From owner-freebsd-pkg-fallout@freebsd.org Sat Aug 22 23:49:43 2020 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 60E873A8E56 for ; Sat, 22 Aug 2020 23:49:43 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.nyi.freebsd.org (unknown [127.0.1.3]) by mx1.freebsd.org (Postfix) with ESMTP id 4BYw932FSgz40Zt for ; Sat, 22 Aug 2020 23:49:43 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.nyi.freebsd.org (Postfix) id 4C9F83A8E55; Sat, 22 Aug 2020 23:49:43 +0000 (UTC) Delivered-To: pkg-fallout@mailman.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.nyi.freebsd.org (Postfix) with ESMTP id 4C6413A9295 for ; Sat, 22 Aug 2020 23:49:43 +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 "Let's Encrypt Authority X3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4BYw931mQbz40fZ; Sat, 22 Aug 2020 23:49:43 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy18.nyi.freebsd.org (beefy18.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:f3]) (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 did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 2101A1E503; Sat, 22 Aug 2020 23:49:43 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy18.nyi.freebsd.org (localhost [127.0.0.1]) by beefy18.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id 07MNnh5E046003; Sat, 22 Aug 2020 23:49:43 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy18.nyi.freebsd.org (8.15.2/8.15.2/Submit) id 07MNnhIQ046002; Sat, 22 Aug 2020 23:49:43 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sat, 22 Aug 2020 23:49:43 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202008222349.07MNnhIQ046002@beefy18.nyi.freebsd.org> To: jwb@FreeBSD.org Subject: [package - head-amd64-default][biology/tophat] Failed for tophat-2.1.1_1 in build Cc: pkg-fallout@FreeBSD.org X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.33 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 22 Aug 2020 23:49:43 -0000 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: jwb@FreeBSD.org Last committer: antoine@FreeBSD.org Ident: $FreeBSD: head/biology/tophat/Makefile 528058 2020-03-08 17:01:46Z antoine $ Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p545731_s364466/logs/tophat-2.1.1_1.log Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p545731_s364466 Log: =>> Building biology/tophat build started at Sat Aug 22 23:49:16 UTC 2020 port directory: /usr/ports/biology/tophat package name: tophat-2.1.1_1 building for: FreeBSD head-amd64-default-job-07 13.0-CURRENT FreeBSD 13.0-CURRENT 1300110 amd64 maintained by: jwb@FreeBSD.org Makefile ident: $FreeBSD: head/biology/tophat/Makefile 528058 2020-03-08 17:01:46Z antoine $ Poudriere version: 3.2.8-5-gc81843e5 Host OSVERSION: 1300100 Jail OSVERSION: 1300110 Job Id: 07 !!! Jail is newer than host. (Jail: 1300110, Host: 1300100) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300110 UNAME_v=FreeBSD 13.0-CURRENT 1300110 UNAME_r=13.0-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=3.2.8-5-gc81843e5 MASTERMNT=/usr/local/poudriere/data/.m/head-amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/head-amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=head-amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/head-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-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PYTHON="/usr/local/bin/python2.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/tophat/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/tophat/work HOME=/wrkdirs/usr/ports/biology/tophat/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/tophat/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/tophat/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/tophat/work HOME=/wrkdirs/usr/ports/biology/tophat/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/tophat/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 CC="cc" CFLAGS="-O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -Wno-unused -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_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python2.7 PYTHON_LIBDIR=lib/python2.7 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python2.7/site-packages PYTHON_SUFFIX=27 PYTHON_VER=2.7 PYTHON_VERSION=python2.7 PYTHON2="" PYTHON3="@comment " OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/tophat" EXAMPLESDIR="share/examples/tophat" DATADIR="share/tophat" WWWDIR="www/tophat" ETCDIR="etc/tophat" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/tophat DOCSDIR=/usr/local/share/doc/tophat EXAMPLESDIR=/usr/local/share/examples/tophat WWWDIR=/usr/local/www/tophat ETCDIR=/usr/local/etc/tophat --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 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: x86_64-unknown-freebsd13.0 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_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=13.0-CURRENT OSREL=13.0 OSVERSION=1300110 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-- =================================================== ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-09-15. ===> License BSL accepted by the user =========================================================================== =================================================== ===> tophat-2.1.1_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.14.7.txz [head-amd64-default-job-07] Installing pkg-1.14.7... [head-amd64-default-job-07] Extracting pkg-1.14.7: .......... done ===> tophat-2.1.1_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of tophat-2.1.1_1 =========================================================================== =================================================== =========================================================================== =================================================== ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-09-15. ===> License BSL accepted by the user ===> Fetching all distfiles required by tophat-2.1.1_1 for building =========================================================================== =================================================== ===> NOTICE: This port is deprecated; you may wish to reconsider installing it: Uses deprecated version of python. It is scheduled to be removed on or after 2020-09-15. ===> License BSL accepted by the user ===> Fetching all distfiles required by tophat-2.1.1_1 for building => SHA256 Checksum OK for tophat-2.1.1.tar.gz. =========================================================================== =================================================== checking for size_t... (cached) yes checking for ptrdiff_t... (cached) yes checking for an ANSI C-conforming const... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking for gzread in -lz... yes checking for stdlib.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for memset... (cached) yes checking for strdup... (cached) yes checking for strrchr... (cached) yes checking for strtol... (cached) yes checking for strsep... (cached) yes checking build system type... amd64-portbld-freebsd13.0 checking host system type... amd64-portbld-freebsd13.0 checking how to create a pax tar archive... gnutar checking dependency style of cc... (cached) gcc3 checking dependency style of c++... (cached) gcc3 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating config.h config.status: executing depfiles commands -- tophat 2.1.1 Configuration Results -- C++ compiler: c++ -I./SeqAn-1.4.2 -std=gnu++98 -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -I./samtools-0.1.18 -pthread -I/usr/local/include Linker flags: -L./samtools-0.1.18 -L/usr/local/lib -fstack-protector-strong BOOST libraries: -lboost_thread GCC version: FreeBSD clang version 11.0.0 (git@github.com:llvm/llvm-project.git llvmorg-11.0.0-rc1-47-gff47911ddfc) Host System type: amd64-portbld-freebsd13.0 Install prefix: /usr/local Install eprefix: ${prefix} See config.h for further configuration information. Email bug reports to . =========================================================================== =================================================== ===> Building for tophat-2.1.1_1 gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1' gmake all-recursive gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1' Making all in src gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src' Makefile:1679: warning: overriding recipe for target 'libbam.a' Makefile:1203: warning: ignoring old recipe for target 'libbam.a' cd ./samtools-0.1.18 && gmake samtools_0.1.18 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src/samtools-0.1.18' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src/samtools-0.1.18' cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bgzf.c -o bgzf.o bgzf.c:275:17: warning: implicit conversion from 'const int' to 'bgzf_byte_t' (aka 'signed char') changes value from 139 to -117 [-Wconstant-conversion] buffer[1] = GZIP_ID2; ~ ^~~~~~~~ bgzf.c:283:17: warning: implicit conversion from 'const int' to 'bgzf_byte_t' (aka 'signed char') changes value from 255 to -1 [-Wconstant-conversion] buffer[9] = OS_UNKNOWN; ~ ^~~~~~~~~~ 2 warnings generated. cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kstring.c -o kstring.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_aux.c -o bam_aux.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam.c -o bam.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_import.c -o bam_import.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam.c -o sam.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_index.c -o bam_index.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_pileup.c -o bam_pileup.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_lpileup.c -o bam_lpileup.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_md.c -o bam_md.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. razf.c -o razf.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. faidx.c -o faidx.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bedidx.c -o bedidx.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. knetfile.c -o knetfile.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_sort.c -o bam_sort.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_header.c -o sam_header.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_reheader.c -o bam_reheader.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kprobaln.c -o kprobaln.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_cat.c -o bam_cat.o ar cr libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o /usr/bin/ranlib libbam.a gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src/samtools-0.1.18' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src/samtools-0.1.18/bcftools' cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf.c -o bcf.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. vcf.c -o vcf.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcfutils.c -o bcfutils.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. prob1.c -o prob1.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. em.c -o em.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kfunc.c -o kfunc.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. kmin.c -o kmin.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. index.c -o index.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. fet.c -o fet.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. mut.c -o mut.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I.. -I. bcf2qcall.c -o bcf2qcall.o ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src/samtools-0.1.18/bcftools' cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_tview.c -o bam_tview.o bam_tview.c:434:2: warning: "No curses library is available; tview is disabled." [-W#warnings] #warning "No curses library is available; tview is disabled." ^ 1 warning generated. cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_plcmd.c -o bam_plcmd.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sam_view.c -o sam_view.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdup.c -o bam_rmdup.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_rmdupse.c -o bam_rmdupse.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_mate.c -o bam_mate.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_stat.c -o bam_stat.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam_color.c -o bam_color.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bamtk.c -o bamtk.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. kaln.c -o kaln.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2bcf.c -o bam2bcf.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2bcf_indel.c -o bam2bcf_indel.o bam2bcf_indel.c:32:52: warning: for loop has empty body [-Wempty-body] for (r = p; *r && *r != '\t' && *r != '\n'; ++r); lp = r - p; ^ bam2bcf_indel.c:32:52: note: put the semicolon on a separate line to silence this warning bam2bcf_indel.c:33:52: warning: for loop has empty body [-Wempty-body] for (r = q; *r && *r != '\t' && *r != '\n'; ++r); lq = r - q; ^ bam2bcf_indel.c:33:52: note: put the semicolon on a separate line to silence this warning 2 warnings generated. cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. errmod.c -o errmod.o errmod.c:79:8: warning: self-comparison always evaluates to false [-Wtautological-compare] if (m > m) return -1; ^ 1 warning generated. cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. sample.c -o sample.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. cut_target.c -o cut_target.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. phase.c -o phase.o cc -c -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0 -I. bam2depth.c -o bam2depth.o cc -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -O2 -pipe -Wno-unused -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -O -o samtools_0.1.18 bam_tview.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lm -lz #-lcurses ld: error: undefined symbol: __ks_insertsort_uint32_t >>> referenced by bam2bcf_indel.c:12 >>> bam2bcf_indel.o:(ks_combsort_uint32_t) >>> referenced by bam2bcf_indel.c:12 >>> bam2bcf_indel.o:(ks_introsort_uint32_t) ld: error: undefined symbol: __ks_insertsort_uint16_t >>> referenced by errmod.c:4 >>> errmod.o:(ks_combsort_uint16_t) >>> referenced by errmod.c:4 >>> errmod.o:(ks_introsort_uint16_t) ld: error: undefined symbol: __ks_insertsort_rseq >>> referenced by phase.c:51 >>> phase.o:(ks_combsort_rseq) >>> referenced by phase.c:51 >>> phase.o:(ks_introsort_rseq) ld: error: undefined symbol: unpackInt16 >>> referenced by bgzf.c:497 >>> bgzf.o:(bgzf_read_block) in archive libbam.a >>> referenced by bgzf.c:407 >>> bgzf.o:(check_header) in archive libbam.a >>> referenced by bgzf.c:410 >>> bgzf.o:(check_header) in archive libbam.a ld: error: undefined symbol: packInt16 >>> referenced by bgzf.c:344 >>> bgzf.o:(deflate_block) in archive libbam.a ld: error: undefined symbol: packInt32 >>> referenced by bgzf.c:347 >>> bgzf.o:(deflate_block) in archive libbam.a >>> referenced by bgzf.c:348 >>> bgzf.o:(deflate_block) in archive libbam.a ld: error: undefined symbol: __ks_insertsort_off >>> referenced by bam_index.c:52 >>> bam_index.o:(ks_combsort_off) in archive libbam.a >>> referenced by bam_index.c:52 >>> bam_index.o:(ks_introsort_off) in archive libbam.a ld: error: undefined symbol: __ks_insertsort_uint64_t >>> referenced by bedidx.c:12 >>> bedidx.o:(ks_combsort_uint64_t) in archive libbam.a >>> referenced by bedidx.c:12 >>> bedidx.o:(ks_introsort_uint64_t) in archive libbam.a ld: error: undefined symbol: __ks_insertsort_heap >>> referenced by bam_sort.c:53 >>> bam_sort.o:(ks_combsort_heap) in archive libbam.a >>> referenced by bam_sort.c:53 >>> bam_sort.o:(ks_introsort_heap) in archive libbam.a ld: error: undefined symbol: __ks_insertsort_sort >>> referenced by bam_sort.c:309 >>> bam_sort.o:(ks_combsort_sort) in archive libbam.a >>> referenced by bam_sort.c:309 >>> bam_sort.o:(ks_introsort_sort) in archive libbam.a cc: error: linker command failed with exit code 1 (use -v to see invocation) gmake[4]: *** [Makefile:50: samtools_0.1.18] Error 1 gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src/samtools-0.1.18' gmake[3]: *** [Makefile:1679: libbam.a] Error 2 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1/src' gmake[2]: *** [Makefile:313: all-recursive] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1' gmake[1]: *** [Makefile:253: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/tophat/work/tophat-2.1.1' *** Error code 1 Stop. make: stopped in /usr/ports/biology/tophat