From owner-freebsd-pkg-fallout@freebsd.org Thu Dec 27 01:52:09 2018 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 8153D133E534 for ; Thu, 27 Dec 2018 01:52:09 +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 AF2A780080 for ; Thu, 27 Dec 2018 01:52:08 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id 72D78133E52E; Thu, 27 Dec 2018 01:52:08 +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 1602E133E52B for ; Thu, 27 Dec 2018 01:52:08 +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 BB0828007C for ; Thu, 27 Dec 2018 01:52:07 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy14.nyi.freebsd.org (beefy14.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:e1]) (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 AECE949D2 for ; Thu, 27 Dec 2018 01:52:07 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy14.nyi.freebsd.org (localhost [127.0.0.1]) by beefy14.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id wBR1q7Nd078281 for ; Thu, 27 Dec 2018 01:52:07 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy14.nyi.freebsd.org (8.15.2/8.15.2/Submit) id wBR1q7fi078277; Thu, 27 Dec 2018 01:52:07 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Thu, 27 Dec 2018 01:52:07 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201812270152.wBR1q7fi078277@beefy14.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 112mips-quarterly][biology/stringtie] Failed for stringtie-1.3.4.d in build X-Rspamd-Queue-Id: BB0828007C X-Spamd-Bar: -- Authentication-Results: mx1.freebsd.org X-Spamd-Result: default: False [-2.98 / 15.00]; local_wl_from(0.00)[FreeBSD.org]; NEURAL_HAM_MEDIUM(-1.00)[-1.000,0]; NEURAL_HAM_SHORT(-0.98)[-0.983,0]; 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: Thu, 27 Dec 2018 01:52:10 -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: mzaki@niid.go.jp Last committer: yuri@FreeBSD.org Ident: $FreeBSD: branches/2018Q4/biology/stringtie/Makefile 474480 2018-07-11 21:32:39Z yuri $ Log URL: http://beefy14.nyi.freebsd.org/data/112mips-quarterly/488499/logs/stringtie-1.3.4.d.log Build URL: http://beefy14.nyi.freebsd.org/build.html?mastername=112mips-quarterly&build=488499 Log: =>> Building biology/stringtie build started at Thu Dec 27 01:50:22 UTC 2018 port directory: /usr/ports/biology/stringtie package name: stringtie-1.3.4.d building for: FreeBSD 112mips-quarterly-job-12 11.2-RELEASE-p7 FreeBSD 11.2-RELEASE-p7 1102000 mips maintained by: mzaki@niid.go.jp Makefile ident: $FreeBSD: branches/2018Q4/biology/stringtie/Makefile 474480 2018-07-11 21:32:39Z yuri $ Poudriere version: 3.2.8 Host OSVERSION: 1300002 Jail OSVERSION: 1102000 Job Id: 12 ---Begin Environment--- POUDRIEREPATH=/usr/local/bin/poudriere SCRIPTPATH=/usr/local/share/poudriere/bulk.sh OLDPWD=/usr/local/poudriere/data/.m/112mips-quarterly/ref/.p SCRIPTPREFIX=/usr/local/share/poudriere MASTERNAME=112mips-quarterly P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS PWD=/usr/local/poudriere/data/.m/112mips-quarterly/ref/.p/pool SAVED_TERM= PACKAGE_BUILDING=yes POUDRIERE_BUILD_TYPE=bulk MASTERMNT=/usr/local/poudriere/data/.m/112mips-quarterly/ref POUDRIERE_VERSION=3.2.8 LIBEXECPREFIX=/usr/local/libexec/poudriere USER=root QEMU_EMULATING=1 LOCALBASE=/usr/local PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin HOME=/root STATUS=1 MAIL=/var/mail/root BLOCKSIZE=K UNAME_r=11.2-RELEASE-p7 UNAME_v=FreeBSD 11.2-RELEASE-p7 1102000 OSVERSION=1102000 ABI_FILE=/usr/lib/crt1.o UNAME_m=mips UNAME_p=mips SHELL=/bin/csh ---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-- mzaki@niid.go.jp --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/stringtie/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/stringtie/work HOME=/wrkdirs/usr/ports/biology/stringtie/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/stringtie/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/stringtie/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/stringtie/work HOME=/wrkdirs/usr/ports/biology/stringtie/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/stringtie/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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -G0 -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -G0 -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=11.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/stringtie" EXAMPLESDIR="share/examples/stringtie" DATADIR="share/stringtie" WWWDIR="www/stringtie" ETCDIR="etc/stringtie" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/stringtie DOCSDIR=/usr/local/share/doc/stringtie EXAMPLESDIR=/usr/local/share/examples/stringtie WWWDIR=/usr/local/www/stringtie ETCDIR=/usr/local/etc/stringtie --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=mips MACHINE_ARCH=mips 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 # 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_9d218390=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=Using built-in specs. Target: mips-undermydesk-freebsd Configured with: FreeBSD/mips system compiler Thread model: posix gcc version 4.2.1 20070831 patched [FreeBSD] "/usr/bin/ld" "--eh-frame-hdr" "-EB" "-EB" "-melf32btsmip_fbsd" "--enable-new-dtags" "-dynamic-linker" "/libexec/ld-elf.so.1" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "-L/usr/lib" "/dev/null" "-lstdc++" "-lm" "-lgcc_s" "-lgcc" "-lc" "-lgcc_s" "-lgcc" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=cc1: error: unrecognized command line option "-std=c11" CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=cc1: error: unrecognized command line option "-std=gnu11" CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=cc1plus: error: unrecognized command line option "-std=c++0x" CC_OUTPUT_9d218390_f00456e5=cc1plus: error: unrecognized command line option "-std=c++11" CC_OUTPUT_9d218390_65ad290d=cc1plus: error: unrecognized command line option "-std=c++14" CC_OUTPUT_9d218390_f2776b26=cc1plus: error: unrecognized command line option "-std=c++17" CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=cc1plus: error: unrecognized command line option "-std=gnu++11" CC_OUTPUT_9d218390_160933ec=cc1plus: error: unrecognized command line option "-std=gnu++14" CC_OUTPUT_9d218390_fb62803b=cc1plus: error: unrecognized command line option "-std=gnu++17" _OBJC_CCVERSION_9d218390=cc (GCC) 4.2.1 20070831 patched [FreeBSD] Copyright (C) 2007 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. _OBJC_ALTCCVERSION_9d218390=none ARCH=mips OPSYS=FreeBSD _OSRELEASE=11.2-RELEASE-p7 OSREL=11.2 OSVERSION=1102000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ AS=/nxb-bin/usr/bin/as NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 131072 stack size (kbytes, -s) 8192 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 ART20 MIT accepted by the user =========================================================================== =================================================== ===> stringtie-1.3.4.d depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [112mips-quarterly-job-12] Installing pkg-1.10.5_5... [112mips-quarterly-job-12] Extracting pkg-1.10.5_5: .......... done ===> stringtie-1.3.4.d depends on file: /usr/local/sbin/pkg - found ===> Returning to build of stringtie-1.3.4.d =========================================================================== =================================================== =========================================================================== =================================================== ===> License ART20 MIT accepted by the user ===> Fetching all distfiles required by stringtie-1.3.4.d for building =========================================================================== =================================================== ===> License ART20 MIT accepted by the user ===> Fetching all distfiles required by stringtie-1.3.4.d for building => SHA256 Checksum OK for stringtie-1.3.4d.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License ART20 MIT accepted by the user ===> Fetching all distfiles required by stringtie-1.3.4.d for building ===> Extracting for stringtie-1.3.4.d => SHA256 Checksum OK for stringtie-1.3.4d.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for stringtie-1.3.4.d ===> Applying FreeBSD patches for stringtie-1.3.4.d =========================================================================== =================================================== ===> stringtie-1.3.4.d depends on executable: gmake - not found ===> Installing existing package /packages/All/gmake-4.2.1_2.txz [112mips-quarterly-job-12] Installing gmake-4.2.1_2... [112mips-quarterly-job-12] `-- Installing gettext-runtime-0.19.8.1_1... [112mips-quarterly-job-12] | `-- Installing indexinfo-0.3.1... [112mips-quarterly-job-12] | `-- Extracting indexinfo-0.3.1: .... done [112mips-quarterly-job-12] `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [112mips-quarterly-job-12] Extracting gmake-4.2.1_2: .......... done ===> stringtie-1.3.4.d depends on executable: gmake - found ===> Returning to build of stringtie-1.3.4.d =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for stringtie-1.3.4.d =========================================================================== =================================================== ===> Building for stringtie-1.3.4.d gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/stringtie/work/stringtie-1.3.4d' cd ./samtools-0.1.18 && gmake lib gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/stringtie/work/stringtie-1.3.4d/samtools-0.1.18' /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bgzf.c -o bgzf.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C bgzf.c: In function 'cache_block': bgzf.c:445: warning: comparison between signed and unsigned bgzf.c: In function 'bgzf_read_block': bgzf.c:484: warning: comparison between signed and unsigned /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. kstring.c -o kstring.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C kstring.c: In function 'ksprintf': kstring.c:15: warning: comparison between signed and unsigned /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_aux.c -o bam_aux.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam.c -o bam.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C bam.c: In function 'swap_endian_data': bam.c:168: warning: comparison between signed and unsigned bam.c:171: warning: comparison between signed and unsigned /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_import.c -o bam_import.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C bam_import.c: In function 'ks_getuntil2': bam_import.c:17: warning: comparison between signed and unsigned bam_import.c: In function 'append_text': bam_import.c:179: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t' bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 3 has type 'size_t' bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 4 has type 'size_t' bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 5 has type 'size_t' bam_import.c:186: warning: format '%ld' expects type 'long int', but argument 6 has type 'size_t' bam_import.c: In function 'sam_read1': bam_import.c:354: warning: comparison between signed and unsigned bam_import.c:424: warning: comparison between signed and unsigned /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. sam.c -o sam.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_index.c -o bam_index.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C bam_index.c: In function 'merge_chunks': bam_index.c:126: warning: comparison between signed and unsigned bam_index.c: In function 'bam_index_core': bam_index.c:195: warning: comparison between signed and unsigned bam_index.c:207: warning: comparison between signed and unsigned bam_index.c: In function 'bam_index_save': bam_index.c:283: warning: comparison between signed and unsigned bam_index.c:288: warning: comparison between signed and unsigned bam_index.c: In function 'bam_index_load_core': bam_index.c:364: warning: comparison between signed and unsigned bam_index.c: In function 'download_from_remote': bam_index.c:447: warning: unused parameter 'url' bam_index.c: In function 'reg2bins': bam_index.c:556: warning: comparison between signed and unsigned bam_index.c:557: warning: comparison between signed and unsigned bam_index.c:558: warning: comparison between signed and unsigned bam_index.c:559: warning: comparison between signed and unsigned bam_index.c:560: warning: comparison between signed and unsigned bam_index.c: In function 'is_overlap': bam_index.c:567: warning: signed and unsigned type in conditional expression bam_index.c: In function 'bam_iter_query': bam_index.c:621: warning: comparison between signed and unsigned /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_pileup.c -o bam_pileup.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C bam_pileup.c: In function 'resolve_cigar2': bam_pileup.c:95: warning: comparison between signed and unsigned bam_pileup.c:119: warning: comparison between signed and unsigned bam_pileup.c:140: warning: comparison between signed and unsigned bam_pileup.c:140: warning: comparison between signed and unsigned bam_pileup.c: In function 'bam_plp_next': bam_pileup.c:204: warning: comparison between signed and unsigned bam_pileup.c:206: warning: comparison between signed and unsigned bam_pileup.c:228: warning: comparison between signed and unsigned bam_pileup.c: In function 'bam_plp_push': bam_pileup.c:253: warning: comparison between signed and unsigned bam_pileup.c:259: warning: comparison between signed and unsigned /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_lpileup.c -o bam_lpileup.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_md.c -o bam_md.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C bam_md.c: In function 'bam_fillmd1_core': bam_md.c:107: warning: comparison between signed and unsigned bam_md.c:110: warning: comparison between signed and unsigned /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. razf.c -o razf.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C razf.c: In function 'add_zindex': razf.c:81: warning: unused parameter 'in' /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. faidx.c -o faidx.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bedidx.c -o bedidx.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C bedidx.c: In function 'ks_getuntil2': bedidx.c:15: warning: comparison between signed and unsigned /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_sort.c -o bam_sort.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C bam_sort.c: In function 'bam_sort_core_ext': bam_sort.c:405: warning: comparison between signed and unsigned /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. sam_header.c -o sam_header.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C sam_header.c: In function 'nextline': sam_header.c:165: warning: comparison between signed and unsigned /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_reheader.c -o bam_reheader.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. kprobaln.c -o kprobaln.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C /nxb-bin/usr/bin/cc -c -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 -I. bam_cat.c -o bam_cat.o cc1: warning: command line option "-fno-rtti" is valid for C++/ObjC++ but not for C ar -csru 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 bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/stringtie/work/stringtie-1.3.4d/samtools-0.1.18' /nxb-bin/usr/bin/c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -c gclib/GBase.cpp -o gclib/GBase.o /nxb-bin/usr/bin/c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -c gclib/GArgs.cpp -o gclib/GArgs.o /nxb-bin/usr/bin/c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -c gclib/GStr.cpp -o gclib/GStr.o /nxb-bin/usr/bin/c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -c gclib/GBam.cpp -o gclib/GBam.o /nxb-bin/usr/bin/c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -c gclib/gdna.cpp -o gclib/gdna.o /nxb-bin/usr/bin/c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -c gclib/codons.cpp -o gclib/codons.o /nxb-bin/usr/bin/c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -c gclib/GFaSeqGet.cpp -o gclib/GFaSeqGet.o /nxb-bin/usr/bin/c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -c gclib/gff.cpp -o gclib/gff.o /nxb-bin/usr/bin/c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -c gclib/GThreads.cpp -o gclib/GThreads.o /nxb-bin/usr/bin/c++ -DNDEBUG -g -Wall -Wextra -I. -I./gclib -I./samtools-0.1.18 -fsigned-char -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -fno-strict-aliasing -fno-exceptions -fno-rtti -O2 -pipe -G0 -fno-strict-aliasing -c rlink.cpp -o rlink.o In file included from rlink.h:10, from rlink.cpp:1: ./gclib/GIntHash.hh:229: error: integer constant is too large for 'long' type ./gclib/GIntHash.hh:231: error: integer constant is too large for 'long' type gmake[1]: *** [Makefile:125: rlink.o] Error 1 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/stringtie/work/stringtie-1.3.4d' *** Error code 1 Stop. make: stopped in /usr/ports/biology/stringtie