6rA0kxOPATlbg2rZg/9Ux9kzsYyoK cMo1+THOePrne8kl2WInGpRrWjN/i6ZYLocRI8VdgfMXtQC9GpBHgdVkuheBuvRnLYSA5N S/BddEbF/24icDxmzHB1xvyrmAG1c9j7Sc0F9/pdVpu1QncHVT/iW5N6vwLFIERUPpYaxx mVMCzpuM5H3TaVgFukEThr+lTPVlu7YdbwEUWCG542BITIgtJ4nQd11WJ/NFBGKOw+YpfT /7xQ/ttlWEAiwelM3DI0Tsv7IXrwmEOoeD3xEE0y2qjK01t2TRuzxBTH5JQokQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1687753406; a=rsa-sha256; cv=none; b=PsROrFsEsd3VkX5lVyA/Za/81RNMwsd9vMlJkH/68c1KU5cDYsedM/hIEAhCK1w1sESEHj zjsCpbr//VDSG1zGLoAIMeY0WZH561sjcUF6Orf6q8MyIuyTNFjy6zwGHZTllRUnV0HsJD 3lqu+kSFVuU9Ikc+7tnvrMV6L5J0kB0qks+EQhLET0fZG7l/5XatH6GMevKLgQ298xWkN8 tZkKwoVlZCVH/Zg/AG8m66CzXFyv4jBhWR+QPcipCp8ChFczKZgdQw6gE/srMqEKSRBrF5 3IpM54Aq4sZkdBXidj8s+Cw0z8OMhFh6yFg3N+VXzeUSKR8xn7KXGCF4JVTUOw== Received: from beefy17.nyi.freebsd.org (beefy17.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:20]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4QqF8G1cRDzwBZ for ; Mon, 26 Jun 2023 04:23:26 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 2a8e by beefy17.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy17.nyi.freebsd.org); Mon, 26 Jun 2023 04:23:26 +0000 To: yuri@FreeBSD.org Subject: [package - main-i386-default][biology/ncbi-toolkit] Failed for ncbi-toolkit-2017.01.06_7 in build Cc: pkg-fallout@FreeBSD.org Date: Mon, 26 Jun 2023 04:23:26 +0000 Message-Id: <649912be.2a8e.56797ae7@beefy17.nyi.freebsd.org> From: X-ThisMailContainsUnwantedMimeParts: N List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org 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: yuri@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy17/data/main-i386-default/p4785b313b958_se8efee297c/logs/ncbi-toolkit-2017.01.06_7.log Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p4785b313b958_se8efee297c Log: =>> Building biology/ncbi-toolkit build started at Mon Jun 26 04:15:58 UTC 2023 port directory: /usr/ports/biology/ncbi-toolkit package name: ncbi-toolkit-2017.01.06_7 building for: FreeBSD main-i386-default-job-12 14.0-CURRENT FreeBSD 14.0-CURRENT 1400091 i386 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400089 Jail OSVERSION: 1400091 Job Id: 12 !!! Jail is newer than host. (Jail: 1400091, Host: 1400089) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh UNAME_p=i386 UNAME_m=i386 OSVERSION=1400091 UNAME_v=FreeBSD 14.0-CURRENT 1400091 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-i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-i386-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--- ===> The following configuration options are available for ncbi-toolkit-2017.01.06_7: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.cache HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ncbi-toolkit/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-- MOTIFLIB="-L/usr/local/lib -lXm" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.cache HOME=/wrkdirs/usr/ports/biology/ncbi-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/ncbi-toolkit/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 -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-DLIBICONV_PLUG" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasi ng -DLIBICONV_PLUG " 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="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/ncbi-toolkit" EXAMPLESDIR="share/examples/ncbi-toolkit" DATADIR="share/ncbi-toolkit" WWWDIR="www/ncbi-toolkit" ETCDIR="etc/ncbi-toolkit" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/ncbi-toolkit DOCSDIR=/usr/local/share/doc/ncbi-toolkit EXAMPLESDIR=/usr/local/share/examples/ncbi-toolkit WWWDIR=/usr/local/www/ncbi-toolkit ETCDIR=/usr/local/etc/ncbi-toolkit --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 #### _CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: i386-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: i386-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" "-m" "elf_i386_fbsd" "-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: i386-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400091 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) 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-- =================================================== =========================================================================== =================================================== ===> ncbi-toolkit-2017.01.06_7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [main-i386-default-job-12] Installing pkg-1.19.1_1... [main-i386-default-job-12] Extracting pkg-1.19.1_1: .......... done ===> ncbi-toolkit-2017.01.06_7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of ncbi-toolkit-2017.01.06_7 =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_7 for building =========================================================================== =================================================== ===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_7 for building => SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Fetching all distfiles required by ncbi-toolkit-2017.01.06_7 for building ===> Extracting for ncbi-toolkit-2017.01.06_7 => SHA256 Checksum OK for ncbi-toolkit-2017.01.06/ncbi.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for ncbi-toolkit-2017.01.06_7 ===> Applying FreeBSD patches for ncbi-toolkit-2017.01.06_7 from /usr/ports/biology/ncbi-toolkit/files =========================================================================== =================================================== ===> ncbi-toolkit-2017.01.06_7 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF get.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF maketables.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF pcre.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF pcreposix.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF study.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] rm -f libregexp.a ar cru libregexp.a chartables.o get.o maketables.o pcre.o pcreposix.o study.o cp -p libregexp.a ../lib ranlib ../lib/libregexp.a cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF aa_ungapped.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_diagnostics.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_engine.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_extend.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_filter.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_gapalign.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_hits.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_itree.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_lookup.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_message.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_options.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_seg.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_seqsrc.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_sw.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_setup.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_stat.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_traceback.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_util.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF gapinfo.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF greedy_align.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF link_hsps.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF lookup_wrap.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF na_ungapped.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF ncbi_math.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF ncbi_std.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF pattern.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF phi_extend.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF phi_lookup.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF lookup_util.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_encoding.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_psi.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_psi_priv.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_kappa.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF matrix_freq_ratios.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_hspstream.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_parameters.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_posit.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF phi_gapalign.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_program.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_query_info.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_tune.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_aalookup.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_nalookup.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] blast_nalookup.c:901:5: warning: array index 4294967295 refers past the last possible element for an array in 32-bit address space containing 32-bit (4-byte) elements (max possible 1073741824 elements) [-Warray-bounds] mb_lt->hashtable[(Int8)0xffffffff] = 0; ^ ~~~~~~~~~~~~~~~~ ../include/algo/blast/core/blast_nalookup.h:253:5: note: array 'hashtable' declared here Int4* hashtable; /**< Array of positions */ ^ ../include/ncbistd.h:178:21: note: expanded from macro 'Int4' #define Int4 Nlm_Int4 ^ 1 warning generated. cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_aascan.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_nascan.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_dynarray.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF split_query.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF gencode_singleton.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF index_ungapped.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF hspfilter_collector.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_hspstream_mt_utils.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_traceback_mt_priv.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF boost_erf.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF jumper.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] rm -f libblast.a ar cru libblast.a aa_ungapped.o blast_diagnostics.o blast_engine.o blast_extend.o blast_filter.o blast_gapalign.o blast_hits.o blast_itree.o blast_lookup.o blast_message.o blast_options.o blast_seg.o blast_seqsrc.o blast_sw.o blast_setup.o blast_stat.o blast_traceback.o blast_util.o gapinfo.o greedy_align.o link_hsps.o lookup_wrap.o na_ungapped.o ncbi_math.o ncbi_std.o pattern.o phi_extend.o phi_lookup.o lookup_util.o blast_encoding.o blast_psi.o blast_psi_priv.o blast_kappa.o matrix_freq_ratios.o blast_hspstream.o blast_parameters.o blast_posit.o phi_gapalign.o blast_program.o blast_query_info.o blast_tune.o blast_aalookup.o blast_nalookup.o blast_aascan.o blast_nascan.o blast_dynarray.o split_query.o gencode_singleton.o index_ungapped.o hspfilter_collector.o blast_hspstream_mt_utils.o blast_traceback_mt_priv.o boost_erf.o jumper.o cp -p libblast.a ../lib ranlib ../lib/libblast.a cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_api.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_input.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_format.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] blast_format.c:160:16: warning: expression which evaluates to zero treated as a null pointer constant of type 'BlastOutput *' (aka 'struct struct_BlastOutput *') [-Wnon-literal-null-conversion] return FALSE; ^~~~~ ../include/ncbistd.h:247:15: note: expanded from macro 'FALSE' #define FALSE ((Nlm_Boolean)0) ^~~~~~~~~~~~~~~~ 1 warning generated. cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_mtlock.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_options_api.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_prelim.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_returns.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_seq.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_seqalign.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_tabular.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF repeats_filter.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF seqsrc_multiseq.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF seqsrc_readdb.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF twoseq_api.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF dust_filter.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF blast_message_api.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] cc -DNDEBUG -O2 -pipe -DLIBICONV_PLUG -Wno-error=int-conversion -fstack-protector-strong -fno-strict-aliasing -c -I../include -I/usr/local/include -L/usr/local/lib -DWIN_MOTIF hspfilter_queue.c cc: warning: argument unused during compilation: '-L/usr/local/lib' [-Wunused-command-line-argument] hspfilter_queue.c:157:24: error: incompatible function pointer types assigning to 'BlastHSPWriterInitFn' (aka 'int (*)(void *, void *)') from 'int (*)(void *, BlastHSPResults *)' (aka 'int (*)(void *, struct BlastHSPResults *)') [-Wincompatible-function-pointer-types] writer->InitFnPtr = &s_BlastHSPQueueInit; ^ ~~~~~~~~~~~~~~~~~~~~ hspfilter_queue.c:158:24: error: incompatible function pointer types assigning to 'BlastHSPWriterFinalFn' (aka 'int (*)(void *, void *)') from 'int (*)(void *, BlastHSPResults *)' (aka 'int (*)(void *, struct BlastHSPResults *)') [-Wincompatible-function-pointer-types] writer->FinalFnPtr = &s_BlastHSPQueueFinal; ^ ~~~~~~~~~~~~~~~~~~~~~ hspfilter_queue.c:189:26: error: incompatible function pointer types assigning to 'BlastHSPWriterNewFn' (aka 'struct BlastHSPWriter *(*)(void *, struct BlastQueryInfo *, struct BLAST_SequenceBlk *)') from 'BlastHSPWriter *(*)(void *, BlastQueryInfo *)' (aka 'struct BlastHSPWriter *(*)(void *, struct BlastQueryInfo *)') [-Wincompatible-function-pointer-types] writer_info->NewFnPtr = &s_BlastHSPQueueNew; ^ ~~~~~~~~~~~~~~~~~~~ 3 errors generated. *** Error code 1 Stop. make[1]: stopped in /wrkdirs/usr/ports/biology/ncbi-toolkit/work/ncbi/build Fatal error building NCBI core libraries. Please be sure that you have X11 and Motif libraries installed. The NCBI toolkit FAQ at ftp://ftp.ncbi.nih.gov/toolbox/FAQ.html may be helpful. *** Error code 1 Stop. make: stopped in /usr/ports/biology/ncbi-toolkit