From owner-freebsd-pkg-fallout@freebsd.org Sun Mar 24 05:56:21 2019 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 3EB52154B9B2 for ; Sun, 24 Mar 2019 05:56:21 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.ysv.freebsd.org (mailman.ysv.freebsd.org [IPv6:2001:1900:2254:206a::50:5]) by mx1.freebsd.org (Postfix) with ESMTP id A71A76DAB0 for ; Sun, 24 Mar 2019 05:56:20 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id 62C2B154B9B1; Sun, 24 Mar 2019 05:56:20 +0000 (UTC) Delivered-To: pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 055A0154B9B0 for ; Sun, 24 Mar 2019 05:56:20 +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) server-signature RSA-PSS (4096 bits) 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 9212D6DAAD; Sun, 24 Mar 2019 05:56:19 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy12.nyi.freebsd.org (beefy12.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:ef]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) server-signature RSA-PSS (4096 bits)) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 7662F1C021; Sun, 24 Mar 2019 05:56:19 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy12.nyi.freebsd.org (localhost [127.0.0.1]) by beefy12.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id x2O5uJeV059568; Sun, 24 Mar 2019 05:56:19 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy12.nyi.freebsd.org (8.15.2/8.15.2/Submit) id x2O5uJ0L059567; Sun, 24 Mar 2019 05:56:19 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sun, 24 Mar 2019 05:56:19 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201903240556.x2O5uJ0L059567@beefy12.nyi.freebsd.org> To: danilo@FreeBSD.org Subject: [package - head-amd64-default][biology/iolib] Failed for io_lib-1.14.10 in build Cc: pkg-fallout@FreeBSD.org X-Rspamd-Queue-Id: 9212D6DAAD X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.97 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-1.000,0]; NEURAL_HAM_SHORT(-0.97)[-0.971,0]; ASN(0.00)[asn:11403, ipnet:2610:1c1:1::/48, country:US]; NEURAL_HAM_LONG(-1.00)[-1.000,0] X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.29 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sun, 24 Mar 2019 05:56:21 -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: danilo@FreeBSD.org Last committer: linimon@FreeBSD.org Ident: $FreeBSD: head/biology/iolib/Makefile 484209 2018-11-05 19:42:37Z linimon $ Log URL: http://beefy12.nyi.freebsd.org/data/head-amd64-default/p496699_s345461/logs/io_lib-1.14.10.log Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p496699_s345461 Log: =>> Building biology/iolib build started at Sun Mar 24 05:54:22 UTC 2019 port directory: /usr/ports/biology/iolib package name: io_lib-1.14.10 building for: FreeBSD head-amd64-default-job-16 13.0-CURRENT FreeBSD 13.0-CURRENT 1300017 amd64 maintained by: danilo@FreeBSD.org Makefile ident: $FreeBSD: head/biology/iolib/Makefile 484209 2018-11-05 19:42:37Z linimon $ Poudriere version: 3.2.8-3-g02cc9753 Host OSVERSION: 1300009 Jail OSVERSION: 1300017 Job Id: 16 !!! Jail is newer than host. (Jail: 1300017, Host: 1300009) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/csh OSVERSION=1300017 UNAME_v=FreeBSD 13.0-CURRENT 1300017 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=3.2.8-3-g02cc9753 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-- danilo@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/iolib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/iolib/work HOME=/wrkdirs/usr/ports/biology/iolib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/iolib/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=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/iolib/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/iolib/work HOME=/wrkdirs/usr/ports/biology/iolib/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/iolib/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 -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-- OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/io_lib" EXAMPLESDIR="share/examples/io_lib" DATADIR="share/io_lib" WWWDIR="www/io_lib" ETCDIR="etc/io_lib" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/io_lib DOCSDIR=/usr/local/share/doc/io_lib EXAMPLESDIR=/usr/local/share/examples/io_lib WWWDIR=/usr/local/www/io_lib ETCDIR=/usr/local/etc/io_lib --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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: x86_64-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) 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 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) 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=1300017 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=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) 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-- =================================================== ===> License BSD3CLAUSE accepted by the user =========================================================================== =================================================== ===> io_lib-1.14.10 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [head-amd64-default-job-16] Installing pkg-1.10.5_5... [head-amd64-default-job-16] Extracting pkg-1.10.5_5: .......... done ===> io_lib-1.14.10 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of io_lib-1.14.10 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by io_lib-1.14.10 for building =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by io_lib-1.14.10 for building => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE accepted by the user ===> Fetching all distfiles required by io_lib-1.14.10 for building ===> Extracting for io_lib-1.14.10 => SHA256 Checksum OK for jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for io_lib-1.14.10 ===> Applying FreeBSD patches for io_lib-1.14.10 =========================================================================== =================================================== ===> io_lib-1.14.10 depends on package: autoconf>=2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69_2.txz [head-amd64-default-job-16] Installing autoconf-2.69_2... mv -f .deps/libstaden_read_la-strings.Tpo .deps/libstaden_read_la-strings.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-traceType.lo -MD -MP -MF .deps/libstaden_read_la-traceType.Tpo -c -o libstaden_read_la-traceType.lo `test -f 'traceType.c' || echo './'`traceType.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-traceType.lo -MD -MP -MF .deps/libstaden_read_la-traceType.Tpo -c traceType.c -fPIC -DPIC -o .libs/libstaden_read_la-traceType.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-traceType.lo -MD -MP -MF .deps/libstaden_read_la-traceType.Tpo -c traceType.c -o libstaden_read_la-traceType.o >/dev/null 2>&1 mv -f 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../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-vlen.lo -MD -MP -MF .deps/libstaden_read_la-vlen.Tpo -c -o libstaden_read_la-vlen.lo `test -f 'vlen.c' || echo './'`vlen.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-vlen.lo -MD -MP -MF .deps/libstaden_read_la-vlen.Tpo -c vlen.c -fPIC -DPIC -o .libs/libstaden_read_la-vlen.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-vlen.lo -MD -MP -MF .deps/libstaden_read_la-vlen.Tpo -c vlen.c -o libstaden_read_la-vlen.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-vlen.Tpo .deps/libstaden_read_la-vlen.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-hash_table.lo -MD -MP -MF .deps/libstaden_read_la-hash_table.Tpo -c -o libstaden_read_la-hash_table.lo `test -f 'hash_table.c' || echo './'`hash_table.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-hash_table.lo -MD -MP -MF .deps/libstaden_read_la-hash_table.Tpo -c hash_table.c -fPIC -DPIC -o .libs/libstaden_read_la-hash_table.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-hash_table.lo -MD -MP -MF .deps/libstaden_read_la-hash_table.Tpo -c hash_table.c -o libstaden_read_la-hash_table.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-hash_table.Tpo .deps/libstaden_read_la-hash_table.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-jenkins_lookup3.lo -MD -MP -MF .deps/libstaden_read_la-jenkins_lookup3.Tpo -c -o libstaden_read_la-jenkins_lookup3.lo `test -f 'jenkins_lookup3.c' || echo './'`jenkins_lookup3.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-jenkins_lookup3.lo -MD -MP -MF .deps/libstaden_read_la-jenkins_lookup3.Tpo -c jenkins_lookup3.c -fPIC -DPIC -o .libs/libstaden_read_la-jenkins_lookup3.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-jenkins_lookup3.lo -MD -MP -MF .deps/libstaden_read_la-jenkins_lookup3.Tpo -c jenkins_lookup3.c -o libstaden_read_la-jenkins_lookup3.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-jenkins_lookup3.Tpo .deps/libstaden_read_la-jenkins_lookup3.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c -o libstaden_read_la-mFILE.lo `test -f 'mFILE.c' || echo './'`mFILE.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c mFILE.c -fPIC -DPIC -o .libs/libstaden_read_la-mFILE.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-mFILE.lo -MD -MP -MF .deps/libstaden_read_la-mFILE.Tpo -c mFILE.c -o libstaden_read_la-mFILE.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-mFILE.Tpo .deps/libstaden_read_la-mFILE.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-pooled_alloc.lo -MD -MP -MF .deps/libstaden_read_la-pooled_alloc.Tpo -c -o libstaden_read_la-pooled_alloc.lo `test -f 'pooled_alloc.c' || echo './'`pooled_alloc.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-pooled_alloc.lo -MD -MP -MF .deps/libstaden_read_la-pooled_alloc.Tpo -c pooled_alloc.c -fPIC -DPIC -o .libs/libstaden_read_la-pooled_alloc.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-pooled_alloc.lo -MD -MP -MF .deps/libstaden_read_la-pooled_alloc.Tpo -c pooled_alloc.c -o libstaden_read_la-pooled_alloc.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-pooled_alloc.Tpo .deps/libstaden_read_la-pooled_alloc.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c -o libstaden_read_la-bam.lo `test -f 'bam.c' || echo './'`bam.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c bam.c -fPIC -DPIC -o .libs/libstaden_read_la-bam.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-bam.lo -MD -MP -MF .deps/libstaden_read_la-bam.Tpo -c bam.c -o libstaden_read_la-bam.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-bam.Tpo .deps/libstaden_read_la-bam.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c -o libstaden_read_la-sam_header.lo `test -f 'sam_header.c' || echo './'`sam_header.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c sam_header.c -fPIC -DPIC -o .libs/libstaden_read_la-sam_header.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-sam_header.lo -MD -MP -MF .deps/libstaden_read_la-sam_header.Tpo -c sam_header.c -o libstaden_read_la-sam_header.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-sam_header.Tpo .deps/libstaden_read_la-sam_header.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-rANS_static.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static.Tpo -c -o libstaden_read_la-rANS_static.lo `test -f 'rANS_static.c' || echo './'`rANS_static.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-rANS_static.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static.Tpo -c rANS_static.c -fPIC -DPIC -o .libs/libstaden_read_la-rANS_static.o rANS_static.c:274:20: warning: unused function 'RansDecSymbolInit' [-Wunused-function] static inline void RansDecSymbolInit(RansDecSymbol* s, uint32_t start, uint32_t freq) ^ rANS_static.c:318:20: warning: unused function 'RansDecAdvanceSymbol' [-Wunused-function] static inline void RansDecAdvanceSymbol(RansState* r, uint8_t** pptr, RansDecSymbol const* sym, uint32_t scale_bits) ^ rANS_static.c:336:20: warning: unused function 'RansDecAdvanceSymbolStep' [-Wunused-function] static inline void RansDecAdvanceSymbolStep(RansState* r, RansDecSymbol const* sym, uint32_t scale_bits) ^ rANS_static.c:348:20: warning: unused function 'RansDecRenorm' [-Wunused-function] static inline void RansDecRenorm(RansState* r, uint8_t** pptr) { ^ rANS_static.c:470:20: warning: unused function 'RansDecAdvanceSymbol32' [-Wunused-function] static inline void RansDecAdvanceSymbol32(RansState* r, uint8_t** pptr, RansDecSymbol32 const* sym, uint32_t scale_bits) ^ 5 warnings generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-rANS_static.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static.Tpo -c rANS_static.c -o libstaden_read_la-rANS_static.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-rANS_static.Tpo .deps/libstaden_read_la-rANS_static.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-rANS_static4x16pr.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static4x16pr.Tpo -c -o libstaden_read_la-rANS_static4x16pr.lo `test -f 'rANS_static4x16pr.c' || echo './'`rANS_static4x16pr.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-rANS_static4x16pr.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static4x16pr.Tpo -c rANS_static4x16pr.c -fPIC -DPIC -o .libs/libstaden_read_la-rANS_static4x16pr.o rANS_static4x16pr.c:107:20: warning: unused function 'RansEncPut' [-Wunused-function] static inline void RansEncPut(RansState* r, uint8_t** pptr, uint32_t start, uint32_t freq, uint32_t scale_bits) ^ rANS_static4x16pr.c:149:24: warning: unused function 'RansDecGet' [-Wunused-function] static inline uint32_t RansDecGet(RansState* r, uint32_t scale_bits) ^ rANS_static4x16pr.c:282:20: warning: unused function 'RansDecSymbolInit' [-Wunused-function] static inline void RansDecSymbolInit(RansDecSymbol* s, uint32_t start, uint32_t freq) ^ rANS_static4x16pr.c:334:20: warning: unused function 'RansDecAdvanceSymbol' [-Wunused-function] static inline void RansDecAdvanceSymbol(RansState* r, uint8_t** pptr, RansDecSymbol const* sym, uint32_t scale_bits) ^ rANS_static4x16pr.c:352:20: warning: unused function 'RansDecAdvanceSymbolStep' [-Wunused-function] static inline void RansDecAdvanceSymbolStep(RansState* r, RansDecSymbol const* sym, uint32_t scale_bits) ^ 5 warnings generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-rANS_static4x16pr.lo -MD -MP -MF .deps/libstaden_read_la-rANS_static4x16pr.Tpo -c rANS_static4x16pr.c -o libstaden_read_la-rANS_static4x16pr.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-rANS_static4x16pr.Tpo .deps/libstaden_read_la-rANS_static4x16pr.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c -o libstaden_read_la-cram_codecs.lo `test -f 'cram_codecs.c' || echo './'`cram_codecs.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c cram_codecs.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_codecs.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_codecs.lo -MD -MP -MF .deps/libstaden_read_la-cram_codecs.Tpo -c cram_codecs.c -o libstaden_read_la-cram_codecs.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_codecs.Tpo .deps/libstaden_read_la-cram_codecs.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c -o libstaden_read_la-cram_encode.lo `test -f 'cram_encode.c' || echo './'`cram_encode.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c cram_encode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_encode.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_encode.lo -MD -MP -MF .deps/libstaden_read_la-cram_encode.Tpo -c cram_encode.c -o libstaden_read_la-cram_encode.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_encode.Tpo .deps/libstaden_read_la-cram_encode.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c -o libstaden_read_la-cram_decode.lo `test -f 'cram_decode.c' || echo './'`cram_decode.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c cram_decode.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_decode.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_decode.lo -MD -MP -MF .deps/libstaden_read_la-cram_decode.Tpo -c cram_decode.c -o libstaden_read_la-cram_decode.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_decode.Tpo .deps/libstaden_read_la-cram_decode.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c -o libstaden_read_la-cram_stats.lo `test -f 'cram_stats.c' || echo './'`cram_stats.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c cram_stats.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_stats.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_stats.lo -MD -MP -MF .deps/libstaden_read_la-cram_stats.Tpo -c cram_stats.c -o libstaden_read_la-cram_stats.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_stats.Tpo .deps/libstaden_read_la-cram_stats.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c -o libstaden_read_la-cram_io.lo `test -f 'cram_io.c' || echo './'`cram_io.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_io.o cram_io.c:3742:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ ./cram_io.h:105:311: note: expanded from macro 'itf8_put' #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~^~~~~~~~~~~~~~~~~ cram_io.c:3742:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ ./cram_io.h:105:345: note: expanded from macro 'itf8_put' #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~~~~~~^~~~~ cram_io.c:3742:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ ./cram_io.h:105:367: note: expanded from macro 'itf8_put' #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~~~~~~^~~~~ cram_io.c:3742:8: warning: implicit conversion from 'int' to 'char' changes value from 255 to -1 [-Wconstant-conversion] cp += itf8_put(cp, -2); ^~~~~~~~~~~~~~~~ ./cram_io.h:105:388: note: expanded from macro 'itf8_put' #define itf8_put(c,v) ((!((v)&~0x7f))?((c)[0]=(v),1):(!((v)&~0x3fff))?((c)[0]=((v)>>8)|0x80,(c)[1]=(v)&0xff,2):(!((v)&~0x1fffff))?((c)[0]=((v)>>16)|0xc0,(c)[1]=((v)>>8)&0xff,(c)[2]=(v)&0xff,3):(!((v)&~0xfffffff))?((c)[0]=((v)>>24)|0xe0,(c)[1]=((v)>>16)&0xff,(c)[2]=((v)>>8)&0xff,(c)[3]=(v)&0xff,4):((c)[0]=0xf0|(((v)>>28)&0xff),(c)[1]=((v)>>20)&0xff,(c)[2]=((v)>>12)&0xff,(c)[3]=((v)>>4)&0xff,(c)[4]=(v)&0xf,5)) ~~~~~~~~~^~~~~ 4 warnings generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_io.lo -MD -MP -MF .deps/libstaden_read_la-cram_io.Tpo -c cram_io.c -o libstaden_read_la-cram_io.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_io.Tpo .deps/libstaden_read_la-cram_io.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c -o libstaden_read_la-cram_index.lo `test -f 'cram_index.c' || echo './'`cram_index.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c cram_index.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_index.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_index.lo -MD -MP -MF .deps/libstaden_read_la-cram_index.Tpo -c cram_index.c -o libstaden_read_la-cram_index.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_index.Tpo .deps/libstaden_read_la-cram_index.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c -o libstaden_read_la-zfio.lo `test -f 'zfio.c' || echo './'`zfio.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c zfio.c -fPIC -DPIC -o .libs/libstaden_read_la-zfio.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-zfio.lo -MD -MP -MF .deps/libstaden_read_la-zfio.Tpo -c zfio.c -o libstaden_read_la-zfio.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-zfio.Tpo .deps/libstaden_read_la-zfio.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c -o libstaden_read_la-dstring.lo `test -f 'dstring.c' || echo './'`dstring.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c dstring.c -fPIC -DPIC -o .libs/libstaden_read_la-dstring.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-dstring.lo -MD -MP -MF .deps/libstaden_read_la-dstring.Tpo -c dstring.c -o libstaden_read_la-dstring.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-dstring.Tpo .deps/libstaden_read_la-dstring.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-string_alloc.lo -MD -MP -MF .deps/libstaden_read_la-string_alloc.Tpo -c -o libstaden_read_la-string_alloc.lo `test -f 'string_alloc.c' || echo './'`string_alloc.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. 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crc32.c -fPIC -DPIC -o .libs/libstaden_read_la-crc32.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-crc32.lo -MD -MP -MF .deps/libstaden_read_la-crc32.Tpo -c crc32.c -o libstaden_read_la-crc32.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-crc32.Tpo .deps/libstaden_read_la-crc32.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c -o libstaden_read_la-scram.lo `test -f 'scram.c' || echo './'`scram.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -fPIC -DPIC -o .libs/libstaden_read_la-scram.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-scram.lo -MD -MP -MF .deps/libstaden_read_la-scram.Tpo -c scram.c -o libstaden_read_la-scram.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-scram.Tpo .deps/libstaden_read_la-scram.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c -o libstaden_read_la-thread_pool.lo `test -f 'thread_pool.c' || echo './'`thread_pool.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-thread_pool.lo -MD -MP -MF .deps/libstaden_read_la-thread_pool.Tpo -c thread_pool.c -fPIC -DPIC -o .libs/libstaden_read_la-thread_pool.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe 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libstaden_read_la-binning.lo -MD -MP -MF .deps/libstaden_read_la-binning.Tpo -c binning.c -o libstaden_read_la-binning.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-binning.Tpo .deps/libstaden_read_la-binning.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c -o libstaden_read_la-cram_bambam.lo `test -f 'cram_bambam.c' || echo './'`cram_bambam.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c cram_bambam.c -fPIC -DPIC -o .libs/libstaden_read_la-cram_bambam.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-cram_bambam.lo -MD -MP -MF .deps/libstaden_read_la-cram_bambam.Tpo -c cram_bambam.c -o libstaden_read_la-cram_bambam.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-cram_bambam.Tpo .deps/libstaden_read_la-cram_bambam.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c -o libstaden_read_la-bgzip.lo `test -f 'bgzip.c' || echo './'`bgzip.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c bgzip.c -fPIC -DPIC -o .libs/libstaden_read_la-bgzip.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-bgzip.lo -MD -MP -MF .deps/libstaden_read_la-bgzip.Tpo -c bgzip.c -o libstaden_read_la-bgzip.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-bgzip.Tpo .deps/libstaden_read_la-bgzip.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-tokenise_name3.lo -MD -MP -MF .deps/libstaden_read_la-tokenise_name3.Tpo -c -o libstaden_read_la-tokenise_name3.lo `test -f 'tokenise_name3.c' || echo './'`tokenise_name3.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-tokenise_name3.lo -MD -MP -MF .deps/libstaden_read_la-tokenise_name3.Tpo -c tokenise_name3.c -fPIC -DPIC -o .libs/libstaden_read_la-tokenise_name3.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-tokenise_name3.lo -MD -MP -MF .deps/libstaden_read_la-tokenise_name3.Tpo -c tokenise_name3.c -o libstaden_read_la-tokenise_name3.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-tokenise_name3.Tpo .deps/libstaden_read_la-tokenise_name3.Plo /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-fqzcomp_qual.lo -MD -MP -MF .deps/libstaden_read_la-fqzcomp_qual.Tpo -c -o libstaden_read_la-fqzcomp_qual.lo `test -f 'fqzcomp_qual.c' || echo './'`fqzcomp_qual.c libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-fqzcomp_qual.lo -MD -MP -MF .deps/libstaden_read_la-fqzcomp_qual.Tpo -c fqzcomp_qual.c -fPIC -DPIC -o .libs/libstaden_read_la-fqzcomp_qual.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I.. -I.. -I/usr/local/include -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT libstaden_read_la-fqzcomp_qual.lo -MD -MP -MF .deps/libstaden_read_la-fqzcomp_qual.Tpo -c fqzcomp_qual.c -o libstaden_read_la-fqzcomp_qual.o >/dev/null 2>&1 mv -f .deps/libstaden_read_la-fqzcomp_qual.Tpo .deps/libstaden_read_la-fqzcomp_qual.Plo /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -version-info 13:0:0 -fstack-protector -o libstaden-read.la -rpath /usr/local/lib libstaden_read_la-Read.lo libstaden_read_la-scf_extras.lo libstaden_read_la-translate.lo libstaden_read_la-compression.lo libstaden_read_la-ztr.lo libstaden_read_la-ztr_translate.lo libstaden_read_la-deflate_interlaced.lo libstaden_read_la-fpoint.lo libstaden_read_la-seqIOABI.lo libstaden_read_la-seqIOALF.lo libstaden_read_la-expFileIO.lo libstaden_read_la-seqIOPlain.lo libstaden_read_la-misc_scf.lo libstaden_read_la-read_scf.lo libstaden_read_la-write_scf.lo libstaden_read_la-sff.lo libstaden_read_la-srf.lo libstaden_read_la-array.lo libstaden_read_la-compress.lo libstaden_read_la-error.lo libstaden_read_la-files.lo libstaden_read_la-find.lo libstaden_read_la-mach-io.lo libstaden_read_la-open_trace_file.lo libstaden_read_la-read_alloc.lo libstaden_read_la-strings.lo libstaden_read_la-traceType.lo l ibstaden_read_la-xalloc.lo libstaden_read_la-vlen.lo libstaden_read_la-hash_table.lo libstaden_read_la-jenkins_lookup3.lo libstaden_read_la-mFILE.lo libstaden_read_la-pooled_alloc.lo libstaden_read_la-bam.lo libstaden_read_la-sam_header.lo libstaden_read_la-rANS_static.lo libstaden_read_la-rANS_static4x16pr.lo libstaden_read_la-cram_codecs.lo libstaden_read_la-cram_encode.lo libstaden_read_la-cram_decode.lo libstaden_read_la-cram_stats.lo libstaden_read_la-cram_io.lo libstaden_read_la-cram_index.lo libstaden_read_la-zfio.lo libstaden_read_la-dstring.lo libstaden_read_la-string_alloc.lo libstaden_read_la-md5.lo libstaden_read_la-crc32.lo libstaden_read_la-scram.lo libstaden_read_la-thread_pool.lo libstaden_read_la-binning.lo libstaden_read_la-cram_bambam.lo libstaden_read_la-bgzip.lo libstaden_read_la-tokenise_name3.lo libstaden_read_la-fqzcomp_qual.lo -lz -L/usr/local/lib -lcurl -lm -llzma -lbz2 libtool: link: cc -shared -fPIC -DPIC .libs/libstaden_read_la-Read.o .libs/libstaden_read_la-scf_extras.o .libs/libstaden_read_la-translate.o .libs/libstaden_read_la-compression.o .libs/libstaden_read_la-ztr.o .libs/libstaden_read_la-ztr_translate.o .libs/libstaden_read_la-deflate_interlaced.o .libs/libstaden_read_la-fpoint.o .libs/libstaden_read_la-seqIOABI.o .libs/libstaden_read_la-seqIOALF.o .libs/libstaden_read_la-expFileIO.o .libs/libstaden_read_la-seqIOPlain.o .libs/libstaden_read_la-misc_scf.o .libs/libstaden_read_la-read_scf.o .libs/libstaden_read_la-write_scf.o .libs/libstaden_read_la-sff.o .libs/libstaden_read_la-srf.o .libs/libstaden_read_la-array.o .libs/libstaden_read_la-compress.o .libs/libstaden_read_la-error.o .libs/libstaden_read_la-files.o .libs/libstaden_read_la-find.o .libs/libstaden_read_la-mach-io.o .libs/libstaden_read_la-open_trace_file.o .libs/libstaden_read_la-read_alloc.o .libs/libstaden_read_la-strings.o .libs/libstaden_read_la-traceType.o .libs/libstade n_read_la-xalloc.o .libs/libstaden_read_la-vlen.o .libs/libstaden_read_la-hash_table.o .libs/libstaden_read_la-jenkins_lookup3.o .libs/libstaden_read_la-mFILE.o .libs/libstaden_read_la-pooled_alloc.o .libs/libstaden_read_la-bam.o .libs/libstaden_read_la-sam_header.o .libs/libstaden_read_la-rANS_static.o .libs/libstaden_read_la-rANS_static4x16pr.o .libs/libstaden_read_la-cram_codecs.o .libs/libstaden_read_la-cram_encode.o .libs/libstaden_read_la-cram_decode.o .libs/libstaden_read_la-cram_stats.o .libs/libstaden_read_la-cram_io.o .libs/libstaden_read_la-cram_index.o .libs/libstaden_read_la-zfio.o .libs/libstaden_read_la-dstring.o .libs/libstaden_read_la-string_alloc.o .libs/libstaden_read_la-md5.o .libs/libstaden_read_la-crc32.o .libs/libstaden_read_la-scram.o .libs/libstaden_read_la-thread_pool.o .libs/libstaden_read_la-binning.o .libs/libstaden_read_la-cram_bambam.o .libs/libstaden_read_la-bgzip.o .libs/libstaden_read_la-tokenise_name3.o .libs/libstaden_read_la-fqzcomp_qual.o -lz -L/usr/local/lib -lcurl -lm -llzma -lbz2 -O! 2 -fstack-protector -fstack-protector -Wl,-soname -Wl,libstaden-read.so.13 -o .libs/libstaden-read.so.13.0.0 libtool: link: (cd ".libs" && rm -f "libstaden-read.so.13" && ln -s "libstaden-read.so.13.0.0" "libstaden-read.so.13") libtool: link: (cd ".libs" && rm -f "libstaden-read.so" && ln -s "libstaden-read.so.13.0.0" "libstaden-read.so") libtool: link: ar cru .libs/libstaden-read.a libstaden_read_la-Read.o libstaden_read_la-scf_extras.o libstaden_read_la-translate.o libstaden_read_la-compression.o libstaden_read_la-ztr.o libstaden_read_la-ztr_translate.o libstaden_read_la-deflate_interlaced.o libstaden_read_la-fpoint.o libstaden_read_la-seqIOABI.o libstaden_read_la-seqIOALF.o libstaden_read_la-expFileIO.o libstaden_read_la-seqIOPlain.o libstaden_read_la-misc_scf.o libstaden_read_la-read_scf.o libstaden_read_la-write_scf.o libstaden_read_la-sff.o libstaden_read_la-srf.o libstaden_read_la-array.o libstaden_read_la-compress.o libstaden_read_la-error.o libstaden_read_la-files.o libstaden_read_la-find.o libstaden_read_la-mach-io.o libstaden_read_la-open_trace_file.o libstaden_read_la-read_alloc.o libstaden_read_la-strings.o libstaden_read_la-traceType.o libstaden_read_la-xalloc.o libstaden_read_la-vlen.o libstaden_read_la-hash_table.o libstaden_read_la-jenkins_lookup3.o libstaden_read_la-mFILE.o libstaden_read_la-pooled_ alloc.o libstaden_read_la-bam.o libstaden_read_la-sam_header.o libstaden_read_la-rANS_static.o libstaden_read_la-rANS_static4x16pr.o libstaden_read_la-cram_codecs.o libstaden_read_la-cram_encode.o libstaden_read_la-cram_decode.o libstaden_read_la-cram_stats.o libstaden_read_la-cram_io.o libstaden_read_la-cram_index.o libstaden_read_la-zfio.o libstaden_read_la-dstring.o libstaden_read_la-string_alloc.o libstaden_read_la-md5.o libstaden_read_la-crc32.o libstaden_read_la-scram.o libstaden_read_la-thread_pool.o libstaden_read_la-binning.o libstaden_read_la-cram_bambam.o libstaden_read_la-bgzip.o libstaden_read_la-tokenise_name3.o libstaden_read_la-fqzcomp_qual.o libtool: link: ranlib .libs/libstaden-read.a libtool: link: ( cd ".libs" && rm -f "libstaden-read.la" && ln -s "../libstaden-read.la" "libstaden-read.la" ) gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/io_lib' Making all in progs gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/progs' cc -DHAVE_CONFIG_H -I. -I.. -I.. -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -MT convert_trace.o -MD -MP -MF .deps/convert_trace.Tpo -c -o convert_trace.o convert_trace.c mv -f .deps/convert_trace.Tpo .deps/convert_trace.Po /bin/sh ../libtool --tag=CC --mode=link cc -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -fstack-protector -o convert_trace convert_trace.o ../io_lib/libstaden-read.la -lm -llzma -lbz2 libtool: link: cc -Wall -O2 -pipe -fstack-protector -fno-strict-aliasing -fstack-protector -o .libs/convert_trace convert_trace.o ../io_lib/.libs/libstaden-read.so -L/usr/local/lib -lz -lcurl -lm -llzma -lbz2 -Wl,-rpath -Wl,/usr/local/lib ld: error: ../io_lib/.libs/libstaden-read.so: undefined reference to pthread_create cc: error: linker command failed with exit code 1 (use -v to see invocation) gmake[3]: *** [Makefile:644: convert_trace] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10/progs' gmake[2]: *** [Makefile:750: all-recursive] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10' gmake[1]: *** [Makefile:495: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/iolib/work/io_lib-io_lib-1-14-10' *** Error code 1 Stop. make: stopped in /usr/ports/biology/iolib