=>> Building biology/viennarna build started at Sat Dec 27 17:09:47 EST 2025 port directory: /usr/ports/biology/viennarna package name: viennarna-2.7.0_2 building for: FreeBSD 143amd64-deluxe-desktop-job-01 14.3-RELEASE-p2 FreeBSD 14.3-RELEASE-p2 amd64 maintained by: yuri@FreeBSD.org Makefile datestamp: -rw-r--r-- 1 root wheel 1979 Dec 16 05:29 /usr/ports/biology/viennarna/Makefile Ports top last git commit: 3dd9e2202282 Ports top unclean checkout: yes Port dir last git commit: 042fe38f0395 Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.4 Host OSVERSION: 1403000 Jail OSVERSION: 1403000 Job Id: 01 ---Begin Environment--- SHELL=/bin/sh OSVERSION=1403000 UNAME_v=FreeBSD 14.3-RELEASE-p2 UNAME_r=14.3-RELEASE-p2 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 MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.4 MASTERMNT=/mnt/data/.m/143amd64-deluxe-desktop/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM=screen GID=0 OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 UID=0 PWD=/mnt/data/.m/143amd64-deluxe-desktop/01/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=143amd64-deluxe-desktop SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/mnt/data/.m/143amd64-deluxe-desktop/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.4 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for viennarna-2.7.0_2: 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-- F77="gfortran14" F90="gfortran14" FC="gfortran14" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc14" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc14" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc14" MAKE=/usr/local/bin/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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" DEFAULT_AUTOCONF=2.72 CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran14" F90="gfortran14" FC="gfortran14" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc14" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc14" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc14" 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 ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" DEFAULT_AUTOCONF=2.72 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=" -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 " LIBS="-L/usr/local/lib" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Dregister= -isystem /usr/local/include " 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=14.3 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.42.0 PERL_VER=5.42 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/5.42 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 FORCE_PACKAGE=yes PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### #### # Work around some weirdness when fetching golang modules GO_TAGS+=netcgo .if ${.CURDIR:M*/www/chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/www/ungoogled-chromium*} MAKE_JOBS_NUMBER=24 .endif .if ${.CURDIR:M*/lang/rust*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/lang/gcc*} MAKE_JOBS_NUMBER=10 .endif .if ${.CURDIR:M*/www/iridium*} MAKE_JOBS_NUMBER=16 .endif .if ${.CURDIR:M*/devel/electron*} MAKE_JOBS_NUMBER=20 .endif .if ${.CURDIR:M*/databases/mongodb*} MAKE_JOBS_NUMBER=12 .endif .if ${.CURDIR:M*/devel/llvm*} MAKE_JOBS_NUMBER=16 .endif # Speed things up a bit MAKE_JOBS_NUMBER?=8 #### #### #MAKE_JOBS_NUMBER?=4 # Alows us to build ports non-interactivly DISABLE_LICENSES=yes LICENSES_ACCEPTED+= DCC # Enable SNDIO on anything that supports it #OPTIONS_SET+=PULSEAUDIO OPTIONS_SET+=SNDIO # Yes we have MS Windows x11-fonts_webfonts_SET+=EXTRAFONTS CLEARTYPE # Desktop Specific Options sysutils_gksu_UNSET+=NAUTILUS x11-wm_compiz-fusion_UNSET+=EMERALD accessibility_redshift_SET+=GUI VIDMODE # These ports default to other audio servers, audio_espeak_UNSET+=PORTAUDIO www_qt5-webengine_UNSET+=ALSA www_qt6-webengine_UNSET+=ALSA audio_rhvoice_UNSET+=AO comms_morse_UNSET+=OSS audio_harp_UNSET+=OSS # Somehow these options are being set and result in ports being rebuilt needlessly becuase they are actually turned off audio_alsa-plugins_SET+=FFMPEG JACK PULSEAUDIO SAMPLERATE SPEEX #### Misc Poudriere #### .include "/etc/make.conf.ports_env" ---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) 8192 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 pipebuf (-y) unlimited --End resource limits-- =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> viennarna-2.7.0_2 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.5.1.pkg [143amd64-deluxe-desktop-job-01] Installing pkg-2.5.1... [143amd64-deluxe-desktop-job-01] Extracting pkg-2.5.1: .......... done ===> viennarna-2.7.0_2 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of viennarna-2.7.0_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by viennarna-2.7.0_2 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Fetching all distfiles required by viennarna-2.7.0_2 for building => SHA256 Checksum OK for ViennaRNA-2.7.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Fetching all distfiles required by viennarna-2.7.0_2 for building ===> Extracting for viennarna-2.7.0_2 => SHA256 Checksum OK for ViennaRNA-2.7.0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Patching for viennarna-2.7.0_2 ===> Applying FreeBSD patches for viennarna-2.7.0_2 from /usr/ports/biology/viennarna/files =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> viennarna-2.7.0_2 depends on executable: bash - not found ===> Installing existing package /packages/All/bash-5.3.9.pkg [143amd64-deluxe-desktop-job-01] Installing bash-5.3.9... [143amd64-deluxe-desktop-job-01] `-- Installing gettext-runtime-0.26... [143amd64-deluxe-desktop-job-01] | `-- Installing indexinfo-0.3.1_1... [143amd64-deluxe-desktop-job-01] | `-- Extracting indexinfo-0.3.1_1: . done [143amd64-deluxe-desktop-job-01] `-- Extracting gettext-runtime-0.26: .......... done [143amd64-deluxe-desktop-job-01] Extracting bash-5.3.9: .......... done ===> viennarna-2.7.0_2 depends on executable: bash - found ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on package: lapacke>0 - not found ===> Installing existing package /packages/All/lapacke-3.12.1.pkg [143amd64-deluxe-desktop-job-01] Installing lapacke-3.12.1... [143amd64-deluxe-desktop-job-01] `-- Installing blas-3.12.1... [143amd64-deluxe-desktop-job-01] | `-- Installing gcc14-14.2.0_4... [143amd64-deluxe-desktop-job-01] | | `-- Installing binutils-2.44,1... [143amd64-deluxe-desktop-job-01] | | `-- Installing zstd-1.5.7_1... [143amd64-deluxe-desktop-job-01] | | `-- Extracting zstd-1.5.7_1: .......... done [143amd64-deluxe-desktop-job-01] | | `-- Extracting binutils-2.44,1: .......... done [143amd64-deluxe-desktop-job-01] | | `-- Installing gmp-6.3.0... [143amd64-deluxe-desktop-job-01] | | `-- Extracting gmp-6.3.0: .......... done [143amd64-deluxe-desktop-job-01] | | `-- Installing mpc-1.3.1_1... [143amd64-deluxe-desktop-job-01] | | `-- Installing mpfr-4.2.2,1... [143amd64-deluxe-desktop-job-01] | | `-- Extracting mpfr-4.2.2,1: .......... done [143amd64-deluxe-desktop-job-01] | | `-- Extracting mpc-1.3.1_1: ...... done [143amd64-deluxe-desktop-job-01] | `-- Extracting gcc14-14.2.0_4: .......... done [143amd64-deluxe-desktop-job-01] `-- Extracting blas-3.12.1: ..... done [143amd64-deluxe-desktop-job-01] `-- Installing lapack-3.12.1... [143amd64-deluxe-desktop-job-01] `-- Extracting lapack-3.12.1: .......... done [143amd64-deluxe-desktop-job-01] Extracting lapacke-3.12.1: .......... done ===== Message from gcc14-14.2.0_4: -- To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc14 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> viennarna-2.7.0_2 depends on package: lapacke>0 - found ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on package: libgd>0 - not found ===> Installing existing package /packages/All/libgd-2.3.3_13,1.pkg [143amd64-deluxe-desktop-job-01] Installing libgd-2.3.3_13,1... [143amd64-deluxe-desktop-job-01] `-- Installing fontconfig-2.17.1,1... [143amd64-deluxe-desktop-job-01] | `-- Installing expat-2.7.3... [143amd64-deluxe-desktop-job-01] | `-- Extracting expat-2.7.3: .......... done [143amd64-deluxe-desktop-job-01] | `-- Installing freetype2-2.14.1... [143amd64-deluxe-desktop-job-01] | | `-- Installing brotli-1.2.0,1... [143amd64-deluxe-desktop-job-01] | | `-- Extracting brotli-1.2.0,1: .......... done [143amd64-deluxe-desktop-job-01] | | `-- Installing png-1.6.53... [143amd64-deluxe-desktop-job-01] | | `-- Extracting png-1.6.53: .......... done [143amd64-deluxe-desktop-job-01] | `-- Extracting freetype2-2.14.1: .......... done [143amd64-deluxe-desktop-job-01] `-- Extracting fontconfig-2.17.1,1: .......... done [143amd64-deluxe-desktop-job-01] `-- Installing jpeg-turbo-3.1.3... [143amd64-deluxe-desktop-job-01] `-- Extracting jpeg-turbo-3.1.3: .......... done [143amd64-deluxe-desktop-job-01] `-- Installing tiff-4.7.1... [143amd64-deluxe-desktop-job-01] | `-- Installing jbigkit-2.1_3... [143amd64-deluxe-desktop-job-01] | `-- Extracting jbigkit-2.1_3: .......... done [143amd64-deluxe-desktop-job-01] | `-- Installing lerc-4.0.0... [143amd64-deluxe-desktop-job-01] | `-- Extracting lerc-4.0.0: ..... done [143amd64-deluxe-desktop-job-01] | `-- Installing libdeflate-1.25... [143amd64-deluxe-desktop-job-01] | `-- Extracting libdeflate-1.25: .......... done [143amd64-deluxe-desktop-job-01] `-- Extracting tiff-4.7.1: .......... done [143amd64-deluxe-desktop-job-01] `-- Installing webp-1.6.0... [143amd64-deluxe-desktop-job-01] | `-- Installing giflib-5.2.2... [143amd64-deluxe-desktop-job-01] | `-- Extracting giflib-5.2.2: .......... done [143amd64-deluxe-desktop-job-01] `-- Extracting webp-1.6.0: .......... done [143amd64-deluxe-desktop-job-01] Extracting libgd-2.3.3_13,1: .......... done ==> Running trigger: fontconfig.ucl Running fc-cache to build fontconfig cache... ===== Message from freetype2-2.14.1: -- The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. If LONG_PCF_NAMES port's option was enabled, the PCF family names may include the foundry and information whether they contain wide characters. For example, "Sony Fixed" or "Misc Fixed Wide", instead of "Fixed". This can be disabled at run time with using pcf:no-long-family-names property, if needed. Example: FREETYPE_PROPERTIES=pcf:no-long-family-names=1 How to recreate fontconfig cache with using such environment variable, if needed: # env FREETYPE_PROPERTIES=pcf:no-long-family-names=1 fc-cache -fsv The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/index.html, if documentation was installed). ===> viennarna-2.7.0_2 depends on package: libgd>0 - found ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on executable: swig - not found ===> Installing existing package /packages/All/swig-4.3.1.pkg [143amd64-deluxe-desktop-job-01] Installing swig-4.3.1... [143amd64-deluxe-desktop-job-01] `-- Installing pcre2-10.47_1... [143amd64-deluxe-desktop-job-01] `-- Extracting pcre2-10.47_1: .......... done [143amd64-deluxe-desktop-job-01] Extracting swig-4.3.1: .......... done ===> viennarna-2.7.0_2 depends on executable: swig - found ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on executable: xxd - not found ===> Installing existing package /packages/All/xxd-9.1.1948.pkg [143amd64-deluxe-desktop-job-01] Installing xxd-9.1.1948... [143amd64-deluxe-desktop-job-01] Extracting xxd-9.1.1948: .. done ===> viennarna-2.7.0_2 depends on executable: xxd - found ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on executable: bison - not found ===> Installing existing package /packages/All/bison-3.8.2_2,1.pkg [143amd64-deluxe-desktop-job-01] Installing bison-3.8.2_2,1... [143amd64-deluxe-desktop-job-01] `-- Installing libtextstyle-0.26... [143amd64-deluxe-desktop-job-01] `-- Extracting libtextstyle-0.26: .......... done [143amd64-deluxe-desktop-job-01] `-- Installing m4-1.4.20,1... [143amd64-deluxe-desktop-job-01] `-- Extracting m4-1.4.20,1: .......... done [143amd64-deluxe-desktop-job-01] Extracting bison-3.8.2_2,1: .......... done ===> viennarna-2.7.0_2 depends on executable: bison - found ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on executable: gfortran14 - found ===> viennarna-2.7.0_2 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [143amd64-deluxe-desktop-job-01] Installing gmake-4.4.1... [143amd64-deluxe-desktop-job-01] Extracting gmake-4.4.1: .......... done ===> viennarna-2.7.0_2 depends on package: gmake>=4.4.1 - found ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-2.4.3,1.pkg [143amd64-deluxe-desktop-job-01] Installing pkgconf-2.4.3,1... [143amd64-deluxe-desktop-job-01] Extracting pkgconf-2.4.3,1: .......... done ===> viennarna-2.7.0_2 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on file: /usr/local/bin/as - found ===> viennarna-2.7.0_2 depends on package: autoconf>=2.72_1 - not found ===> Installing existing package /packages/All/autoconf-2.72_1.pkg [143amd64-deluxe-desktop-job-01] Installing autoconf-2.72_1... [143amd64-deluxe-desktop-job-01] `-- Installing autoconf-switch-20220527... [143amd64-deluxe-desktop-job-01] `-- Extracting autoconf-switch-20220527: ....... done [143amd64-deluxe-desktop-job-01] `-- Installing perl5-5.42.0_1... [143amd64-deluxe-desktop-job-01] `-- Extracting perl5-5.42.0_1: .......... done [143amd64-deluxe-desktop-job-01] Extracting autoconf-2.72_1: .......... done ===> viennarna-2.7.0_2 depends on package: autoconf>=2.72_1 - found ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on package: automake>=1.18.1 - not found ===> Installing existing package /packages/All/automake-1.18.1.pkg [143amd64-deluxe-desktop-job-01] Installing automake-1.18.1... [143amd64-deluxe-desktop-job-01] Extracting automake-1.18.1: .......... done ===> viennarna-2.7.0_2 depends on package: automake>=1.18.1 - found ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on executable: libtoolize - not found ===> Installing existing package /packages/All/libtool-2.5.4_1.pkg [143amd64-deluxe-desktop-job-01] Installing libtool-2.5.4_1... [143amd64-deluxe-desktop-job-01] Extracting libtool-2.5.4_1: .......... done ===> viennarna-2.7.0_2 depends on executable: libtoolize - found ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on package: perl5>=5.42.r<5.43 - found ===> viennarna-2.7.0_2 depends on file: /usr/local/libdata/pkgconfig/ice.pc - not found ===> Installing existing package /packages/All/libICE-1.1.2,1.pkg [143amd64-deluxe-desktop-job-01] Installing libICE-1.1.2,1... [143amd64-deluxe-desktop-job-01] Extracting libICE-1.1.2,1: .......... done ===> viennarna-2.7.0_2 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found ===> Installing existing package /packages/All/libX11-1.8.12,1.pkg [143amd64-deluxe-desktop-job-01] Installing libX11-1.8.12,1... [143amd64-deluxe-desktop-job-01] `-- Installing libxcb-1.17.0... [143amd64-deluxe-desktop-job-01] | `-- Installing libXau-1.0.12... [143amd64-deluxe-desktop-job-01] | `-- Extracting libXau-1.0.12: .......... done [143amd64-deluxe-desktop-job-01] | `-- Installing libXdmcp-1.1.5... [143amd64-deluxe-desktop-job-01] | | `-- Installing xorgproto-2024.1... [143amd64-deluxe-desktop-job-01] | | `-- Extracting xorgproto-2024.1: .......... done [143amd64-deluxe-desktop-job-01] | `-- Extracting libXdmcp-1.1.5: ...... done [143amd64-deluxe-desktop-job-01] `-- Extracting libxcb-1.17.0: .......... done [143amd64-deluxe-desktop-job-01] Extracting libX11-1.8.12,1: .......... done ===> viennarna-2.7.0_2 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on file: /usr/local/libdata/pkgconfig/xext.pc - not found ===> Installing existing package /packages/All/libXext-1.3.6,1.pkg [143amd64-deluxe-desktop-job-01] Installing libXext-1.3.6,1... [143amd64-deluxe-desktop-job-01] Extracting libXext-1.3.6,1: .......... done ===> viennarna-2.7.0_2 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> Returning to build of viennarna-2.7.0_2 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> viennarna-2.7.0_2 depends on shared library: libdlib.so - not found ===> Installing existing package /packages/All/dlib-cpp-20.0_1.pkg [143amd64-deluxe-desktop-job-01] Installing dlib-cpp-20.0_1... [143amd64-deluxe-desktop-job-01] `-- Installing libSM-1.2.6,1... [143amd64-deluxe-desktop-job-01] `-- Extracting libSM-1.2.6,1: ........ done [143amd64-deluxe-desktop-job-01] `-- Installing sqlite3-3.50.4_2,1... [143amd64-deluxe-desktop-job-01] | `-- Installing libedit-3.1.20251016_1,1... [143amd64-deluxe-desktop-job-01] | `-- Extracting libedit-3.1.20251016_1,1: .......... done [143amd64-deluxe-desktop-job-01] `-- Extracting sqlite3-3.50.4_2,1: .......... done [143amd64-deluxe-desktop-job-01] Extracting dlib-cpp-20.0_1: .......... done ===> viennarna-2.7.0_2 depends on shared library: libdlib.so - found (/usr/local/lib/libdlib.so) ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on shared library: libgmp.so - found (/usr/local/lib/libgmp.so) ===> viennarna-2.7.0_2 depends on shared library: libgsl.so - not found ===> Installing existing package /packages/All/gsl-2.7.1_1.pkg [143amd64-deluxe-desktop-job-01] Installing gsl-2.7.1_1... [143amd64-deluxe-desktop-job-01] Extracting gsl-2.7.1_1: .......... done ===> viennarna-2.7.0_2 depends on shared library: libgsl.so - found (/usr/local/lib/libgsl.so) ===> Returning to build of viennarna-2.7.0_2 ===> viennarna-2.7.0_2 depends on shared library: liblapack.so - found (/usr/local/lib/liblapack.so) ===> viennarna-2.7.0_2 depends on shared library: libmpfr.so - found (/usr/local/lib/libmpfr.so) =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Configuring for viennarna-2.7.0_2 libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:41: installing 'config/compile' configure.ac:14: installing 'config/missing' interfaces/Python/Makefile.am: installing 'config/depcomp' libtoolize: putting auxiliary files in AC_CONFIG_AUX_DIR, 'config'. libtoolize: copying file 'config/ltmain.sh' libtoolize: putting macros in AC_CONFIG_MACRO_DIRS, 'm4'. libtoolize: copying file 'm4/libtool.m4' libtoolize: copying file 'm4/ltoptions.m4' libtoolize: copying file 'm4/ltsugar.m4' libtoolize: copying file 'm4/ltversion.m4' libtoolize: copying file 'm4/lt~obsolete.m4' configure.ac:15: installing 'config/compile' configure.ac:22: installing 'config/missing' interfaces/Perl/Makefile.am: installing 'config/depcomp' configure: loading site script /usr/ports/Templates/config.site checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking for stdio.h... 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(cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking xargs -n works... yes checking whether UID '65534' is supported by ustar format... yes checking whether GID '65534' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar checking dependency style of cc... gcc3 checking if malloc debugging is wanted... no checking build system type... amd64-portbld-freebsd14.3 checking host system type... amd64-portbld-freebsd14.3 checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking dependency style of c++... gcc3 checking how to run the C++ preprocessor... c++ -E checking for gcc... (cached) cc checking whether the compiler supports GNU C... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to enable C11 features... (cached) none needed checking whether cc understands -c and -o together... (cached) yes checking how to run the C preprocessor... cpp checking whether the compiler supports GNU Fortran 77... yes checking whether gfortran14 accepts -g... yes checking whether /usr/local/bin/gmake sets $(MAKE)... (cached) yes checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for gawk... (cached) /usr/bin/awk checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... (cached) /usr/bin/fgrep checking whether ln -s works... yes checking the archiver (/usr/local/bin/ar) interface... ar checking how to print strings... printf checking for a sed that does not truncate output... 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(cached) 524288 checking how to convert amd64-portbld-freebsd14.3 file names to amd64-portbld-freebsd14.3 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd14.3 file names to toolchain format... func_convert_file_noop checking for /usr/local/bin/ld option to reload object files... -r checking for file... file checking for objdump... /usr/local/bin/objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... /usr/local/bin/ranlib checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/local/bin/nm output from cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/local/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd14.3 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... c++ -E checking for ld used by c++... /usr/local/bin/ld checking if the linker (/usr/local/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/local/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/usr/local/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd14.3 ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for gfortran14 option to produce PIC... -fPIC checking if gfortran14 PIC flag -fPIC works... yes checking if gfortran14 static flag -static works... yes checking if gfortran14 supports -c -o file.o... yes checking if gfortran14 supports -c -o file.o... (cached) yes checking whether the gfortran14 linker (/usr/local/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd14.3 ld.so checking how to hardcode library paths into programs... immediate checking for exp in -lm... yes checking for _Bool... (cached) yes checking for stdbool.h that conforms to C99 or later... (cached) yes checking for malloc.h... yes checking for float.h... (cached) yes checking for limits.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for math.h... (cached) yes checking for stdarg.h... (cached) yes checking for GNU libc compatible malloc... (cached) yes checking for GNU libc compatible realloc... yes checking for working strtod... (cached) yes checking for floor... yes checking for strdup... (cached) yes checking for strstr... (cached) yes checking for strchr... (cached) yes checking for strrchr... (cached) yes checking for strstr... (cached) yes checking for strtol... (cached) yes checking for strtoul... (cached) yes checking for pow... yes checking for rint... yes checking for sqrt... yes checking for erand48... yes checking for memset... (cached) yes checking for memmove... (cached) yes checking for erand48... (cached) yes checking for asprintf... (cached) yes checking for vasprintf... (cached) yes checking for an ANSI C-conforming const... yes checking for size_t... (cached) yes checking for inline... inline checking for _Generic... yes checking for egrep -e... (cached) /usr/bin/egrep checking for pdflatex... no checking for bibtex... no checking for makeindex... no checking pkg-config is at least version 0.9.0... yes checking for C compiler vendor... clang checking for perl... (cached) /usr/local/bin/perl checking whether C compiler accepts -fno-strict-aliasing... yes checking whether C++ compiler accepts -fno-strict-aliasing... yes checking whether the linker accepts -fno-strict-aliasing... yes checking whether the C compiler allows unnamed unions of unnamed structs... yes checking whether the C++ compiler allows unnamed unions of unnamed structs... yes checking whether C compiler accepts -flto... yes checking whether C compiler accepts -flto=auto... yes checking whether C++ compiler accepts -flto... yes checking whether C++ compiler accepts -flto=auto... yes checking whether C compiler accepts -ffat-lto-objects... yes checking whether C++ compiler accepts -ffat-lto-objects... yes configure: WARNING: Unknown target host, deactivating LTO support checking for ./src/libsvm-3.35/svm.cpp... yes checking for ./src/libsvm-3.35/svm.h... yes checking for cblas_dgemm in -lgslcblas... yes checking for gsl_blas_dgemm in -lgsl... yes checking for gsl/gsl_multimin.h... yes checking whether we can compile and link programs with gsl support... yes checking for OpenMP flag of C compiler... -fopenmp checking for OpenMP flag of C++ compiler... -fopenmp checking for omp.h... yes checking for the correct linker flags to use for OpenMP... -lomp checking whether cc is Clang... yes checking whether pthreads work with "-pthread" and "-lpthread"... yes checking whether Clang needs flag to prevent "argument unused" warning when linking with -pthread... no checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE checking whether more special flags are required for pthreads... no checking for PTHREAD_PRIO_INHERIT... yes checking compiler support for AVX 512 instructions... yes checking compiler support for SSE 4.1 instructions... yes checking whether C compiler accepts -ftree-vectorize... yes checking for mpfr.h... yes checking whether we can compile programs with mpfr support... yes checking for ./src/ViennaRNA/plotting/naview/naview.c... yes checking for ./src/ViennaRNA/plotting/naview/naview.h... yes checking for ./interfaces/Makefile.am... yes checking for swig... /usr/local/bin/swig checking SWIG version... 4.3.1 checking for SWIG library... /usr/local/share/swig/4.3.1 checking for doxygen... no checking for dot... no checking for grep... /usr/bin/grep checking for perl... /usr/local/bin/perl checking for sphinx-build... no checking for sphinx-build3... no checking for doc/doxygen/xml/index.xml... yes configure: WARNING: sphinx-build is required to build the reference manual configure: WARNING: Python module build required to build the reference manual configure: WARNING: Could not find pdflatex! configure: WARNING: deactivating automatic (re)generation of reference manual! configure: WARNING: makeindex command not found on your system! configure: WARNING: deactivating automatic (re)generation of reference manual! configure: WARNING: bibtex command not found on your system! configure: WARNING: deactivating automatic (re)generation of reference manual! checking for doc/RNAlib-2.7.0.pdf... yes checking for doc/build/html/index.html... yes configure: WARNING: Could not find pdflatex! configure: WARNING: deactivating automatic (re)generation of CLA! checking for doc/CLA/ViennaRNA-CLA-Individual.pdf... yes checking for doc/CLA/ViennaRNA-CLA-Entity.pdf... yes checking for check >= 0.9.4... no configure: WARNING: check not found -- will not build C-library Unit tests checking for diff... /usr/bin/diff checking for xxd... /usr/local/bin/xxd checking for gengetopt... no checking for help2man... no checking whether c++ supports C++17 features with -std=c++17... yes checking for dlib-1 >= 19.0... yes checking for ./src/Kinfold/Makefile.am... yes checking for ./src/RNAforester/Makefile.am... yes checking for ./src/Cluster/Makefile.am... yes checking for ./src/Kinwalker/Makefile.am... yes checking for ./src/RNAlocmin/Makefile.am... yes checking for ./src/RNAxplorer/Makefile.am... yes checking for openblas/lapacke.h... no checking for lapacke/lapacke.h... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating packaging/macosx/Makefile config.status: creating packaging/macosx/Distribution.xml config.status: creating packaging/macosx/resources/welcome.txt config.status: creating src/ViennaRNA/plotting/naview/Makefile config.status: creating doc/doxygen/doxygen.conf config.status: creating doc/conf.py config.status: creating doc/source/conf.py config.status: creating doc/source/install.rst config.status: creating tests/Makefile config.status: creating tests/RNApath.py config.status: creating tests/RNAHelpers.pm config.status: creating tests/test-env.sh config.status: creating src/ViennaRNA/static/templates_postscript.h config.status: creating src/ViennaRNA/static/templates_svg.h config.status: creating src/ViennaRNA/static/energy_parameter_sets.h config.status: creating interfaces/parameter_sets.i config.status: creating src/Cluster/Makefile config.status: creating src/ViennaRNA/vrna_config.h config.status: creating misc/Makefile config.status: creating interfaces/Makefile config.status: creating Makefile config.status: creating RNAlib2.pc config.status: creating src/Utils/Makefile config.status: creating src/bin/Makefile config.status: creating src/Makefile config.status: creating src/ViennaRNA/Makefile config.status: creating src/Utils/python_wrapper config.status: creating src/ViennaRNA/static/Makefile config.status: creating man/Makefile config.status: creating man/cmdlopt.sh config.status: creating doc/doxygen/Makefile config.status: creating doc/Makefile config.status: creating doc/source/man/Makefile config.status: creating doc/CLA/Makefile config.status: creating examples/Makefile config.status: creating packaging/viennarna.spec config.status: creating packaging/PKGBUILD config.status: creating packaging/win_installer_archlinux_i686.nsi config.status: creating packaging/win_installer_archlinux_x86_64.nsi config.status: creating packaging/win_installer_fedora_i686.nsi config.status: creating packaging/win_installer_fedora_x86_64.nsi config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands === configuring in src/Kinfold (/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold) configure: running /usr/local/bin/bash ./configure --disable-option-checking '--prefix=/usr/local' '--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' '--localstatedir=/var' '--mandir=/usr/local/share/man' '--disable-silent-rules' '--infodir=/usr/local/share/info/' '--build=amd64-portbld-freebsd14.3' 'build_alias=amd64-portbld-freebsd14.3' 'CC=cc' 'CFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing' 'LDFLAGS=-Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' 'CXX=c++' 'CXXFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Dregister= -isystem /usr/local/include' 'CPP=cpp' 'F77=gfortran14' 'FFLAGS=-O -Wl,-rpath=/usr/local/lib/gcc14' 'PKG_CONFIG=pkgconf' 'PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/viennarna/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig' 'AR=/usr/local/bin/ar' 'RANLIB=/usr/local/bin/ranlib' 'NM=/usr/local/bin/nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB' 'VRNA_LIBS=-fno-strict-aliasing -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++' --cache-file=/dev/null --srcdir=. configure: loading site script /usr/ports/Templates/config.site checking whether /usr/local/bin/gmake supports nested variables... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking xargs -n works... yes checking whether UID '65534' is supported by ustar format... yes checking whether GID '65534' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar checking if malloc debugging is wanted... no checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking dependency style of cc... gcc3 checking build system type... amd64-portbld-freebsd14.3 checking host system type... amd64-portbld-freebsd14.3 checking for strdup... (cached) yes checking for memset... (cached) yes checking for strchr... (cached) yes checking pkg-config is at least version 0.9.0... yes checking for RNAlib2 >= 2.2.0... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for exp in -lm... yes checking for an ANSI C-conforming const... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Example/Makefile config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in src/RNAforester (/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester) configure: running /usr/local/bin/bash ./configure --disable-option-checking '--prefix=/usr/local' '--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' '--localstatedir=/var' '--mandir=/usr/local/share/man' '--disable-silent-rules' '--infodir=/usr/local/share/info/' '--build=amd64-portbld-freebsd14.3' 'build_alias=amd64-portbld-freebsd14.3' 'CC=cc' 'CFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing' 'LDFLAGS=-Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' 'CXX=c++' 'CXXFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Dregister= -isystem /usr/local/include' 'CPP=cpp' 'F77=gfortran14' 'FFLAGS=-O -Wl,-rpath=/usr/local/lib/gcc14' 'PKG_CONFIG=pkgconf' 'PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/viennarna/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig' 'AR=/usr/local/bin/ar' 'RANLIB=/usr/local/bin/ranlib' 'NM=/usr/local/bin/nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB' 'VRNA_LIBS=-fno-strict-aliasing -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++' --cache-file=/dev/null --srcdir=. configure: loading site script /usr/ports/Templates/config.site checking whether /usr/local/bin/gmake supports nested variables... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking xargs -n works... yes checking whether UID '65534' is supported by ustar format... yes checking whether GID '65534' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking for gcc... cc checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking for flex... flex checking for lex output file root... lex.yy checking for lex library... none needed checking for library containing yywrap... -lfl checking whether yytext is a pointer... yes checking for bison... bison -y checking for c++ option to support OpenMP... -fopenmp checking pkg-config is at least version 0.9.0... yes checking for RNAlib2... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for g2.h... yes checking for an ANSI C-conforming const... yes checking for inline... inline checking for size_t... (cached) yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in g2-0.72 (/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/g2-0.72) configure: running /usr/local/bin/bash ./configure --disable-option-checking '--prefix=/usr/local' '--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' '--localstatedir=/var' '--mandir=/usr/local/share/man' '--disable-silent-rules' '--infodir=/usr/local/share/info/' '--build=amd64-portbld-freebsd14.3' 'build_alias=amd64-portbld-freebsd14.3' 'CC=cc' 'CFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing' 'LDFLAGS=-Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' 'CXX=c++' 'CXXFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Dregister= -isystem /usr/local/include' 'CPP=cpp' 'F77=gfortran14' 'FFLAGS=-O -Wl,-rpath=/usr/local/lib/gcc14' 'PKG_CONFIG=pkgconf' 'PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/viennarna/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig' 'AR=/usr/local/bin/ar' 'RANLIB=/usr/local/bin/ranlib' 'NM=/usr/local/bin/nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB' 'VRNA_LIBS=-fno-strict-aliasing -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++' --cache-file=/dev/null --srcdir=. configure: loading site script /usr/ports/Templates/config.site checking build system type... amd64-portbld-freebsd14.3 checking host system type... amd64-portbld-freebsd14.3 checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking how to run the C preprocessor... cpp checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking for a BSD-compatible install... /usr/bin/install -c checking for find... find checking for makedepend... : checking for dlopen in -ldl... yes checking for X... libraries /usr/local/lib, headers /usr/local/include checking whether -R must be followed by a space... neither works checking for gethostbyname... (cached) yes checking for connect... yes checking for remove... yes checking for shmat... yes checking for IceConnectionNumber in -lICE... yes checking for main in -lm... yes checking for main in -lX11... yes checking for main in -lXext... yes checking for main in -lgd... yes checking for gdImagePng... yes checking for gdImageGif... yes checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for limits.h... (cached) yes configure: creating ./config.status config.status: creating Makefile config.status: creating demo/Makefile config.status: creating g2_perl/Makefile.PL config.status: creating g2_python/Makefile Supported devices: PostScript FIG X11 Xdbe GD GD (GIF) Unsupported devices: Win32 Run 'make depend' to create dependencies. === configuring in src/Kinwalker (/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker) configure: running /usr/local/bin/bash ./configure --disable-option-checking '--prefix=/usr/local' '--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' '--localstatedir=/var' '--mandir=/usr/local/share/man' '--disable-silent-rules' '--infodir=/usr/local/share/info/' '--build=amd64-portbld-freebsd14.3' 'build_alias=amd64-portbld-freebsd14.3' 'CC=cc' 'CFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing' 'LDFLAGS=-Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' 'CXX=c++' 'CXXFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Dregister= -isystem /usr/local/include' 'CPP=cpp' 'F77=gfortran14' 'FFLAGS=-O -Wl,-rpath=/usr/local/lib/gcc14' 'PKG_CONFIG=pkgconf' 'PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/viennarna/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig' 'AR=/usr/local/bin/ar' 'RANLIB=/usr/local/bin/ranlib' 'NM=/usr/local/bin/nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB' 'VRNA_LIBS=-fno-strict-aliasing -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++' --cache-file=/dev/null --srcdir=. configure: loading site script /usr/ports/Templates/config.site checking whether /usr/local/bin/gmake supports nested variables... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking xargs -n works... yes checking whether UID '65534' is supported by ustar format... yes checking whether GID '65534' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking dependency style of c++... gcc3 checking how to run the C++ preprocessor... c++ -E checking for gcc... cc checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking how to run the C preprocessor... cpp checking whether c++ supports C++14 features with -std=c++14... yes checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for malloc.h... yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for inline... inline checking pkg-config is at least version 0.9.0... yes checking for RNAlib2... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating man/Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in src/RNAlocmin (/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAlocmin) configure: running /usr/local/bin/bash ./configure --disable-option-checking '--prefix=/usr/local' '--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' '--localstatedir=/var' '--mandir=/usr/local/share/man' '--disable-silent-rules' '--infodir=/usr/local/share/info/' '--build=amd64-portbld-freebsd14.3' 'build_alias=amd64-portbld-freebsd14.3' 'CC=cc' 'CFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing' 'LDFLAGS=-Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' 'CXX=c++' 'CXXFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Dregister= -isystem /usr/local/include' 'CPP=cpp' 'F77=gfortran14' 'FFLAGS=-O -Wl,-rpath=/usr/local/lib/gcc14' 'PKG_CONFIG=pkgconf' 'PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/viennarna/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig' 'AR=/usr/local/bin/ar' 'RANLIB=/usr/local/bin/ranlib' 'NM=/usr/local/bin/nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB' 'VRNA_LIBS=-fno-strict-aliasing -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++' --cache-file=/dev/null --srcdir=. configure: loading site script /usr/ports/Templates/config.site checking for gcc... cc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for wchar.h... (cached) yes checking for minix/config.h... (cached) no checking whether it is safe to define __EXTENSIONS__... yes checking whether _XOPEN_SOURCE should be defined... no checking whether /usr/local/bin/gmake supports nested variables... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking xargs -n works... yes checking whether UID '65534' is supported by ustar format... yes checking whether GID '65534' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar checking dependency style of cc... gcc3 checking build system type... amd64-portbld-freebsd14.3 checking host system type... amd64-portbld-freebsd14.3 checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking dependency style of c++... gcc3 checking how to run the C++ preprocessor... c++ -E checking for gcc... (cached) cc checking whether the compiler supports GNU C... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to enable C11 features... (cached) none needed checking whether cc understands -c and -o together... (cached) yes checking how to run the C preprocessor... cpp checking whether c++ supports C++11 features by default... yes checking for strchr... (cached) yes checking for strdup... (cached) yes checking for strtol... (cached) yes checking for limits.h... (cached) yes checking for _Bool... (cached) yes checking for stdbool.h that conforms to C99 or later... (cached) yes checking for inline... inline checking for GNU libc compatible malloc... (cached) yes checking for GNU libc compatible realloc... yes checking for working strtod... (cached) yes checking for size_t... (cached) yes checking pkg-config is at least version 0.9.0... yes checking for RNAlib2... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating config.h config.status: executing depfiles commands === configuring in src/RNAxplorer (/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer) configure: running /usr/local/bin/bash ./configure --disable-option-checking '--prefix=/usr/local' '--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' '--localstatedir=/var' '--mandir=/usr/local/share/man' '--disable-silent-rules' '--infodir=/usr/local/share/info/' '--build=amd64-portbld-freebsd14.3' 'build_alias=amd64-portbld-freebsd14.3' 'CC=cc' 'CFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing' 'LDFLAGS=-Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14' 'LIBS=-L/usr/local/lib' 'CPPFLAGS=-isystem /usr/local/include' 'CXX=c++' 'CXXFLAGS=-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Dregister= -isystem /usr/local/include' 'CPP=cpp' 'F77=gfortran14' 'FFLAGS=-O -Wl,-rpath=/usr/local/lib/gcc14' 'PKG_CONFIG=pkgconf' 'PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/viennarna/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig' 'AR=/usr/local/bin/ar' 'RANLIB=/usr/local/bin/ranlib' 'NM=/usr/local/bin/nm' 'VRNA_CFLAGS=-I$(top_srcdir)/../../src/ViennaRNA -I$(top_srcdir)/../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB' 'VRNA_LIBS=-fno-strict-aliasing -L$(top_builddir)/../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++' --cache-file=/dev/null --srcdir=. configure: loading site script /usr/ports/Templates/config.site checking whether /usr/local/bin/gmake supports nested variables... yes checking for a BSD-compatible install... /usr/bin/install -c checking whether sleep supports fractional seconds... yes checking filesystem timestamp resolution... 0.01 checking whether build environment is sane... yes checking for a race-free mkdir -p... (cached) /bin/mkdir -p checking for gawk... (cached) /usr/bin/awk checking whether /usr/local/bin/gmake sets $(MAKE)... yes checking xargs -n works... yes checking whether UID '65534' is supported by ustar format... yes checking whether GID '65534' is supported by ustar format... yes checking how to create a ustar tar archive... (cached) /usr/bin/tar checking whether the Fortran 77 compiler works... yes checking for Fortran 77 compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether the compiler supports GNU Fortran 77... yes checking whether gfortran14 accepts -g... yes checking build system type... amd64-portbld-freebsd14.3 checking host system type... amd64-portbld-freebsd14.3 checking how to get verbose linking output from gfortran14... -v checking for Fortran 77 libraries of gfortran14... -L/usr/local/lib/gcc14 -L/usr/local/lib -L/usr/local/lib/gcc14/gcc/x86_64-portbld-freebsd14.3/14.2.0 -L/usr/local/lib/gcc14/gcc/x86_64-portbld-freebsd14.3/14.2.0/../../../../../x86_64-portbld-freebsd14.3/lib -L/usr/local/lib/gcc14/gcc/x86_64-portbld-freebsd14.3/14.2.0/../../.. -lgfortran -lm -lquadmath checking whether /usr/local/bin/gmake supports the include directive... yes (GNU style) checking for gcc... cc checking whether the compiler supports GNU C... yes checking whether cc accepts -g... yes checking for cc option to enable C11 features... none needed checking whether cc understands -c and -o together... yes checking dependency style of cc... gcc3 checking for dummy main to link with Fortran 77 libraries... none checking for Fortran 77 name-mangling scheme... lower case, underscore, no extra underscore checking if sgemm_ is being linked in already... no checking for sgemm_ in -lflexiblas... no checking for sgemm_ in -lopenblas... no checking for ATL_xerbla in -latlas... no checking for sgemm_ in -lblas... yes checking for dgemm_ in -ldgemm... no checking for sgemm_ in -lmkl... no checking for sgemm_ in -framework Accelerate... no checking for sgemm_ in -lcxml... no checking for sgemm_ in -ldxml... no checking for sgemm_ in -lscs... no checking for sgemm_ in -lcomplib.sgimath... no checking for sgemm_ in -lblas... (cached) yes checking for sgemm_ in -lessl... no checking for sgemm_ in -lblas... (cached) yes checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for cheev_... no checking for cheev_ in -llapack... yes checking for openblas/lapacke.h... no checking for lapacke/lapacke.h... yes checking for gcc... (cached) cc checking whether the compiler supports GNU C... (cached) yes checking whether cc accepts -g... (cached) yes checking for cc option to enable C11 features... (cached) none needed checking whether cc understands -c and -o together... (cached) yes checking dependency style of cc... (cached) gcc3 checking how to run the C preprocessor... cpp checking whether the compiler supports GNU C++... yes checking whether c++ accepts -g... yes checking for c++ option to enable C++11 features... none needed checking dependency style of c++... gcc3 checking for malloc.h... yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for inline... inline checking the archiver (/usr/local/bin/ar) interface... ar checking how to print strings... printf checking for a sed that does not truncate output... (cached) /usr/bin/sed checking for grep that handles long lines and -e... (cached) /usr/bin/grep checking for egrep... (cached) /usr/bin/egrep checking for fgrep... (cached) /usr/bin/fgrep checking for ld used by cc... /usr/local/bin/ld checking if the linker (/usr/local/bin/ld) is GNU ld... yes checking for BSD- or MS-compatible name lister (nm)... /usr/local/bin/nm checking the name lister (/usr/local/bin/nm) interface... BSD nm checking whether ln -s works... yes checking the maximum length of command line arguments... (cached) 524288 checking how to convert amd64-portbld-freebsd14.3 file names to amd64-portbld-freebsd14.3 format... func_convert_file_noop checking how to convert amd64-portbld-freebsd14.3 file names to toolchain format... func_convert_file_noop checking for /usr/local/bin/ld option to reload object files... -r checking for file... file checking for objdump... /usr/local/bin/objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ranlib... /usr/local/bin/ranlib checking for archiver @FILE support... @ checking for strip... strip checking command to parse /usr/local/bin/nm output from cc object... failed checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/local/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd14.3 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking how to run the C++ preprocessor... c++ -E checking for ld used by c++... /usr/local/bin/ld checking if the linker (/usr/local/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/local/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/usr/local/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd14.3 ld.so checking how to hardcode library paths into programs... immediate checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... no checking for gfortran14 option to produce PIC... -fPIC checking if gfortran14 PIC flag -fPIC works... yes checking if gfortran14 static flag -static works... yes checking if gfortran14 supports -c -o file.o... yes checking if gfortran14 supports -c -o file.o... (cached) yes checking whether the gfortran14 linker (/usr/local/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd14.3 ld.so checking how to hardcode library paths into programs... immediate checking for pkg-config... true checking pkg-config is at least version 0.9.0... yes checking for RNAlib2 >= 2.4.12... yes checking for exp in -lm... yes checking for malloc.h... (cached) yes checking for float.h... (cached) yes checking for limits.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for strings.h... (cached) yes checking for unistd.h... (cached) yes checking for unistd.h... (cached) yes checking for math.h... (cached) yes checking for strdup... (cached) yes checking for C compiler vendor... clang checking for gengetopt... no checking for help2man... no checking for OpenMP flag of C compiler... -fopenmp checking for OpenMP flag of C++ compiler... -fopenmp checking for ./interfaces/Makefile.am... yes checking for swig... /usr/local/bin/swig checking SWIG version... 4.3.1 checking for SWIG library... /usr/local/share/swig/4.3.1 checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating doc/Makefile chmod: doc/cmdlopt.sh: No such file or directory config.status: creating doc/cmdlopt.sh config.status: creating interfaces/Makefile config.status: creating Makefile config.status: creating src/Makefile config.status: creating packaging/RNAxplorer.spec config.status: creating packaging/PKGBUILD config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands configure: Configured successful with the following options: RNAxplorerlib Scripting Interfaces: Python3 Interface: no Files will be installed in the following directories: Executables: /usr/local/bin Python3 Interface: Not to be installed (binaries): (scripts): configure: ====================================== ViennaRNA Package 2.7.0 ====================================== Successfully configured with the following options: Sub Packages ------------ * Kinfold : yes * RNAforester : yes * Analyse{Dists,Seqs} : yes * RNAlocmin : yes * Kinwalker : yes * RNAxplorer : yes Extra Libraries --------------- * Support Vector Machine : yes * GNU Scientific Library : yes * GNU MPFR : yes Features -------- * Use hash for NR Sampling : no * C11 features : yes * TTY colors : yes * Float Precision(PF} : no * Deprecation Warnings : no * Debug Log Messages : no Optimizations ------------- * Auto Vectorization : yes * Explicit SIMD Extension : yes * Link Time Optimization : yes * POSIX Threads : yes * OpenMP : yes Scripting Language Interfaces ----------------------------- * Perl 5 : no * Python 3.x : no * Python 2.x : no Documentation ------------- * Reference Manual (PDF) : yes * Reference Manual (HTML) : yes * CLA (PDF) : yes Unit Tests ---------- * Executable Programs : yes * C-Library : no * Perl 5 Interface : no * Python 3.x Interface : no * Python 2.x Interface : no MacOS X ------- * Universal Binary : no * Installer : no * SDK : no Install Directories ------------------- * Executables : /usr/local/bin * Libraries : /usr/local/lib * Header files : /usr/local/include * Extra Data : /usr/local/share * Man pages : /usr/local/share/man * Documentation : /usr/local/share/doc/ViennaRNA (HTML) : /usr/local/share/doc/ViennaRNA/html (PDF) : /usr/local/share/doc/ViennaRNA * Perl5 Interface : Not to be installed (binaries) : (scripts) : * Python 3.x Interface : Not to be installed (binaries) : (scripts) : * Python 2.x Interface : Not to be installed (binaries) : (scripts) : You can run 'make', 'make check', and 'make install' now! =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building for viennarna-2.7.0_2 /usr/local/bin/gmake all-recursive gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0' Making all in src gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src' Making all in ViennaRNA gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA' Making all in static gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/static' /usr/local/bin/gmake all-am gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/static' gmake[5]: Nothing to be done for 'all-am'. gmake[5]: Leaving directory 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/usr/local/include -fno-strict-aliasing -MT naview.lo -MD -MP -MF .deps/naview.Tpo -c naview.c -fPIC -DPIC -o .libs/naview.o mv -f .deps/naview.Tpo .deps/naview.Plo /usr/local/bin/bash ../../../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o libRNA_naview.la naview.lo -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: /usr/local/bin/ar cr .libs/libRNA_naview.a .libs/naview.o libtool: link: /usr/local/bin/ranlib .libs/libRNA_naview.a libtool: link: ( cd ".libs" && rm -f "libRNA_naview.la" && ln -s "../libRNA_naview.la" "libRNA_naview.la" ) gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/plotting/naview' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA' depbase=`echo fold_compound.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT fold_compound.lo -MD -MP -MF $depbase.Tpo -c -o fold_compound.lo fold_compound.c &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo dist_vars.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT dist_vars.lo -MD -MP -MF $depbase.Tpo -c -o dist_vars.lo dist_vars.c &&\ mv 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stringdist.lo -MD -MP -MF $depbase.Tpo -c -o stringdist.lo stringdist.c &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo ProfileAln.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT ProfileAln.lo -MD -MP -MF $depbase.Tpo -c -o ProfileAln.lo ProfileAln.c &&\ mv -f $depbase.Tpo $depbase.Plo depbase=`echo duplex.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem 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-DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT duplex.lo -MD -MP -MF .deps/duplex.Tpo -c duplex.c -fPIC -DPIC -o .libs/duplex.o depbase=`echo mm.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT mm.lo -MD -MP -MF $depbase.Tpo -c -o mm.lo mm.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing 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-fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT ../cephes/const.lo -MD -MP -MF $depbase.Tpo -c -o ../cephes/const.lo ../cephes/const.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT ../cephes/kn.lo -MD -MP -MF ../cephes/.deps/kn.Tpo -c ../cephes/kn.c -fPIC -DPIC -o ../cephes/.libs/kn.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT ../cephes/const.lo -MD -MP -MF ../cephes/.deps/const.Tpo -c ../cephes/const.c -fPIC -DPIC -o ../cephes/.libs/const.o ../cephes/kn.c:94:8: warning: a function definition without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 94 | double kn( nn, depbase=`echo ../cephes/mtherr.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ x/usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT ../cephes/mtherr.lo -MD -MP -MF $depbase.Tpo -c -o ../cephes/mtherr.lo ../cephes/mtherr.c &&\ mv -f $depbase.Tpo $depbase.Plo ) | ^ 1 warning generated. libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize 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probing/.libs/probing.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT probabilities/probs_structures.lo -MD -MP -MF probabilities/.deps/probs_structures.Tpo -c probabilities/probs_structures.c -fPIC -DPIC -o probabilities/.libs/probs_structures.o libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT probing/SHAPE.lo -MD -MP -MF probing/.deps/SHAPE.Tpo -c probing/SHAPE.c -fPIC -DPIC -o probing/.libs/SHAPE.o In file included from plotting/RNApuzzler/RNApuzzler.c:20: In file included from plotting/RNApuzzler/includes/resolveIntersections.inc:15: plotting/RNApuzzler/includes/handleAncestorIntersections.inc:64:11: warning: 10 enumeration values not handled in switch: 'noIntersection', 'LxL', 'LxS'... 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-DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -I../../src/libsvm-3.35 -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT io/libRNA_utils_la-file_formats_msa.lo -MD -MP -MF io/.deps/libRNA_utils_la-file_formats_msa.Tpo -c -o io/libRNA_utils_la-file_formats_msa.lo `test -f 'io/file_formats_msa.c' || echo './'`io/file_formats_msa.c na_realloc: requested silibtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -I../../src/libsvm-3.35 -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT io/libRNA_utils_la-io_utils.lo -MD -MP -MF io/.deps/libRNA_utils_la-io_utils.Tpo -c io/io_utils.c -fPIC -DPIC -o io/.libs/libRNA_utils_la-io_utils.o ze: %d\n", size);libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -I../../src/libsvm-3.35 -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT io/libRNA_utils_la-file_formats.lo -MD -MP -MF io/.deps/libRNA_utils_la-file_formats.Tpo -c io/file_formats.c -fPIC -DPIC -o io/.libs/libRNA_utils_la-file_formats.o | ~~ ^~~~ | %zu libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/json -I../../src/libsvm-3.35 -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT io/libRNA_utils_la-file_formats_msa.lo -MD -MP -MF io/.deps/libRNA_utils_la-file_formats_msa.Tpo -c io/file_formats_msa.c -fPIC -DPIC -o 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sequences/.libs/seq_utils.o libtool: link: ( cd ".libs" && rm -f "libRNA_probing.la" && ln -s "../libRNA_probing.la" "libRNA_probing.la" ) libtool: link: /usr/local/bin/ar cr .libs/libRNA_plotting.a plotting/.libs/alignments.o plotting/.libs/layouts.o plotting/.libs/probabilities.o plotting/.libs/structures.o plotting/.libs/plot_utils.o plotting/.libs/svg.o plotting/.libs/eps.o plotting/.libs/gml.o plotting/.libs/xrna.o plotting/.libs/ssv.o plotting/RNApuzzler/.libs/RNApuzzler.o plotting/RNApuzzler/.libs/RNAturtle.o .libs/libRNA_plotting.lax/libRNA_naview.a/naview.o /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o libRNA_utils.la utils/libRNA_utils_la-utils.lo utils/libRNA_utils_la-string_utils.lo utils/libRNA_utils_la-higher_order_functions.lo 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libRNA_structures.la libRNA_subopt.la libRNA_utils.la libRNA_utils_sse41.la libRNA_utils_avx512.la libRNA_svm.la -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: (cd .libs/libRNA_conv.lax/libRNA_backtrack.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_backtrack.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_combinatorics.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_combinatorics.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_concentrations.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_concentrations.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_constraints.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_constraints.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_datastructures.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_datastructures.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_eval.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_eval.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_grammar.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_grammar.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_inverse.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_inverse.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_landscape.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_landscape.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_mfe.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_mfe.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_params.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_params.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_partfunc.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_partfunc.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_plotting.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_plotting.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_probabilities.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_probabilities.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_probing.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_probing.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_sampling.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_sampling.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_sequences.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_sequences.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_structures.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_structures.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_subopt.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_subopt.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_utils.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_utils.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_utils_sse41.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_utils_sse41.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_utils_avx512.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_utils_avx512.a") libtool: link: (cd .libs/libRNA_conv.lax/libRNA_svm.a && /usr/local/bin/ar x "/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/./.libs/libRNA_svm.a") libtool: link: /usr/local/bin/ar cr .libs/libRNA_conv.a .libs/fold_compound.o .libs/dist_vars.o .libs/treedist.o .libs/ProfileDist.o .libs/RNAstruct.o .libs/stringdist.o .libs/ProfileAln.o .libs/duplex.o .libs/mm.o .libs/2Dfold.o .libs/2Dpfold.o .libs/plex_functions.o .libs/ali_plex.o .libs/c_plex.o .libs/plex.o .libs/snofold.o .libs/snoop.o 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.libs/libRNA.lax/libRNA_conv.a/sequence.o .libs/libRNA.lax/libRNA_conv.a/snofold.o .libs/libRNA.lax/libRNA_conv.a/snoop.o .libs/libRNA.lax/libRNA_conv.a/soft.o .libs/libRNA.lax/libRNA_conv.a/soft_cb_multi.o .libs/libRNA.lax/libRNA_conv.a/sparse_mx.o .libs/libRNA.lax/libRNA_conv.a/ssv.o .libs/libRNA.lax/libRNA_conv.a/stream_output.o .libs/libRNA.lax/libRNA_conv.a/string.o .libs/libRNA.lax/libRNA_conv.a/stringdist.o .libs/libRNA.lax/libRNA_conv.a/structure_benchmark.o .libs/libRNA.lax/libRNA_conv.a/structure_dotbracket.o .libs/libRNA.lax/libRNA_conv.a/structure_helix.o .libs/libRNA.lax/libRNA_conv.a/structure_metrics.o .libs/libRNA.lax/libRNA_conv.a/structure_pairtable.o .libs/libRNA.lax/libRNA_conv.a/structure_problist.o .libs/libRNA.lax/libRNA_conv.a/structure_shapes.o .libs/libRNA.lax/libRNA_conv.a/structure_tree.o .libs/libRNA.lax/libRNA_conv.a/structure_utils.o .libs/libRNA.lax/libRNA_conv.a/structures.o .libs/libRNA.lax/libRNA_conv.a/subopt.o .libs/libRNA.lax/libRNA_conv.a/subopt_gquad.o .libs/libRNA.lax/libRNA_conv.a/subopt_zuker.o .libs/libRNA.lax/libRNA_conv.a/svg.o .libs/libRNA.lax/libRNA_conv.a/treedist.o .libs/libRNA.lax/libRNA_conv.a/unstructured_domains.o .libs/libRNA.lax/libRNA_conv.a/walk.o .libs/libRNA.lax/libRNA_conv.a/xrna.o libtool: link: /usr/local/bin/ranlib .libs/libRNA.a libtool: link: rm -fr .libs/libRNA.lax libtool: link: ( cd ".libs" && rm -f "libRNA.la" && ln -s "../libRNA.la" "libRNA.la" ) ( \ /usr/local/bin/bash ../../libtool --config > libtoolconfig.tmp && \ ( \. ./libtoolconfig.tmp; cp "$objdir/libRNA.a" ./ ) && \ rm -f libtoolconfig.tmp \ ) gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA' Making all in bin gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/bin' depbase=`echo RNAfold_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAfold_cmdl.o -MD -MP -MF $depbase.Tpo -c -o RNAfold_cmdl.o RNAfold_cmdl.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo RNAfold.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAfold.o -MD -MP -MF $depbase.Tpo -c -o RNAfold.o RNAfold.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo gengetopt_helpers.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool 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-DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAalifold.o -MD -MP -MF $depbase.Tpo -c -o RNAalifold.o RNAalifold.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo RNAplfold_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAplfold_cmdl.o -MD -MP -MF $depbase.Tpo -c -o RNAplfold_cmdl.o RNAplfold_cmdl.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo RNAplfold.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAplfold.o -MD -MP -MF $depbase.Tpo -c -o RNAplfold.o RNAplfold.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo RNAup_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ RNAalifold.ccc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAup_cmdl.o -MD -MP -MF $depbase.Tpo -c -o RNAup_cmdl.o RNAup_cmdl.c &&\ :mv -f $depbase.Tpo $depbase.Po 1109depbase=`echo RNAup.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ :cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAup.o -MD -MP -MF $depbase.Tpo -c -o RNAup.o RNAup.c &&\ 7mv -f $depbase.Tpo $depbase.Po : warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] 1109 | THREADSAFE_FILE_OUdepbase=`echo RNAaliduplex_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ Tcc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAaliduplex_cmdl.o -MD -MP -MF $depbase.Tpo -c -o RNAaliduplex_cmdl.o RNAaliduplex_cmdl.c &&\ mv -f $depbase.Tpo $depbase.Po PUdepbase=`echo RNAaliduplex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAaliduplex.o -MD -MP -MF $depbase.Tpo -c -o RNAaliduplex.o RNAaliduplex.c &&\ mv -f $depbase.Tpo $depbase.Po T({ | ^~~~~~~~~~~~~~~~~~~~~~~~ 1110 | aliout = fopen(filename_out, "w"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1111 | ifdepbase=`echo RNALalifold_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNALalifold_cmdl.o -MD -MP -MF $depbase.Tpo -c -o RNALalifold_cmdl.o RNALalifold_cmdl.c &&\ (mv -f $depbase.Tpo $depbase.Po !aliout) | ~~~~~~~~~~~~ 1112 | vrna_log_warning("can't open %s ... skipping output", filename_out); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1113 | else | ~~~~ 1114 | print_aliout(vc, pl, opt->bppmThreshold, mfe_structure, aliout); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1115 | 1116 | depbase=`echo RNALalifold.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNALalifold.o -MD -MP -MF $depbase.Tpo -c -o RNALalifold.o RNALalifold.c &&\ mv -f $depbase.Tpo $depbase.Po fclose(aliout); | ~~~~~~~~~~~~~~~ 1117 | }); | ~~ ./parallel_helpers.h:27:7: note: expanded from macro 'THREADSAFE_FILE_OUTPUT' 27 | (a); \ | ^ RNAalifold.c:1109:30: note: '{' token is here 1109 | depbase=`echo RNA2Dfold_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNA2Dfold_cmdl.o -MD -MP -MF $depbase.Tpo -c -o RNA2Dfold_cmdl.o RNA2Dfold_cmdl.c &&\ mv -f $depbase.Tpo $depbase.Po THREADSAFE_FILE_OUTPUT({ | ^ ./parallel_helpers.h:27:8: note: expanded from macro 'THREADSAFE_FILE_OUTPUT' 27 | (a); \ | ^ RNAalifold.c:1117:7: depbase=`echo RNA2Dfold.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ warning: cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNA2Dfold.o -MD -MP -MF $depbase.Tpo -c -o RNA2Dfold.o RNA2Dfold.c &&\ '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro]mv -f $depbase.Tpo $depbase.Po 1117 | }); | ^ ./parallel_helpers.h:27:8: note: expanded from macro 'THREADSAFE_FILE_OUTPUT' 27 | (a); \ | ^ RNAalifold.c:1109:7: note: ')' token is here 1109 | THREADSAFE_FILE_OUTPUT({ | ^~~~~~~~~~~~~~~~~~~~~~~~depbase=`echo RNAparconv_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAparconv_cmdl.o -MD -MP -MF $depbase.Tpo -c -o RNAparconv_cmdl.o RNAparconv_cmdl.c &&\ mv -f $depbase.Tpo $depbase.Po 1110 | aliout = fopen(filename_out, "w"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1111 | if (!aliout) | ~~~~~~~~~~~~ 1112 | vrna_log_warning("can't open %s ... skipping output", filename_out); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ depbase=`echo RNAparconv.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAparconv.o -MD -MP -MF $depbase.Tpo -c -o RNAparconv.o RNAparconv.c &&\ mv -f $depbase.Tpo $depbase.Po 1113 | depbase=`echo RNAPKplex_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAPKplex_cmdl.o -MD -MP -MF $depbase.Tpo -c -o RNAPKplex_cmdl.o RNAPKplex_cmdl.c &&\ else | ~~~~ mv -f $depbase.Tpo $depbase.Po 1114 | print_aliout(vc, pl, opt->bppmThreshold, mfe_structure, aliout); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1115 | 1116 | fclose(aliout); | ~~~~~~~~~~~~~~~ 1117 | }); | ~~ ./parallel_helpers.h:27:9: note: expanded from macro 'THREADSAFE_FILE_OUTPUT' 27 | (a); \ | ^ RNAalifold.c:1109:7: warning: '(' and '{' tokens introducing statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] 1109 | THREADSAFE_FILEdepbase=`echo RNAPKplex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAPKplex.o -MD -MP -MF $depbase.Tpo -c -o RNAPKplex.o RNAPKplex.c &&\ mv -f $depbase.Tpo $depbase.Po _Odepbase=`echo RNAplex_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAplex_cmdl.o -MD -MP -MF $depbase.Tpo -c -o RNAplex_cmdl.o RNAplex_cmdl.c &&\ mv -f $depbase.Tpo $depbase.Po UTPUT({ | ^~~~~~~~~~~~~~~~~~~~~~~~ 1110 | aliout = fopen(filename_out, "w"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1111 | if (!aliout) | ~~~~~~~~~~~~ 1112 | vrna_log_warning("can't open %s ... skipping output", filename_out); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1113 | else | ~~~~ 1114 | print_aliout(vc, pl, opt->bppmThreshold, mfe_structure, aliout); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1115 | 1116 | fclose(aliout); | ~~~~~~~~~~~~~~~ depbase=`echo RNAplex.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAplex.o -MD -MP -MF $depbase.Tpo -c -o RNAplex.o RNAplex.c &&\ mv -f $depbase.Tpo $depbase.Po 1117 | }); | ~~ ./parallel_helpers.h:30:7: note: expanded from macro 'THREADSAFE_FILE_OUTPUT' 30 | (a); \ | ^ RNAalifold.c:1109:30: note: '{' token is here 1109 | THREADSAFE_FILE_OUTPUT({ | ^ ./parallel_helpers.h:30:8: note: expanded from macro 'THREADSAFE_FILE_OUTPUT' 30 | (a); \ | ^ depbase=`echo RNAsnoop_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ RNAalifold.c:1117:7: warning: '}' and ')' tokens terminating statement expression appear in different macro expansion contexts [-Wcompound-token-split-by-macro] cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAsnoop_cmdl.o -MD -MP -MF $depbase.Tpo -c -o RNAsnoop_cmdl.o RNAsnoop_cmdl.c &&\ 1117 | }); | ^ mv -f $depbase.Tpo $depbase.Po ./parallel_helpers.h:30:8: note: expanded from macro 'THREADSAFE_FILE_OUTPUT' 30 | (a); \ | ^ RNAalifold.c:1109:7: note: ')' token is here 1109 | THREADSAFE_FILE_OUTPUT({ | ^~~~~~~~~~~~~~~~~~~~~~~~ 1110 | aliout = fopen(filename_out, "w"); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1111 | if (!aliout) | ~~~~~~~~~~~~ 1112 | vrna_log_warning("can't open %s ... skipping output", filename_out); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1113 | depbase=`echo RNAsnoop.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAsnoop.o -MD -MP -MF $depbase.Tpo -c -o RNAsnoop.o RNAsnoop.c &&\ mv -f $depbase.Tpo $depbase.Po elRNAplex.c:s2104e: 46: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source] | 2104 ~~~~ | 1114 | i f ( s sc a n f ( nparmienst[_0a]l,i o"u%t2(5v5c[,^ /p]l/,% lolpdt--%>lblpdp"m,T hbrleas,h o&lbde,g mfe_structure, aliouti)n;,depbase=`echo RNApvmin_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNApvmin_cmdl.o -MD -MP -MF $depbase.Tpo -c -o RNApvmin_cmdl.o RNApvmin_cmdl.c &&\ mv -f $depbase.Tpo $depbase.Po &| e ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ depbase=`echo RNApvmin.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ ncc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNApvmin.o -MD -MP -MF $depbase.Tpo -c -o RNApvmin.o RNApvmin.c &&\ mv -f $depbase.Tpo $depbase.Po d1115)depbase=`echo RNAdos_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ | cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAdos_cmdl.o -MD -MP -MF $depbase.Tpo -c -o RNAdos_cmdl.o RNAdos_cmdl.c &&\ mv -f $depbase.Tpo $depbase.Po 1116 | =f=c l3o)se(aliout); | ~~~~~~~~~~~~~~~ /1117* | i n i t i a}l)i;z e | l ~~ o./parallel_helpers.h:c30:9a: tnote: iexpanded from macro 'THREADSAFE_FILE_OUTPUT' o n30 | _ f l a (ga;); *\/ | ^ | ^ RNAplex.c:2120:48: warning: 'sscanf' may overflow; destination buffer in argument 3 has size 255, but the corresponding specifier may require size 256 [-Wfortify-source] 2120 | if (sscanf(names[i], "%255[^/]/%lld-%lld", bla, &begin, &end) == 3) { | ^ depbase=`echo RNAdos.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAdos.o -MD -MP -MF $depbase.Tpo -c -o RNAdos.o RNAdos.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo RNAmultifold_cmdl.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAmultifold_cmdl.o -MD -MP -MF $depbase.Tpo -c -o RNAmultifold_cmdl.o RNAmultifold_cmdl.c &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo RNAmultifold.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT RNAmultifold.o -MD -MP -MF $depbase.Tpo -c -o RNAmultifold.o RNAmultifold.c &&\ mv -f $depbase.Tpo $depbase.Po 4 warnings generated. depbase=`echo ../cthreadpool/thpool.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\ /usr/local/bin/bash ../../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT ../cthreadpool/thpool.lo -MD -MP -MF $depbase.Tpo -c -o ../cthreadpool/thpool.lo ../cthreadpool/thpool.c &&\ mv -f $depbase.Tpo $depbase.Plo libtool: compile: cc -DHAVE_CONFIG_H -I. -I../.. -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I../../src -I../../src/cthreadpool -isystem /usr/local/include -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT ../cthreadpool/thpool.lo -MD -MP -MF ../cthreadpool/.deps/thpool.Tpo -c ../cthreadpool/thpool.c -fPIC -DPIC -o ../cthreadpool/.libs/thpool.o /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -avoid-version -static -flto=auto -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o libhelpers.la gengetopt_helpers.lo input_id_helpers.lo modified_bases_helpers.lo parallel_helpers.lo ../cthreadpool/thpool.lo -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: /usr/local/bin/ar cr .libs/libhelpers.a .libs/gengetopt_helpers.o .libs/input_id_helpers.o .libs/modified_bases_helpers.o .libs/parallel_helpers.o ../cthreadpool/.libs/thpool.o libtool: link: /usr/local/bin/ranlib .libs/libhelpers.a libtool: link: ( cd ".libs" && rm -f "libhelpers.la" && ln -s "../libhelpers.la" "libhelpers.la" ) /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAfold RNAfold_cmdl.o RNAfold.o ../../src/ViennaRNA/libRNA_special_const.la libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAeval RNAeval_cmdl.o RNAeval.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNApdist RNApdist_cmdl.o RNApdist.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAinverse RNAinverse_cmdl.o RNAinverse.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAdistance RNAdistance_cmdl.o RNAdistance.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAheat RNAheat_cmdl.o RNAheat.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAdistance RNAdistance_cmdl.o RNAdistance.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAinverse RNAinverse_cmdl.o RNAinverse.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNApdist RNApdist_cmdl.o RNApdist.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAheat RNAheat_cmdl.o RNAheat.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAeval RNAeval_cmdl.o RNAeval.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAplot RNAplot_cmdl.o RNAplot.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAfold RNAfold_cmdl.o RNAfold.o -L/usr/local/lib/gcc14 ../../src/ViennaRNA/.libs/libRNA_special_const.a -L/usr/local/lib ./.libs/libhelpers.a ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAsubopt RNAsubopt_cmdl.o RNAsubopt.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAcofold RNAcofold_cmdl.o RNAcofold.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNApaln RNApaln_cmdl.o RNApaln.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAduplex RNAduplex_cmdl.o RNAduplex.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNALfold RNALfold_cmdl.o RNALfold.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAalifold RNAalifold_cmdl.o RNAalifold.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib 2 warnings generated. /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAplfold RNAplfold_cmdl.o RNAplfold.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAplot RNAplot_cmdl.o RNAplot.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNApaln RNApaln_cmdl.o RNApaln.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAsubopt RNAsubopt_cmdl.o RNAsubopt.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAduplex RNAduplex_cmdl.o RNAduplex.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAcofold RNAcofold_cmdl.o RNAcofold.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAalifold RNAalifold_cmdl.o RNAalifold.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNALfold RNALfold_cmdl.o RNALfold.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAup RNAup_cmdl.o RNAup.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAaliduplex RNAaliduplex_cmdl.o RNAaliduplex.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNALalifold RNALalifold_cmdl.o RNALalifold.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNA2Dfold RNA2Dfold_cmdl.o RNA2Dfold.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAparconv RNAparconv_cmdl.o RNAparconv.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAPKplex RNAPKplex_cmdl.o RNAPKplex.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAplex RNAplex_cmdl.o RNAplex.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAplfold RNAplfold_cmdl.o RNAplfold.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAsnoop RNAsnoop_cmdl.o RNAsnoop.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAup RNAup_cmdl.o RNAup.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAaliduplex RNAaliduplex_cmdl.o RNAaliduplex.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNALalifold RNALalifold_cmdl.o RNALalifold.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNApvmin RNApvmin_cmdl.o RNApvmin.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNA2Dfold RNA2Dfold_cmdl.o RNA2Dfold.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAparconv RNAparconv_cmdl.o RNAparconv.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAPKplex RNAPKplex_cmdl.o RNAPKplex.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAplex RNAplex_cmdl.o RNAplex.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAdos RNAdos_cmdl.o RNAdos.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib /usr/local/bin/bash ../../libtool --tag=CC --mode=link cc -fno-strict-aliasing -fopenmp -ftree-vectorize -pthread -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -lpthread -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o RNAmultifold RNAmultifold_cmdl.o RNAmultifold.o libhelpers.la ../../src/ViennaRNA/libRNA_conv.la -lmpfr -lgmp -lstdc++ -lstdc++ -lgsl -lgslcblas -lm -L/usr/local/lib libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong 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-L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp libtool: link: cc -fno-strict-aliasing -fopenmp -ftree-vectorize -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -o RNAdos RNAdos_cmdl.o RNAdos.o -L/usr/local/lib/gcc14 ./.libs/libhelpers.a -L/usr/local/lib ../../src/ViennaRNA/.libs/libRNA_conv.a -ldlib -lpthread -lmpfr -lgmp -lstdc++ -lgsl -lgslcblas -lm -pthread -fopenmp gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/bin' Making all in Utils gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Utils' cp python_wrapper RNAconsensus /usr/local/bin/gmake all-am gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Utils' cc -DHAVE_CONFIG_H -I. -I../.. 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-I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT baum.o -MD -MP -MF .deps/baum.Tpo -c -o baum.o baum.c cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cache.o -MD -MP -MF .deps/cache.Tpo -c -o cache.o cache.c cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT globals.o -MD -MP -MF .deps/globals.Tpo -c -o globals.o globals.c cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT nachbar.o -MD -MP -MF .deps/nachbar.Tpo -c -o nachbar.o nachbar.c cc -DHAVE_CONFIG_H -I. -I./src -isystem /usr/local/include -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT cmdline.o -MD -MP -MF .deps/cmdline.Tpo -c -o cmdline.o cmdline.c globals.c:344:5: warning: add explicit braces to avoid dangling else [-Wdangling-else] 344 | nachbar.c e:ls318emain.c: :43G175:T: V8warning: .:format specifies type 'int' but the argument has type 'unsigned long' [-Wformat]s ewarning: eusing the result of an assignment as a condition without parentheses [-Wparentheses]318d | =s175 p | 1r ;i n it| ff ^ ( (fcglobals.co=:rs359mv -f .deps/cache.Tpo .deps/cache.Po mta:rt9c,:h r "(warning: %cformat specifies type 'float *' but the argument has type 'double *' [-Wformat]% -t %m358dp | s, %' %& 6'i.)f2) f ( {s% s% c1| a0 ~^~~~~~~~~~~~~~~~~~n. f3main.c(f:a"175r,:g 8ss:_t irnote: nlplace parentheses around the assignment to silence this warningfe on .(175pG | bA oV u.inffda sr(_bcae=r_sgft,ur lc"lh%)rg+(=1c%)tg;=m %p g,| " ~~ ^~~~~~~~~~~~~~~~~~~~~~~~,' & '| | ) %lu ~~) { | %lg | ^ 359 | ( ) | main.c : 175 : 8 : ¬e: Guse '==' to turn this assignment into an equality comparison A V175. | p h ii_fb o(ucn=dsst[r0c]h,r ( c| t ^~~~~~~~~~~~~~~~~~m pglobals.c,: 360':&9':) )warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat]{ 358| | ^ | ==i f (main.cs:s200c:a10n:f (warning: ausing the result of an assignment as a condition without parentheses [-Wparentheses] r g200 | s _ i niffo .(pcb=osutnrdcsh_ra(rGgA,V ."s%tga=r%tgf=o%rgm",, ' &| ' ~~) ) | { %lg 1| 359 warning ~^~~~~~~~~~~~~~~~~~~~~~~~~~~ | generated . main.c : 200 : 10 : note: &place parentheses around the assignment to silence this warningGmv -f .deps/nachbar.Tpo .deps/nachbar.Po A V200. | p h i _ biofu n(dsc[=0s]t,r c h360r | (mv -f .deps/baum.Tpo .deps/baum.Po G A V . s t a r&tGfAoVr.mp,h i'_&b'o)u)n d{s [ 1| ] ^ , | | ( ) ^~~~~~~~~~~~~~~~~~ main.cglobals.c::200361::109:: note: warning: use '==' to turn this assignment into an equality comparisonformat specifies type 'float *' but the argument has type 'double *' [-Wformat] 200358 | | iiff ((cs=ssctarncfh(ra(rGgAsV_.isntfaor.tpfboorumn,d s'_&a'r)g), "{% g =| % ^g = %| g ==" , main.c| : ~~224 : 12| : %lg warning: using the result of an assignment as a condition without parentheses [-Wparentheses]359 | 224 | &iGfA V(.cp=shtir_cbhoru(ncdtsm[p0,] ,' & '360) | ) { | ~^~~~~~~~~~~~~~~~~~ main.c&:G224A:V12.:p hnote: iplace parentheses around the assignment to silence this warning_ b o224u | n d s [ 1 ] ,i f 361( | c = s t r c h r (&cGtAmVp.,p h'i&_'b)o)u n{d s [| 2 ^ ] ) | = ( )= main.c0:)224 : 12| : ^~~~~~~~~~~~~~~~~~ note: use '==' to turn this assignment into an equality comparison 224 | globals.c : 449 : 8 :i fwarning: format specifies type 'float *' but the argument has type 'double *' [-Wformat]( c =448s | t r c hirf( c(tsmspc,a n'f&(')o)p t{a r g| , ^ " %| g === %g=%g", | ~~ | %lg 449 | &GAV.phi_bounds[0], | ^~~~~~~~~~~~~~~~~~ globals.c:450:8: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat] 448 | if (sscanf(optarg, "%g=%g=%g", | ~~ | %lg 449 | &GAV.3p warninghsi generated_. bounds[0], 450 | mv -f .deps/main.Tpo .deps/main.Po &GAmv -f .deps/cmdline.Tpo .deps/cmdline.Po V.phi_bounds[1], | ^~~~~~~~~~~~~~~~~~ globals.c:451:8: warning: format specifies type 'float *' but the argument has type 'double *' [-Wformat] 448 | if (sscanf(optarg, "%g=%g=%g", | ~~ | %lg 449 | &GAV.phi_bounds[0], 450 | &GAV.phi_bounds[1], 451 | &GAV.phi_bounds[2]) == 0) | ^~~~~~~~~~~~~~~~~~ 7 warnings generated. mv -f .deps/globals.Tpo .deps/globals.Po cc -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -o Kinfold baum.o cache.o globals.o main.o nachbar.o cmdline.o -fno-strict-aliasing -L./../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ -lm -L/usr/local/lib gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold' Making all in src/RNAforester gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester' /usr/local/bin/gmake all-recursive gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester' Making all in g2-0.72 gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/g2-0.72' Makefile:101: warning: overriding recipe for target 'libg2.so' Makefile:98: warning: ignoring old recipe for target 'libg2.so' cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_device.c -o src/g2_device.o cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_control.c -o src/g2_ui_control.o cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_util.c -o src/g2_util.o cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_fif.c -o src/g2_fif.o cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_virtual_device.c -o src/g2_virtual_device.o cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_physical_device.c -o src/g2_physical_device.o cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_graphic_pd.c -o src/g2_graphic_pd.o cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_control_pd.c -o src/g2_control_pd.o cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_graphic.c -o src/g2_ui_graphic.o src/g2_graphic_pd.c:48:25: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 48cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_virtual_device.c -o src/g2_ui_virtual_device.o | src/g2_control_pd.c : 39 : 22: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] pcc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_ui_device.c -o src/g2_ui_device.o 39d | - cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/g2_splines.c -o src/g2_splines.o >pff[g2_Plot].fun(pd->pidd-,> cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/PS/g2_PS.c -o src/PS/g2_PS.o fpsrc/g2_ui_device.cf:d[51g-:2>31_p:Fd lpwarning: u,passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]s h ]| 51. ^ | f udne( vppsrc/g2_graphic_pd.cd--:>>53dp.ipdd,:- >pf25df-[>g:p2 d_warning: pDpassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype])e;l e t| e ^] . fcc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/FIG/g2_FIG.c -o src/FIG/g2_FIG.o 53u | src/g2_control_pd.cn (: d 55e : pv21dp:-- >warning: f>fpassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype][dg2_ Plo t.55]p | .d f-pu>nd(ppd->-ipid, >pddf-,f> [p gd| cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/X11/g2_X11.c -o src/X11/g2_X11.o p2, ^ _ | ^ Savesrc/g2_graphic_pd.c]:.80:25: fwarning: upassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] n 80 | ( pd-p>df-src/FIG/g2_FIG.cf>[:pg478i:d2,54_ :Lp idnwarning: -eformat specifies type 'int' but the argument has type 'unsigned long' [-Wformat]>] p. df477pu | )n1 ;( warning p generated d. | -f ^>p prisrc/g2_control_pd.cid:n,71t :fp22cc -I./src -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DUNIX=1 -DDO_PS=1 -DDO_FIG=1 -DDO_X11=1 -DDO_XDBE=1 -DDO_GD=1 -DDO_GIF=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DHAVE_LIMITS_H=1 -c src/GD/g2_gd.c -o src/GD/g2_gd.o (d:f- i>warning: gppassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]-d >p f,71p | , "| p4 ^d -0src/g2_graphic_pd.c> :f%86fd:[ 25g1:2 _-warning: C1passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]l e0a r86%] | d. f 0u n 5( pp%ddd-- >>%pfdif d[%,gd 2 p_%ddL- i>"np,ed ]p .)| f; ~~u n (| | p ^ %lud - src/g2_control_pd.c>478:p | 87i :d 20, : pwarning: dfpassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]-i> gp -d>87pp | ,e np _d| c- ^o> lfofrsrc/g2_graphic_pd.c[,:g 1152f:_i29Pg:e- n>warning: ]fpassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype].o fn ut115n_ | (s pi dz -e >, p pifddi-,g> -fp>fdf[-og>n2pt_d_Ppso,il zyceLo,il noferi])g.;-f >u fn| o( ^n ptdsrc/g2_control_pd.c-_:>103ps:i30id:z, e warning: *ppassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]sd t- r>103lp | ed npp(,dt -e >x| ft ^f) [,gsrc/g2_graphic_pd.c 2:x_125,S: e29yt:)B ;awarning: cpassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] k | g ^~~~~~~~~~~~~~~~~~~~~~~~~~~r125 o | u n d ] . fpudn-(>pfdf-[>gp2i_dP,o lpydL-i>nped]p.,f unc(opd->pliodr,) ;p d -| > ^p dpsrc/g2_control_pd.c, : | ^ 121:23src/g2_graphic_pd.c:: 159:29: warning: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 159121 | | r v = ppdd-->>ffff[[gg22__ITnrki]a.nfgulne(]p.df-u>np(ipdd,- >ppdi-d>,p dppd,- > p| ^ dp, src/g2_control_pd.c :140| : ^29 : src/g2_graphic_pd.cwarning: :passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 168 :140 | 29 :p dwarning: -passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]> f f168[g2_C | l ea r P al etptde-].f>ufnf([p1gd2 warning-_ generated>Tp. riida,n gplde-]>.pfdupn)(; | ^ pdsrc/g2_control_pd.c:-158>:p20i:d ,warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]p d -158> | p dppd,- > f| f ^[ g2_Insrc/g2_graphic_pd.ck:]201.:f35u:n (warning: ppassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] d -201> | p i d , ppdd-->>fpf[g2_dFpi,l ledTri a ngle].fun/(* pwdh->ipid, pd->tpdp, | ^ esrc/g2_graphic_pd.c: 210*:/35 : | warning: ^passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] src/g2_control_pd.c210: | 160 : 20 : warning: ppassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]d->ff[g2_FilledTriangle].fun(pd->pid, pd-> pdp, | ^ 160 | src/g2_graphic_pd.c:247:30: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] p 247 | pd->ff[g2_Rectangle].fun(pd->pid, pd->pdp, | ^ dsrc/g2_graphic_pd.c:255:30: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] - 255 | pd->ff[g2_Rectangle].fun(pd->pid, pd->pdp, | ^ >ff[src/g2_graphic_pd.c:287:36: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] g 287 | pd->ff[g2_FilledRectangle].fun(pd->pid, pd->pdp, | ^ 2src/g2_graphic_pd.c:295:36: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] _ 295 | pd->ff[g2_FilledRectangle].fun(pd->pid, pd->pdp, | ^ Ink]src/g2_graphic_pd.c:333:28: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] . 333 | pd->ff[g2_Polygon].fun(pd->pid, pd->pdp, | ^ fusrc/g2_graphic_pd.c:342:28: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] n 342 | pd->f(f[g2_Polygon].fun(pd->pid, pd->pdp, | ^ pd->src/g2_graphic_pd.c:376:34: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] p 376 | pd->ff[g2_FilledPolygoin].dfun(pd->pid, pd->pdp, | ^ , src/g2_graphic_pd.c:385:34: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] p 385 | pd->ff[g2_FilledPolygon].fun(pd->pid, pd->pdp, | ^ d->src/g2_graphic_pd.c:413:28: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] p 413 | pd->ff[g2_Eldlipse].fun(pd->pid, pd->pdpp, | ^ ,src/g2_graphic_pd.c:419:28: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 419 | pd->ff[g2_Ellipse].fun(pd->pid, pd->pdp, /* black */ | ^ | src/g2_control_pd.c:169:22: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] ^ 169 | pd->ff[g2_Ink] .fun(pd->pid, pd->pdp, | ^ src/g2_graphic_pd.c:446src/g2_control_pd.c:189:32: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] : 189 | pd->ff[g2_SetFontSize].fun(pd->pid, 34pd->p:dp, is); | ^ src/g2_control_pd.c:193:32: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] warning: 193 | passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 446 | pd->ff[g2_F i pd->ff[g2_SetFontSize].fun(pd->pid, pd->pdp, lds); | ^ ledsrc/g2_control_pd.cE:l217l:i33p:s ewarning: ]passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]. f u217n | ( p d - > ppidd-,> fpfd[-g>2p_dSpe,t L i| n ^e Wsrc/g2_graphic_pd.ci:d452t:h34]:. fwarning: upassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]n ( p452d | - > p i d ,p dp-d>-f>fp[dgp2,_ Fiiwl)l;e d E| l ^l isrc/g2_control_pd.cp:s221e:]33.:f uwarning: npassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]( p d221- | > p i d , ppdd-->>fpfd[pg,2 _ S| e ^t Linsrc/g2_graphic_pd.ce:W482i:d27t:h ]warning: .passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]f u n482( | p d - > p ipdd,- >pfdf-[>gp2d_pC,i rdcwl)e;] . f| u ^n (pd-src/g2_control_pd.c>:p249i:d25,: pwarning: dpassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]- > p249d | p pd->ff[,g2_SetDash].fun(pd- >pid, pd- >pdp, N, id); | ^ | src/g2_control_pd.c:252:25: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] ^ 252 | pd->ff[g2_SetDash] .src/g2_graphic_pd.cf:488:u27n(pd->pid,: pd->p dp, 0, NULL); | ^ warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]src/g2_control_pd.c:259:25: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 259 | pd->ff [488 | g 2 pd->ff_[Sg2e_tCDiarschl]e].fun(.pfdu-n>(ppidd-,> ppidd-,> ppddp-,> p d| p ^, N, src/g2_graphic_pd.cd:d515):;33 : | warning: ^passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] src/g2_control_pd.c :515263 | : 25 : warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]p d -263> | f f [pgd2-_>Ffifl[lge2d_CSiertcDlaes]h.]f.ufnu(np(dp-d>-p>ipdi,d ,p dp-d>-p>dppd,p , | 0 ^, Nsrc/g2_graphic_pd.cU:L521L:)33;: warning: | passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] ^ 521 | src/g2_control_pd.c : 286 : 33p:d -warning: >passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]f f [286g | 2 _ F i l lpedd-C>ifrfc[lge2]_.Qfuuenr(ypPdo-i>nptiedr,] .pfdu-n>(ppddp-,> p i| d ^, pd-src/g2_graphic_pd.c>:p548d:p24,: warning: | passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] ^ src/g2_control_pd.c548: | 291 : 33 : warning: ppassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]d - >291f | f [ g 2 _ Aprdc-]>.fffu[ng(2p_dQ-u>epriydP,o ipndt-e>rp]d.pf,u n (| p ^d -src/g2_graphic_pd.c>:p554i:d24,: pwarning: dpassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]- > p554d | p , p d- >ff| [ ^g2_Arc].fun( pd->src/g2_control_pd.cp:id, 310p:d29-:> pwarning: dpassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]p , 310 | | ^p d->ff[gsrc/g2_graphic_pd.c2:_594G:e30t:P Dwarning: Hpassing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype]a n d594les].fu | n ( p d - >ppdi-d>,f fp[dg-2>_pFdipl,l headnAdrlce]s.)f;u n (| p ^d ->pid, pd->pdp, | ^ src/g2_graphic_pd.c:600:30: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 600 | pd->ff[g2_FilledArc].fun(pd->pid, pd->pdp, | ^ src/g2_graphic_pd.c:641:27: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 641 | pd->ff[g2_String].fun(pd->pid, pd->pdp, | ^ src/g2_graphic_pd.c:646:27: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 646 | pd->21f warningfs[g generated2. _String].fun(pd->pid, pd->pdp, | ^ src/g2_graphic_pd.c:667:26: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 667 | pd->ff[g2_Image].fun(pd->pid, pd->pdp, | ^ src/g2_graphic_pd.c:672:26: warning: passing arguments to a function without a prototype is deprecated in all versions of C and is not supported in C23 [-Wdeprecated-non-prototype] 672 | pd->ff[g2_Image].fun(pd->pid, pd->pdp, | ^ 34 warnings generated. /usr/local/bin/ar cr libg2.a ./src/g2_device.o ./src/g2_ui_control.o ./src/g2_util.o ./src/g2_fif.o ./src/g2_virtual_device.o ./src/g2_physical_device.o ./src/g2_graphic_pd.o ./src/g2_control_pd.o ./src/g2_ui_graphic.o ./src/g2_ui_virtual_device.o ./src/g2_ui_device.o ./src/g2_splines.o ./src/PS/g2_PS.o ./src/FIG/g2_FIG.o ./src/X11/g2_X11.o ./src/GD/g2_gd.o test ! -n "/usr/local/bin/ranlib" || /usr/local/bin/ranlib libg2.a test -d ./include || mkdir ./include cp ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h ./src/GD/g2_gd.h ./include/ gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/g2-0.72' Making all in src gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/src' /usr/local/bin/gmake all-am gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/src' depbase=`echo aligner.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -isystem /usr/local/include -MT aligner.o -MD -MP -MF $depbase.Tpo -c -o aligner.o aligner.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo main.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -isystem /usr/local/include -MT main.o -MD -MP -MF $depbase.Tpo -c -o main.o main.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo forestbase.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -isystem /usr/local/include -MT forestbase.o -MD -MP -MF $depbase.Tpo -c -o forestbase.o forestbase.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo parser.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -isystem /usr/local/include -MT parser.o -MD -MP -MF $depbase.Tpo -c -o parser.o parser.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo progressive_align.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -isystem /usr/local/include -MT progressive_align.o -MD -MP -MF $depbase.Tpo -c -o progressive_align.o progressive_align.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo rna_profile_alignment.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -isystem /usr/local/include -MT rna_profile_alignment.o -MD -MP -MF $depbase.Tpo -c -o rna_profile_alignment.o rna_profile_alignment.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo rna_alignment.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -isystem /usr/local/include -MT rna_alignment.o -MD -MP -MF $depbase.Tpo -c -o rna_alignment.o rna_alignment.cpp &&\ mv -f $depbase.Tpo $depbase.Po depbase=`echo rna_algebra.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -isystem /usr/local/include -MT rna_algebra.o -MD -MP -MF $depbase.Tpo -c -o rna_algebra.o rna_algebra.cpp &&\ mv -f $depbase.Tpo $depbase.Po In file included from forestbase.cpp:10: ./utils/misc.t.cpp:11:20: warning: variable 'maxElemLen' set but not used [-Wunused-but-set-variable] 11 | unsigned int i,maxElemLen; | ^ 1 warning generated. depbase=`echo rna_alphabet.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -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 $depbase.Po depbase=`echo rnaforest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -isystem /usr/local/include -MT rnaforest.o -MD -MP -MF $depbase.Tpo -c -o rnaforest.o rnaforest.cpp &&\ mv -f $depbase.Tpo $depbase.Po In file included from main.cpp:8: In file included from ./aligner.h:18: In file included from ./TED/treeedit.t.cpp:10: ./utils/misc.t.cpp:11:20: warning: variable 'maxElemLen' set but not used [-Wunused-but-set-variable] 11 | unsigned int i,maxElemLen; | ^ In file included from aligner.cpp:3: In file included from ./aligner.h:18: In file included from ./TED/treeedit.t.cpp:10: ./utils/misc.t.cpp:11:20: warning: variable 'maxElemLen' set but not used [-Wunused-but-set-variable] 11 | unsigned int i,maxElemLen; | ^ main.cpp:322:17: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result] 322 | remove(baseStr.begin(),baseStr.end(),'.'); | ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ main.cpp:323:17: warning: ignoring return value of function declared with 'nodiscard' attribute [-Wunused-result] 323 | remove(baseStr.begin(),baseStr.end(),'-'); | ^~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ progressive_align.cpp:136:9: warning: variable 'level' set but not used [-Wunused-but-set-variable] 136 | int level = 1; | ^ depbase=`echo rnafuncs.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -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../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -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 $depbase.Po depbase=`echo anchors/shape.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -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 $depbase.Po depbase=`echo anchors/anchors.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -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 $depbase.Po 3 warnings generated. depbase=`echo frontend/Arguments.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -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../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -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 $depbase.Po anchors/bplex.lpp:5:1: warning: class 'Pair' was previously declared as a struct; this is valid, but may result in linker errors under the Microsoft C++ ABI [-Wmismatched-tags] 5 | class Pair; | ^ anchors/basepair.h:7:8: note: previous use is here 7 | struct Pair { | ^ anchors/bplex.lpp:5:1: note: did you mean struct here? 5 | class Pair; | ^~~~~ | struct anchors/bplex.cpp:1106:16: warning: function 'yyinput' is not needed and will not be emitted [-Wunneeded-internal-declaration] 1106 | static int yyinput (void) | ^~~~~~~ 2 warnings generated. depbase=`echo TED/rnaforestsz.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -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 -Dregister= -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../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -isystem /usr/local/include -I../g2-0.72/include/ -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 $depbase.Po In file included from wmatch/glib.c:1: wmatch/graphtypes.h:49:33: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype] 49 | extern EuclidGraph ReadEuclid(),NewEuclid(); | ^ wmatch/graphtypes.h:71:17: note: conflicting prototype is here 71 | EuclidGraph NewEuclid(int size); | ^ wmatch/graphtypes.h:60:34: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype] 60 | extern MatrixGraph ReadMatrix(), NewMatrix(); | ^ wmatch/graphtypes.h:72:17: note: conflicting prototype is here 72 | MatrixGraph NewMatrix(int size); | ^ wmatch/graphtypes.h:49:20: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype] 49 | extern EuclidGraph ReadEuclid(),NewEuclid(); | ^ wmatch/graphtypes.h:76:17: note: conflicting prototype is here 76 | EuclidGraph ReadEuclid(int *size,char *file); | ^ wmatch/graphtypes.h:60:20: warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype] 60 | exdepbase=`echo wmatch/wmatch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ tecc -DHAVE_CONFIG_H -I. -I.. -I../../../src/ViennaRNA -I../../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -I/usr/local/include -I./anchors -I./frontend -I./TED -I./utils -I./wmatch -isystem /usr/local/include -I../g2-0.72/include/ -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 &&\ rmv -f $depbase.Tpo $depbase.Po n MatrixGraph ReadMatrix(), NewMatrix(); | ^ wmatch/graphtypes.h:78:17: note: conflicting prototype is here 78 | MatrixGraph ReadMatrix(int *sizIn file included from ewmatch/wmatch.c,c:h15a: rwmatch/graphtypes.h :*49f:i33l:e )warning: ;a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype] | 49 ^ | ewmatch/graphtypes.hx:t50e:r12n: Ewarning: ua function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]c l i50d | Gerxatpehr nR eiandtE ueculciddi(s)t,(N)e,weEuuccdliisd(t)s;q ( )| ; ^ wmatch/graphtypes.h| : ^71 :wmatch/graphtypes.h17::80 :note: 9conflicting prototype is here: note: 71conflicting prototype is here | 80 | E u c liindtG reuacpdhi sNte w(EEuucclliidd(Girnatp hs igzrea)p;h , i| n ^t wmatch/graphtypes.hi:,60i:n34t: jwarning: )a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]; | ^ 60wmatch/graphtypes.h:50 | :e22: xwarning: ta function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]e r n50 | MeaxttreirxnG rianpth eRuecaddiMsatt(r)i,xe(u)c,d iNsetwsMqa(t)r;i x (| ) ^; wmatch/graphtypes.h :| 82 ^: 9wmatch/graphtypes.h:: 72note: :conflicting prototype is here17 : 82note: | conflicting prototype is here 72 | i n t eMuactdriisxtGsrqa(pEhu cNlewMiadtGrrixa(pihn tg rsaipzhe,)i;n t | i ^, iwmatch/graphtypes.hn:t49 :j20):; warning: a function declaration without a prototype is deprecated in all versions of C and is treated as a zero-parameter prototype in C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype]| ^ 49 | extern EuclidGraph ReadEuclid(),NewEuclid(); | ^ wmatch/graphtypes.h:76:17: note: conflicting prototype is here 76 | 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 C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype] 60 | extern MatrixGraph ReadMatrix(), NewMatrix(); | ^ wmatch/graphtypes.h:78:17: note: conflicting prototype is here 78 | 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 C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype] 50 | extern int eucdist(),eucdistsq(); | ^ wmatch/graphtypes.h:80:9: note: conflicting prototype is here 80 | 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 C23, conflicting with a subsequent declaration [-Wdeprecated-non-prototype] 50 | extern int eucdist(),eucdistsq(); | ^ wmatch/graphtypes.h:82:9: note: conflicting prototype is here 82 | int eucdistsq(EuclidGraph graph,int i,int j); | ^ 6 warnings generated. 1 warning generated. 6 warnings generated. 1 warning generated. c++ -Wall -std=c++98 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Dregister= -isystem /usr/local/include -L../g2-0.72 -Wl,-rpath=/usr/local/lib/gcc14 -L/usr/local/lib/gcc14 -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 -fno-strict-aliasing -L../../../src/ViennaRNA -lRNA -fopenmp -lgsl -lgslcblas -lpthread -lmpfr -lgmp -lstdc++ -lg2 -L/usr/local/lib gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/src' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/src' Making all in man gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/man' gmake[4]: Nothing to be done for 'all'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/man' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester' Making all in src/Kinwalker gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker' /usr/local/bin/gmake all-recursive gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker' Making all in man gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker/man' gmake[4]: Nothing to be done for 'all'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker/man' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker' c++ -std=c++14 -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Dregister= -isystem /usr/local/include -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.cpp c++ -std=c++14 -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Dregister= -isystem /usr/local/include -MT Energy.o -MD -MP -MF .deps/Energy.Tpo -c -o Energy.o Energy.cpp c++ -std=c++14 -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Dregister= -isystem /usr/local/include -MT MorganHiggs.o -MD -MP -MF .deps/MorganHiggs.Tpo -c -o MorganHiggs.o MorganHiggs.cpp c++ -std=c++14 -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Dregister= -isystem /usr/local/include -MT Node.o -MD -MP -MF .deps/Node.Tpo -c -o Node.o Node.cpp cc -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -MT options.o -MD -MP -MF .deps/options.Tpo -c -o options.o options.c c++ -std=c++14 -DHAVE_CONFIG_H -I. -I./../../src/ViennaRNA -I./../../src -DVRNA_WITH_NAVIEW_LAYOUT -DVRNA_LOG_NO_DEBUG_RNALIB -isystem /usr/local/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -Dregister= -isystem /usr/local/include -MT Util.o -MD -MP -MF .deps/Util.Tpo -c -o Util.o Util.cpp mv -f .deps/options.Tpo .deps/options.Po MorganHiggs.cpp:528:26: warning: adding 'size_t' (aka 'unsigned long') to a string does not append to the string [-Wstring-plus-int] 528 | if(MHS_debug) cout<============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> viennarna-2.7.0_2 depends on executable: gfortran14 - found ===> viennarna-2.7.0_2 depends on package: perl5>=5.42.r<5.43 - found ===> viennarna-2.7.0_2 depends on file: /usr/local/libdata/pkgconfig/ice.pc - found ===> viennarna-2.7.0_2 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found ===> viennarna-2.7.0_2 depends on file: /usr/local/libdata/pkgconfig/xext.pc - found ===> viennarna-2.7.0_2 depends on executable: indexinfo - found =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Staging for viennarna-2.7.0_2 ===> Generating temporary packing list Making install in src gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src' Making install in ViennaRNA gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA' Making install in static gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/static' /usr/local/bin/gmake install-am gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/static' gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/static' gmake[5]: Nothing to be done for 'install-exec-am'. gmake[5]: Nothing to be done for 'install-data-am'. gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/static' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/static' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/static' Making install in plotting/naview gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/plotting/naview' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/plotting/naview' gmake[4]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/plotting/naview' install -m 0644 naview.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/plotting/naview' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/plotting/naview' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA/plotting/naview' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/lib' /usr/local/bin/bash ../../libtool --mode=install /usr/bin/install -c libRNA.la '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/lib' libtool: install: /usr/bin/install -c .libs/libRNA.lai /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/lib/libRNA.la libtool: install: /usr/bin/install -c .libs/libRNA.a /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/lib/libRNA.a libtool: install: chmod 644 /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/lib/libRNA.a libtool: install: /usr/local/bin/ranlib /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/lib/libRNA.a libtool: warning: remember to run 'libtool --finish /usr/local/lib' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA' install -m 0644 vrna_config.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA' install -m 0644 2Dfold.h 2Dpfold.h alifold.h ali_plex.h cofold.h concentrations.h dist_vars.h dp_matrices.h duplex.h edit_cost.h fold_compound.h fold.h fold_vars.h heat_capacity.h mm.h model.h move_set.h part_func_co.h part_func_up.h perturbation_fold.h pk_plex.h plex.h ProfileAln.h profiledist.h ribo.h RNAstruct.h snofold.h snoop.h stringdist.h structured_domains.h treedist.h unstructured_domains.h wrap_dlib.h ../json/json.h ../cephes/mconf.h aln_util.h alphabet.h boltzmann_sampling.h centroid.h char_stream.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA' install -m 0644 commands.h combinatorics.h constraints.h constraints_hard.h constraints_ligand.h constraints_SHAPE.h constraints_soft.h constraints/SHAPE.h convert_epars.h data_structures.h energy_const.h energy_par.h equilibrium_probs.h eval.h exterior_loops.h file_formats.h file_formats_msa.h file_utils.h findpath.h grammar.h gquad.h hairpin_loops.h interior_loops.h inverse.h Lfold.h loop_energies.h LPfold.h MEA.h mfe.h mfe_window.h multibranch_loops.h neighbor.h pair_mat.h params.h part_func.h part_func_window.h pf_multifold.h PKplex.h plot_aln.h plot_layouts.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA' install -m 0644 plot_structure.h plot_utils.h PS_dot.h read_epars.h sequence.h stream_output.h string_utils.h structure_utils.h subopt.h subopt_zuker.h units.h utils.h walk.h naview.h svm_utils.h ../libsvm-3.35/svm.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/backtrack' install -m 0644 backtrack/global.h backtrack/exterior.h backtrack/hairpin.h backtrack/internal.h backtrack/multibranch.h backtrack/gquad.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/backtrack' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/combinatorics' install -m 0644 combinatorics/basic.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/combinatorics' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/constraints' install -m 0644 constraints/basic.h constraints/ligand.h constraints/hard.h constraints/SHAPE.h constraints/soft.h constraints/soft_special.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/constraints' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/datastructures' install -m 0644 datastructures/array.h datastructures/basic.h datastructures/lists.h datastructures/char_stream.h datastructures/stream_output.h datastructures/string.h datastructures/hash_tables.h datastructures/heap.h datastructures/sparse_mx.h datastructures/dp_matrices.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/datastructures' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/eval' install -m 0644 eval/basic.h eval/structures.h eval/exterior.h eval/hairpin.h eval/internal.h eval/multibranch.h eval/gquad.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/eval' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/grammar' install -m 0644 grammar/basic.h grammar/mfe.h grammar/partfunc.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/grammar' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/inverse' install -m 0644 inverse/basic.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/inverse' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/io' install -m 0644 io/utils.h io/file_formats.h io/file_formats_msa.h io/commands.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/io' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/landscape' install -m 0644 landscape/paths.h landscape/findpath.h landscape/neighbor.h landscape/walk.h landscape/move.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/landscape' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/loops' install -m 0644 loops/all.h loops/external.h loops/hairpin.h loops/internal.h loops/multibranch.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/loops' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/mfe' install -m 0644 mfe/global.h mfe/local.h mfe/exterior.h mfe/internal.h mfe/multibranch.h mfe/gquad.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/mfe' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/params' install -m 0644 params/default.h params/constants.h params/basic.h params/io.h params/convert.h params/salt.h params/ribosum.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/params' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/partfunc' install -m 0644 partfunc/global.h partfunc/local.h partfunc/multifold.h partfunc/exterior.h partfunc/internal.h partfunc/multibranch.h partfunc/gquad.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/partfunc' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/plotting' install -m 0644 plotting/alignments.h plotting/layouts.h plotting/probabilities.h plotting/structures.h plotting/utils.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/plotting' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/probabilities' install -m 0644 probabilities/basepairs.h probabilities/structures.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/probabilities' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/probing' install -m 0644 probing/basic.h probing/SHAPE.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/probing' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/plotting/RNApuzzler' install -m 0644 plotting/RNApuzzler/RNApuzzler.h plotting/RNApuzzler/RNAturtle.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/plotting/RNApuzzler' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/sampling' install -m 0644 sampling/basic.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/sampling' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/search' install -m 0644 search/BoyerMoore.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/search' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/sequences' install -m 0644 sequences/alphabet.h sequences/sequence.h sequences/alignments.h sequences/utils.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/sequences' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/structures' install -m 0644 structures/benchmark.h structures/centroid.h structures/dotbracket.h structures/helix.h structures/mea.h structures/metrics.h structures/pairtable.h structures/problist.h structures/shapes.h structures/tree.h structures/utils.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/structures' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/subopt' install -m 0644 subopt/basic.h subopt/wuchty.h subopt/zuker.h subopt/gquad.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/subopt' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/utils' install -m 0644 utils/basic.h utils/strings.h utils/structures.h utils/alignments.h utils/higher_order_functions.h utils/cpu.h utils/units.h utils/log.h utils/svm.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/utils' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/zscore' install -m 0644 zscore/basic.h '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/include/ViennaRNA/zscore' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/ViennaRNA' Making install in bin gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/bin' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' /usr/local/bin/bash ../../libtool --mode=install install -s -m 555 RNAfold RNAeval RNAheat RNApdist RNAdistance RNAinverse RNAplot RNAsubopt RNALfold RNAcofold RNApaln RNAduplex RNAalifold RNAplfold RNAup RNAaliduplex RNALalifold RNA2Dfold RNAparconv RNAPKplex RNAplex RNAsnoop RNApvmin RNAdos RNAmultifold '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' libtool: install: install -m 555 -s RNAfold /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAfold libtool: install: install -m 555 -s RNAeval /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAeval libtool: install: install -m 555 -s RNAheat /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAheat libtool: install: install -m 555 -s RNApdist /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNApdist libtool: install: install -m 555 -s RNAdistance /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAdistance libtool: install: install -m 555 -s RNAinverse /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAinverse libtool: install: install -m 555 -s RNAplot /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAplot libtool: install: install -m 555 -s RNAsubopt /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAsubopt libtool: install: install -m 555 -s RNALfold /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNALfold libtool: install: install -m 555 -s RNAcofold /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAcofold libtool: install: install -m 555 -s RNApaln /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNApaln libtool: install: install -m 555 -s RNAduplex /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAduplex libtool: install: install -m 555 -s RNAalifold /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAalifold libtool: install: install -m 555 -s RNAplfold /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAplfold libtool: install: install -m 555 -s RNAup /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAup libtool: install: install -m 555 -s RNAaliduplex /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAaliduplex libtool: install: install -m 555 -s RNALalifold /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNALalifold libtool: install: install -m 555 -s RNA2Dfold /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNA2Dfold libtool: install: install -m 555 -s RNAparconv /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAparconv libtool: install: install -m 555 -s RNAPKplex /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAPKplex libtool: install: install -m 555 -s RNAplex /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAplex libtool: install: install -m 555 -s RNAsnoop /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAsnoop libtool: install: install -m 555 -s RNApvmin /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNApvmin libtool: install: install -m 555 -s RNAdos /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAdos libtool: install: install -m 555 -s RNAmultifold /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAmultifold gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/bin' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/bin' Making install in Utils gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Utils' /usr/local/bin/gmake install-am gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Utils' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Utils' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' /usr/local/bin/bash ../../libtool --mode=install install -s -m 555 b2ct popt ct2db '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' libtool: install: install -m 555 -s b2ct /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/b2ct libtool: install: install -m 555 -s popt /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/popt libtool: install: install -m 555 -s ct2db /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/ct2db /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' install -m 555 RNAconsensus '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/RNA' install -m 0644 RNAconsensus.py '/wrkdirs/usr/ports/biology/viennarna/work/stage/RNA' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/RNA' install -m 555 RNAconsensus.py '/wrkdirs/usr/ports/biology/viennarna/work/stage/RNA' /usr/local/bin/gmake install-exec-hook gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Utils' target_path=; \ for i in RNAconsensus; \ do \ /usr/bin/sed -i.bak 's#\${exec_prefix}#'/usr/local'#g' /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/$i && rm /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/$i.bak ; \ done gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Utils' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/ViennaRNA/bin' install -m 555 b2mt.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl coloraln.pl refold.pl switch.pl RNAdesign.pl '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/ViennaRNA/bin' /usr/local/bin/gmake install-data-hook gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Utils' for i in b2mt.pl dpzoom.pl mountain.pl relplot.pl rotate_ss.pl cmount.pl coloraln.pl refold.pl switch.pl RNAdesign.pl; \ do \ /usr/local/bin/perl -npi -e 's|^#!\S+|#!'/usr/local/bin/perl'|' /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/ViennaRNA/bin/$i ; \ done gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Utils' gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Utils' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Utils' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Utils' Making install in Cluster gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Cluster' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Cluster' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' /usr/local/bin/bash ../../libtool --mode=install install -s -m 555 AnalyseDists AnalyseSeqs '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' libtool: install: install -m 555 -s AnalyseDists /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/AnalyseDists libtool: install: install -m 555 -s AnalyseSeqs /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/AnalyseSeqs /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' install -m 0644 AnalyseDists.1 AnalyseSeqs.1 '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Cluster' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Cluster' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src' Making install in man gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/man' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/man' gmake[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/info' install -m 0644 ./RNAlib.info '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/info' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' install -m 0644 RNA2Dfold.1 RNAaliduplex.1 RNAalifold.1 RNAcofold.1 RNAduplex.1 RNAeval.1 RNAfold.1 RNAheat.1 RNAinverse.1 RNALalifold.1 RNALfold.1 RNAmultifold.1 RNApaln.1 RNAparconv.1 RNAplfold.1 RNAplot.1 RNApvmin.1 RNAsubopt.1 RNAup.1 RNAPKplex.1 RNAsnoop.1 RNAplex.1 RNAdistance.1 RNApdist.1 RNAdos.1 ct2db.1 '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/man' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/man' Making install in misc gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/misc' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/misc' gmake[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/ViennaRNA' install -m 0644 2Dlandscape_mfe.gri 2Dlandscape_pf.gri rna_turner1999.par rna_turner2004.par rna_andronescu2007.par dna_mathews1999.par dna_mathews2004.par rna_langdon2018.par rna_misc_special_hairpins.par rna_mod_7DA_parameters.json rna_mod_inosine_parameters.json rna_mod_m5C_parameters.json rna_mod_m6A_parameters.json rna_mod_pseudouridine_parameters.json rna_mod_purine_parameters.json rna_mod_dihydrouridine_parameters.json rna_mod_template_parameters.json 2Dlandscape.R '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/ViennaRNA' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/misc' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/misc' Making install in doc/doxygen gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/doxygen' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/doxygen' gmake[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/ViennaRNA' install -m 0644 DoxygenLayout.xml '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/ViennaRNA' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/doxygen' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/doxygen' Making install in interfaces gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/interfaces' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/interfaces' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/interfaces' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/interfaces' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/interfaces' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/interfaces' Making install in doc gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc' Making install in CLA gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/CLA' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/CLA' gmake[3]: Nothing to be done for 'install-exec-am'. for dir in "/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/doc/ViennaRNA"; do \ test -z "$dir" || /bin/mkdir -p "$dir"; \ done test -f ./ViennaRNA-CLA-Individual.pdf || ln -s ./ViennaRNA-CLA-Individual.pdf ./ViennaRNA-CLA-Individual.pdf install -m 0644 ./ViennaRNA-CLA-Individual.pdf /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/doc/ViennaRNA { test ! -h ./ViennaRNA-CLA-Individual.pdf || rm -f ./ViennaRNA-CLA-Individual.pdf; } test -f ./ViennaRNA-CLA-Entity.pdf || ln -s ./ViennaRNA-CLA-Entity.pdf ./ViennaRNA-CLA-Entity.pdf install -m 0644 ./ViennaRNA-CLA-Entity.pdf /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/doc/ViennaRNA { test ! -h ./ViennaRNA-CLA-Entity.pdf || rm -f ./ViennaRNA-CLA-Entity.pdf; } gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/CLA' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/CLA' Making install in source/man gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/source/man' /usr/local/bin/gmake install-am gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/source/man' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/source/man' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/source/man' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/source/man' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/source/man' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc' gmake[3]: Nothing to be done for 'install-exec-am'. Making installdirs in CLA gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/CLA' for dir in "/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/doc/ViennaRNA"; do \ test -z "$dir" || /bin/mkdir -p "$dir"; \ done gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/CLA' Making installdirs in source/man gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/source/man' gmake[4]: Nothing to be done for 'installdirs'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc/source/man' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc' for dir in "/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/doc/ViennaRNA/html" "/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/doc/ViennaRNA" "/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/ViennaRNA"; do \ test -z "$dir" || /bin/mkdir -p "$dir"; \ done gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc' test -d ./build/html || (/bin/mkdir -p ./build && ln -s ./build/html ./build/html) { test ! -h ./build/html || (rm -f ./build/html && rm -rf ./build) } test -f ./RNAlib-2.7.0.pdf || ln -s ./RNAlib-2.7.0.pdf ./RNAlib-2.7.0.pdf install -m 0644 ./RNAlib-2.7.0.pdf /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/doc/ViennaRNA { test ! -h ./RNAlib-2.7.0.pdf || rm -f ./RNAlib-2.7.0.pdf; } /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/ViennaRNA' install -m 0644 viennarna.bib '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/ViennaRNA' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/doc' Making install in src/Kinfold gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold' Making install in Example gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold/Example' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold/Example' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold/Example' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold/Example' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' install -s -m 555 Kinfold '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' install -m 0644 Kinfold.1 '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinfold' Making install in src/RNAforester gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester' Making install in g2-0.72 gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/g2-0.72' Makefile:101: warning: overriding recipe for target 'libg2.so' Makefile:98: warning: ignoring old recipe for target 'libg2.so' test -d /wrkdirs/usr/ports/biology/viennarna/work/stage//usr/local/lib || mkdir -p /wrkdirs/usr/ports/biology/viennarna/work/stage//usr/local/lib test -d /wrkdirs/usr/ports/biology/viennarna/work/stage//usr/local/include || mkdir -p /wrkdirs/usr/ports/biology/viennarna/work/stage//usr/local/include install -m 0644 libg2.a /wrkdirs/usr/ports/biology/viennarna/work/stage//usr/local/lib for IFILE in ./src/g2.h ./src/PS/g2_PS.h ./src/FIG/g2_FIG.h ./src/X11/g2_X11.h ./src/GD/g2_gd.h; do \ install -m 0644 $IFILE /wrkdirs/usr/ports/biology/viennarna/work/stage//usr/local/include; \ done gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/g2-0.72' Making install in src gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/src' /usr/local/bin/gmake install-am gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/src' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/src' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' install -s -m 555 RNAforester '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/src' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/src' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/src' Making install in man gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/man' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/man' gmake[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' install -m 0644 RNAforester.1 '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/man' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester/man' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAforester' Making install in src/Kinwalker gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker' Making install in man gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker/man' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker/man' gmake[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' install -m 0644 kinwalker.1 '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker/man' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker/man' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' install -s -m 555 kinwalker '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/Kinwalker' Making install in src/RNAlocmin gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAlocmin' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAlocmin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' install -s -m 555 RNAlocmin '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' install -m 0644 RNAlocmin.1 '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAlocmin' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAlocmin' Making install in src/RNAxplorer gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer' Making install in src gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/src' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/src' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' /usr/local/bin/bash ../libtool --mode=install install -s -m 555 RNAxplorer '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin' libtool: install: install -m 555 -s RNAxplorer /wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/bin/RNAxplorer gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/src' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/src' Making install in interfaces gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/interfaces' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/interfaces' gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/interfaces' gmake[4]: Nothing to be done for 'install-exec-am'. gmake[4]: Nothing to be done for 'install-data-am'. gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/interfaces' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/interfaces' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/interfaces' Making install in doc gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/doc' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/doc' gmake[3]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' install -m 0644 RNAxplorer.1 '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/man/man1' gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/doc' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer/doc' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/src/RNAxplorer' Making install in tests gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/tests' /usr/local/bin/gmake install-am gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/tests' gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/tests' gmake[3]: Nothing to be done for 'install-exec-am'. gmake[3]: Nothing to be done for 'install-data-am'. gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/tests' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/tests' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/tests' Making install in examples gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/examples' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/examples' gmake[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/examples/ViennaRNA' install -m 0644 callback_subopt.c example1.c example_old.c fold_compound_md.c fold_compound_mfe.c helloworld_mfe.c helloworld_mfe_comparative.c helloworld_probabilities.c soft_constraints_up.c '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/examples/ViennaRNA' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/examples/ViennaRNA/data' install -m 0644 files/alignment_clustal.aln files/alignment_fasta.fa files/alignment_stockholm.stk files/alignment_maf.maf '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/examples/ViennaRNA/data' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/examples/ViennaRNA/perl5' install -m 0644 Perl5/helloworld_mfe.pl Perl5/helloworld_mfe_comparative.pl Perl5/helloworld_nondefault.pl Perl5/maximum_matching.pl Perl5/oo_example1.pl '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/examples/ViennaRNA/perl5' /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/examples/ViennaRNA/python' install -m 0644 Python/boltzmann_sampling.py Python/helloworld_mfe_comparative.py Python/helloworld_mfe.py Python/helloworld_nondefault.py Python/maximum_matching.py Python/oo_example1.py Python/subopt.py Python/RNAfold_MEA.py Python/vrna_logs.py '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/share/examples/ViennaRNA/python' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/examples' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/examples' Making install in packaging/macosx gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/packaging/macosx' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/packaging/macosx' gmake[2]: Nothing to be done for 'install-exec-am'. gmake[2]: Nothing to be done for 'install-data-am'. gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/packaging/macosx' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0/packaging/macosx' gmake[1]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0' gmake[2]: Entering directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0' gmake[2]: Nothing to be done for 'install-exec-am'. /bin/mkdir -p '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/lib/pkgconfig' install -m 0644 RNAlib2.pc '/wrkdirs/usr/ports/biology/viennarna/work/stage/usr/local/lib/pkgconfig' gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.7.0' ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===== env: 'PKG_NOTES=build_timestamp ports_top_git_hash ports_top_checkout_unclean port_git_hash port_checkout_unclean built_by' 'PKG_NOTE_build_timestamp=2025-12-27T22:09:47+0000' 'PKG_NOTE_ports_top_git_hash=3dd9e2202282' 'PKG_NOTE_ports_top_checkout_unclean=yes' 'PKG_NOTE_port_git_hash=042fe38f0395' 'PKG_NOTE_port_checkout_unclean=no' 'PKG_NOTE_built_by=poudriere-git-3.4.4' NO_DEPENDS=yes USER=nobody UID=65534 GID=65534 ===> Building packages for viennarna-2.7.0_2 ===> Building viennarna-2.7.0_2 =========================================================================== =>> Cleaning up wrkdir ===> Cleaning for viennarna-2.7.0_2 build of biology/viennarna | viennarna-2.7.0_2 ended at Sat Dec 27 17:13:23 EST 2025 build time: 00:03:37