From nobody Mon Jun 26 13:54:44 2023 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4QqTqT1vMCz4jLdb for ; Mon, 26 Jun 2023 13:54:45 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4QqTqS6mGjz3xs5 for ; Mon, 26 Jun 2023 13:54:44 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1687787684; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=1pdw+KpEOB3qMQVmbtu6q48Ywv9wdbLzRauE/rp68u0=; b=hxJ5kwUOQYWAlRw3YXgW5N5WCTD6VQ66lRCJze3ZcI0sMBA6dqN57Jx3VWoDVZAkJ2KzsR xAC7dtH3JSofwUryQsEmrPGMiNvDUhTbqbgCMr626VmSkizSv98mld2VPZ225kK4mLvuN6 vWatSqXYYNsOqvi93+c3moqJxYP9XjAThvcWEZ3GZBml/OoeyjtKic8BLhv38ZTErm8FnH PtG6GXShKMcTEyQVGmFw3Ik1a2naG4ka9U9Rx+3cdT7LfXL9FOnfRCqCbFuyLaedGApnAP lCSkGFjPS4a+Pw4pRhkr4GQFFFrEmJTp7thV0x1LJ80tRKe3VB/NAI8LArqS0Q== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1687787684; a=rsa-sha256; cv=none; b=Kr5wju6o2TpVsoK78K8M6hjGcuRH1rq55oeamcUKR5BGBHVB7lAAfLDqTMVf8hkfAO3A7g bM6Dm3TrnDlzq5VjuENLyQGmQgn90rDlj3Q5pbamdETjr0xWKDIvrs2V40iJspZbk+b7p7 G8ZO5AaCoCYOX7DFjEd76IqhHe5ds27dS9C0+wTotpaHFXqovZR8aXdX7wnsgqe98kVykc NvP3efl+Sdrb03K5dHIqpDCuPWGT55+eKKno3VN0bgL0RRhFVhS8Aw5xFSB3q/KJOnfdlX 6lc7Sxcw7gOwrgt5wrc4lAEH0Eb0DZDzDbcSlW04DfBfde9beU4v4w1gbKfmvw== Received: from beefy18.nyi.freebsd.org (beefy18.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:21]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4QqTqS5bwxz1Bxk for ; Mon, 26 Jun 2023 13:54:44 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 231e by beefy18.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on beefy18.nyi.freebsd.org); Mon, 26 Jun 2023 13:54:44 +0000 To: yuri@FreeBSD.org Subject: [package - main-amd64-default][biology/viennarna] Failed for viennarna-2.5.1 in build Cc: pkg-fallout@FreeBSD.org Date: Mon, 26 Jun 2023 13:54:44 +0000 Message-Id: <649998a4.231e.4205e818@beefy18.nyi.freebsd.org> From: X-ThisMailContainsUnwantedMimeParts: N List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org 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-- =================================================== ===> License ViennaRNALicense accepted by the user =========================================================================== =================================================== ===> 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 =========================================================================== =================================================== =========================================================================== =================================================== ===> License ViennaRNALicense accepted by the user ===> Fetching all distfiles required by viennarna-2.5.1 for building =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> 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. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for viennarna-2.5.1 ===> Applying FreeBSD patches for viennarna-2.5.1 from /usr/ports/biology/viennarna/files =========================================================================== =================================================== 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<,std::pair,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 >::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