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Date:      Tue, 15 Jan 2019 02:46:18 GMT
From:      pkg-fallout@FreeBSD.org
To:        pkg-fallout@FreeBSD.org
Subject:   [package - 112mips-quarterly][biology/stringtie] Failed for stringtie-1.3.4.d in build
Message-ID:  <201901150246.x0F2kIkh078984@beefy14.nyi.freebsd.org>

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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/2019Q1/biology/stringtie/Makefile 474480 2018-07-11 21:32:39Z yuri $
Log URL:        http://beefy14.nyi.freebsd.org/data/112mips-quarterly/490334/logs/stringtie-1.3.4.d.log
Build URL:      http://beefy14.nyi.freebsd.org/build.html?mastername=112mips-quarterly&build=490334
Log:

=>> Building biology/stringtie
build started at Tue Jan 15 02:44:32 UTC 2019
port directory: /usr/ports/biology/stringtie
package name: stringtie-1.3.4.d
building for: FreeBSD 112mips-quarterly-job-02 11.2-RELEASE-p8 FreeBSD 11.2-RELEASE-p8 1102000 mips
maintained by: mzaki@niid.go.jp
Makefile ident:      $FreeBSD: branches/2019Q1/biology/stringtie/Makefile 474480 2018-07-11 21:32:39Z yuri $
Poudriere version: 3.2.8
Host OSVERSION: 1300002
Jail OSVERSION: 1102000
Job Id: 02

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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=
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MAKE_ARGS=
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---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
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.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
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#MASTER_SITE_FREEBSD=yes
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LINT=	true
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#### /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.
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ARCH=mips
OPSYS=FreeBSD
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OSREL=11.2
OSVERSION=1102000
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=262144
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UID=0
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MAKE=/nxb-bin/usr/bin/make
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cpu time               (seconds, -t)  unlimited
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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
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pseudo-terminals                (-p)  unlimited
kqueues                         (-k)  unlimited
umtx shared locks               (-o)  unlimited
--End resource limits--
=======================<phase: check-sanity   >============================
===>  License ART20 MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   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-02] Installing pkg-1.10.5_5...
[112mips-quarterly-job-02] 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
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License ART20 MIT accepted by the user
===> Fetching all distfiles required by stringtie-1.3.4.d for building
===========================================================================
=======================<phase: checksum       >============================
===>  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.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  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.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for stringtie-1.3.4.d
===>  Applying FreeBSD patches for stringtie-1.3.4.d
===========================================================================
=======================<phase: build-depends  >============================
===>   stringtie-1.3.4.d depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1_3.txz
[112mips-quarterly-job-02] Installing gmake-4.2.1_3...
[112mips-quarterly-job-02] `-- Installing gettext-runtime-0.19.8.1_2...
[112mips-quarterly-job-02] |   `-- Installing indexinfo-0.3.1...
[112mips-quarterly-job-02] |   `-- Extracting indexinfo-0.3.1: .... done
[112mips-quarterly-job-02] `-- Extracting gettext-runtime-0.19.8.1_2: .......... done
[112mips-quarterly-job-02] Extracting gmake-4.2.1_3: .......... done
===>   stringtie-1.3.4.d depends on executable: gmake - found
===>   Returning to build of stringtie-1.3.4.d
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for stringtie-1.3.4.d
===========================================================================
=======================<phase: build          >============================
===>  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



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