[package - main-amd64-default][biology/viennarna] Failed for viennarna-2.5.1 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Mon, 26 Jun 2023 13:54:44 UTC
You are receiving this mail as a port that you maintain
is failing to build on the FreeBSD package build server.
Please investigate the failure and submit a PR to fix
build.
Maintainer: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/p4785b313b958_se8efee297c/logs/viennarna-2.5.1.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=p4785b313b958_se8efee297c
Log:
=>> Building biology/viennarna
build started at Mon Jun 26 13:49:44 UTC 2023
port directory: /usr/ports/biology/viennarna
package name: viennarna-2.5.1
building for: FreeBSD main-amd64-default-job-05 14.0-CURRENT FreeBSD 14.0-CURRENT 1400091 amd64
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400089
Jail OSVERSION: 1400091
Job Id: 05
!!! Jail is newer than host. (Jail: 1400091, Host: 1400089) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1400091
UNAME_v=FreeBSD 14.0-CURRENT 1400091
UNAME_r=14.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-23-ga7f8d188
MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=main-amd64-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/main-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---
===> The following configuration options are available for viennarna-2.5.1:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--enable-shared --disable-static --with-gsl --with-cluster --with-kinwalker --enable-mpfr --without-python --without-python3 --without-perl --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/viennarna/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/viennarna/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/viennarna/work/.cache HOME=/wrkdirs/usr/ports/biology/viennarna/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/viennarna/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/viennarna/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/usr/local/bin/bash CONFIG_SHELL=/usr/local/bin/bash DEFAULT_AUTOCONF=2.71 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--
--MAKE_ENV--
PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/viennarna/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/viennarna/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/viennarna/work/.cache HOME=/wrkdirs/usr/ports/biology/viennarna/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/viennarna/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/viennarna/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.71 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -is
ystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444"
--End MAKE_ENV--
--PLIST_SUB--
PORTDOCS="" PORTEXAMPLES="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.32 DOCSDIR="share/doc/ViennaRNA" EXAMPLESDIR="share/examples/ViennaRNA" DATADIR="share/viennarna" WWWDIR="www/viennarna" ETCDIR="etc/viennarna"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/viennarna DOCSDIR=/usr/local/share/doc/ViennaRNA EXAMPLESDIR=/usr/local/share/examples/ViennaRNA WWWDIR=/usr/local/www/viennarna ETCDIR=/usr/local/etc/viennarna
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### /usr/local/etc/poudriere.d/make.conf ####
# XXX: We really need this but cannot use it while 'make checksum' does not
# try the next mirror on checksum failure. It currently retries the same
# failed mirror and then fails rather then trying another. It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_53255a77=yes
CC_OUTPUT_921dbbb2_911cfe02=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
CC_OUTPUT_921dbbb2_af59ad06=yes
CC_OUTPUT_921dbbb2_a15f3fcf=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: x86_64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=amd64
OPSYS=FreeBSD
_OSRELEASE=14.0-CURRENT
OSREL=14.0
OSVERSION=1400091
PYTHONBASE=/usr/local
HAVE_COMPAT_IA32_KERN=YES
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 33554432
stack size (kbytes, -s) 524288
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 1024
virtual mem size (kbytes, -v) unlimited
swap limit (kbytes, -w) unlimited
socket buffer size (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
kqueues (-k) unlimited
umtx shared locks (-o) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===> License ViennaRNALicense accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> viennarna-2.5.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.19.1_1.pkg
[main-amd64-default-job-05] Installing pkg-1.19.1_1...
[main-amd64-default-job-05] Extracting pkg-1.19.1_1: .......... done
===> viennarna-2.5.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of viennarna-2.5.1
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License ViennaRNALicense accepted by the user
===> Fetching all distfiles required by viennarna-2.5.1 for building
===========================================================================
=======================<phase: checksum >============================
===> License ViennaRNALicense accepted by the user
===> Fetching all distfiles required by viennarna-2.5.1 for building
=> SHA256 Checksum OK for ViennaRNA-2.5.1.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License ViennaRNALicense accepted by the user
===> Fetching all distfiles required by viennarna-2.5.1 for building
===> Extracting for viennarna-2.5.1
=> SHA256 Checksum OK for ViennaRNA-2.5.1.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for viennarna-2.5.1
===> Applying FreeBSD patches for viennarna-2.5.1 from /usr/ports/biology/viennarna/files
===========================================================================
=======================<phase: build-depends >============================
<snip>
mv -f $depbase.Tpo $depbase.Po
depbase=`echo rna_alphabet.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT rna_alphabet.o -MD -MP -MF $depbase.Tpo -c -o rna_alphabet.o rna_alphabet.cpp &&\
mv -f $depbase.Tpo $depbase.Po
1 warning generated.
depbase=`echo rnaforest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT rnaforest.o -MD -MP -MF $depbase.Tpo -c -o rnaforest.o rnaforest.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo rnafuncs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT rnafuncs.o -MD -MP -MF $depbase.Tpo -c -o rnafuncs.o rnafuncs.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo anchors/bplex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT anchors/bplex.o -MD -MP -MF $depbase.Tpo -c -o anchors/bplex.o anchors/bplex.cpp &&\
mv -f $depbase.Tpo $depbase.Po
anchors/bplex.lpp:5:1: warning: class 'Pair' was previously declared as a struct; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags]
class Pair;
^
./anchors/basepair.h:7:8: note: previous use is here
struct Pair {
^
anchors/bplex.lpp:5:1: note: did you mean struct here?
class Pair;
^~~~~
struct
anchors/bplex.cpp:1106:16: warning: function 'yyinput' is not needed and will not be emitted [-Wunneeded-internal-declaration]
static int yyinput (void)
^
depbase=`echo anchors/shape.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT anchors/shape.o -MD -MP -MF $depbase.Tpo -c -o anchors/shape.o anchors/shape.cpp &&\
mv -f $depbase.Tpo $depbase.Po
2 warnings generated.
depbase=`echo anchors/anchors.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT anchors/anchors.o -MD -MP -MF $depbase.Tpo -c -o anchors/anchors.o anchors/anchors.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo frontend/Arguments.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT frontend/Arguments.o -MD -MP -MF $depbase.Tpo -c -o frontend/Arguments.o frontend/Arguments.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo frontend/rnaforester_options.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT frontend/rnaforester_options.o -MD -MP -MF $depbase.Tpo -c -o frontend/rnaforester_options.o frontend/rnaforester_options.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo TED/rnaforestsz.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
c++ -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -I../g2-0.72/include/ -Wall -std=c++98 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT TED/rnaforestsz.o -MD -MP -MF $depbase.Tpo -c -o TED/rnaforestsz.o TED/rnaforestsz.cpp &&\
mv -f $depbase.Tpo $depbase.Po
depbase=`echo wmatch/glib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -I../g2-0.72/include/ -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT wmatch/glib.o -MD -MP -MF $depbase.Tpo -c -o wmatch/glib.o wmatch/glib.c &&\
mv -f $depbase.Tpo $depbase.Po
In file included from wmatch/glib.c:1:
./wmatch/graphtypes.h:49:33: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]
extern EuclidGraph ReadEuclid(),NewEuclid();
^
./wmatch/graphtypes.h:71:17: note: conflicting prototype is here
EuclidGraph NewEuclid(int size);
^
./wmatch/graphtypes.h:60:34: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]
extern MatrixGraph ReadMatrix(), NewMatrix();
^
./wmatch/graphtypes.h:72:17: note: conflicting prototype is here
MatrixGraph NewMatrix(int size);
^
./wmatch/graphtypes.h:49:20: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]
extern EuclidGraph ReadEuclid(),NewEuclid();
^
./wmatch/graphtypes.h:76:17: note: conflicting prototype is here
EuclidGraph ReadEuclid(int *size,char *file);
^
./wmatch/graphtypes.h:60:20: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]
extern MatrixGraph ReadMatrix(), NewMatrix();
^
./wmatch/graphtypes.h:78:17: note: conflicting prototype is here
MatrixGraph ReadMatrix(int *size,char *file);
^
./wmatch/graphtypes.h:50:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]
extern int eucdist(),eucdistsq();
^
./wmatch/graphtypes.h:80:9: note: conflicting prototype is here
int eucdist (EuclidGraph graph,int i,int j);
^
./wmatch/graphtypes.h:50:22: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]
extern int eucdist(),eucdistsq();
^
./wmatch/graphtypes.h:82:9: note: conflicting prototype is here
int eucdistsq(EuclidGraph graph,int i,int j);
^
depbase=`echo wmatch/wmatch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
cc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -I../g2-0.72/include/ -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT wmatch/wmatch.o -MD -MP -MF $depbase.Tpo -c -o wmatch/wmatch.o wmatch/wmatch.c &&\
mv -f $depbase.Tpo $depbase.Po
In file included from wmatch/wmatch.c:15:
./wmatch/graphtypes.h:49:33: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]
extern EuclidGraph ReadEuclid(),NewEuclid();
^
./wmatch/graphtypes.h:71:17: note: conflicting prototype is here
EuclidGraph NewEuclid(int size);
^
./wmatch/graphtypes.h:60:34: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]
extern MatrixGraph ReadMatrix(), NewMatrix();
^
./wmatch/graphtypes.h:72:17: note: conflicting prototype is here
MatrixGraph NewMatrix(int size);
^
./wmatch/graphtypes.h:49:20: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]
extern EuclidGraph ReadEuclid(),NewEuclid();
^
./wmatch/graphtypes.h:76:17: note: conflicting prototype is here
EuclidGraph ReadEuclid(int *size,char *file);
^
./wmatch/graphtypes.h:60:20: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]
extern MatrixGraph ReadMatrix(), NewMatrix();
^
./wmatch/graphtypes.h:78:17: note: conflicting prototype is here
MatrixGraph ReadMatrix(int *size,char *file);
^
./wmatch/graphtypes.h:50:12: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]
extern int eucdist(),eucdistsq();
^
./wmatch/graphtypes.h:80:9: note: conflicting prototype is here
int eucdist (EuclidGraph graph,int i,int j);
^
./wmatch/graphtypes.h:50:22: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C2x, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]
extern int eucdist(),eucdistsq();
^
./wmatch/graphtypes.h:82:9: note: conflicting prototype is here
int eucdistsq(EuclidGraph graph,int i,int j);
^
6 warnings generated.
6 warnings generated.
c++ -Wall -std=c++98 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -L../g2-0.72 -fstack-protector-strong -o RNAforester anchors/bplex.o anchors/shape.o anchors/anchors.o aligner.o main.o forestbase.o parser.o progressive_align.o rna_profile_alignment.o rna_alignment.o rna_algebra.o rna_alphabet.o rnaforest.o rnafuncs.o frontend/Arguments.o frontend/rnaforester_options.o TED/rnaforestsz.o wmatch/glib.o wmatch/wmatch.o -lg2 -fno-strict-aliasing -L../../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ -L/usr/local/lib
gmake[6]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/RNAforester/src'
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/RNAforester/src'
Making all in man
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/RNAforester/man'
gmake[5]: Nothing to be done for 'all'.
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/RNAforester/man'
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/RNAforester'
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/RNAforester'
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/RNAforester'
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/RNAforester'
Making all in src/Kinwalker
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/Kinwalker'
gmake all-recursive
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/Kinwalker'
Making all in man
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/Kinwalker/man'
gmake[5]: Nothing to be done for 'all'.
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/Kinwalker/man'
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/Kinwalker'
c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp
c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT Energy.o -MD -MP -MF .deps/Energy.Tpo -c -o Energy.o Energy.cpp
mv -f .deps/Energy.Tpo .deps/Energy.Po
c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT MorganHiggs.o -MD -MP -MF .deps/MorganHiggs.Tpo -c -o MorganHiggs.o MorganHiggs.cpp
mv -f .deps/main.Tpo .deps/main.Po
c++ -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT Node.o -MD -MP -MF .deps/Node.Tpo -c -o Node.o Node.cpp
MorganHiggs.cpp:528:26: warning: adding 'size_t' (aka 'unsigned long') to a string does not append to the string [-Wstring-plus-int]
if(MHS_debug) cout<<i+" "+PrintBasePair(mStack.bp[i])<<endl;
~^~~~
MorganHiggs.cpp:528:26: note: use array indexing to silence this warning
Node.cpp:65:38: error: no template named 'binary_function' in namespace 'std'; did you mean '__binary_function'?
struct BasePairConflict :public std::binary_function<std::pair<int,int>,std::pair<int,int>,bool>{
~~~~~^~~~~~~~~~~~~~~
__binary_function
/usr/include/c++/v1/__functional/binary_function.h:49:1: note: '__binary_function' declared here
using __binary_function = __binary_function_keep_layout_base<_Arg1, _Arg2, _Result>;
^
Node.cpp:392:49: error: no member named 'mem_fun' in namespace 'std'; did you mean 'mem_fn'?
if(find_if(extrema.begin(),extrema.end(),std::mem_fun(&Node::IsTranscribed))==extrema.end()){
~~~~~^~~~~~~
mem_fn
/usr/include/c++/v1/__functional/mem_fn.h:52:1: note: 'mem_fn' declared here
mem_fn(_Rp _Tp::* __pm) _NOEXCEPT
^
Node.cpp:471:56: error: no member named 'mem_fun' in namespace 'std'; did you mean 'mem_fn'?
if(find_if(extrema.begin()+i,extrema.end(),std::mem_fun(&Node::IsTranscribed))==extrema.end()) Node::transcribed_front_maximal=true;
~~~~~^~~~~~~
mem_fn
/usr/include/c++/v1/__functional/mem_fn.h:52:1: note: 'mem_fn' declared here
mem_fn(_Rp _Tp::* __pm) _NOEXCEPT
^
Node.cpp:770:98: error: no member named 'bind2nd' in namespace 'std'
std::vector<std::pair<int,int> >::iterator it=remove_if(basepairs.begin(),basepairs.end(),std::bind2nd(BasePairConflict(),bp_to_add));
~~~~~^
4 errors generated.
gmake[5]: *** [Makefile:487: Node.o] Error 1
gmake[5]: *** Waiting for unfinished jobs....
1 warning generated.
mv -f .deps/MorganHiggs.Tpo .deps/MorganHiggs.Po
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/Kinwalker'
gmake[4]: *** [Makefile:507: all-recursive] Error 1
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/Kinwalker'
gmake[3]: *** [Makefile:354: all] Error 2
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1/src/Kinwalker'
gmake[2]: *** [Makefile:692: all-recursive] Error 1
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1'
gmake[1]: *** [Makefile:583: all] Error 2
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.5.1'
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/viennarna