[package - main-arm64-default][biology/augustus] Failed for augustus-gene-prediction-3.5.0_3 in build
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Date: Tue, 25 Jul 2023 21:06:28 UTC
You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Log URL: https://pkg-status.freebsd.org/ampere2/data/main-arm64-default/pe5b71726cc79_s92fd2f39e5/logs/augustus-gene-prediction-3.5.0_3.log Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-arm64-default&build=pe5b71726cc79_s92fd2f39e5 Log: =>> Building biology/augustus build started at Tue Jul 25 20:56:04 UTC 2023 port directory: /usr/ports/biology/augustus package name: augustus-gene-prediction-3.5.0_3 building for: FreeBSD main-arm64-default-job-10 14.0-CURRENT FreeBSD 14.0-CURRENT 1400093 arm64 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400089 Jail OSVERSION: 1400093 Job Id: 10 !!! Jail is newer than host. (Jail: 1400093, Host: 1400089) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1400093 UNAME_v=FreeBSD 14.0-CURRENT 1400093 UNAME_r=14.0-CURRENT BLOCKSIZE=K MAIL=/var/mail/root MM_CHARSET=UTF-8 LANG=C.UTF-8 STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/main-arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-arm64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.9" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/augustus/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/augustus/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/augustus/work/.cache HOME=/wrkdirs/usr/ports/biology/augustus/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/augustus/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/augustus/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/augustus/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/augustus/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/augustus/work/.cache HOME=/wrkdirs/usr/ports/biology/augustus/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/augustus/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/augustus/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 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=" -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/ local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PYTHON_INCLUDEDIR=include/python3.9 PYTHON_LIBDIR=lib/python3.9 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" OSREL=14.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.32.1 PERL_VER=5.32 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.32 DOCSDIR="share/doc/augustus" EXAMPLESDIR="share/examples/augustus" DATADIR="share/augustus" WWWDIR="www/augustus" ETCDIR="etc/augustus" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.9 PYTHON_LIBDIR=/usr/local/lib/python3.9 PYTHON_PLATFORM=freebsd14 PYTHON_SITELIBDIR=/usr/local/lib/python3.9/site-packages PYTHON_SUFFIX=39 PYTHON_EXT_SUFFIX=.cpython-39 PYTHON_VER=3.9 PYTHON_VERSION=python3.9 PYTHON2="@comment " PYTHON3="" PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/augustus DOCSDIR=/usr/local/share/doc/augustus EXAMPLESDIR=/usr/local/share/examples/augustus WWWDIR=/usr/local/www/augustus ETCDIR=/usr/local/etc/augustus --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 16.0.6 (https://github.com/llvm/llvm-project.git llvmorg-16.0.6-0-g7cbf1a259152) Target: aarch64-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400093 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 1048576 stack size (kbytes, -s) 1048576 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> augustus-gene-prediction-3.5.0_3 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.20.4.pkg [main-arm64-default-job-10] Installing pkg-1.20.4... [main-arm64-default-job-10] Extracting pkg-1.20.4: .......... done ===> augustus-gene-prediction-3.5.0_3 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of augustus-gene-prediction-3.5.0_3 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by augustus-gene-prediction-3.5.0_3 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by augustus-gene-prediction-3.5.0_3 for building => SHA256 Checksum OK for Gaius-Augustus-Augustus-v3.5.0_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by augustus-gene-prediction-3.5.0_3 for building ===> Extracting for augustus-gene-prediction-3.5.0_3 => SHA256 Checksum OK for Gaius-Augustus-Augustus-v3.5.0_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for augustus-gene-prediction-3.5.0_3 ===> Applying FreeBSD patches for augustus-gene-prediction-3.5.0_3 from /usr/ports/biology/augustus/files =========================================================================== =======================<phase: build-depends >============================ ===> augustus-gene-prediction-3.5.0_3 depends on package: gmake>=4.3 - not found ===> Installing existing package /packages/All/gmake-4.3_2.pkg [main-arm64-default-job-10] Installing gmake-4.3_2... [main-arm64-default-job-10] `-- Installing gettext-runtime-0.22_1... [main-arm64-default-job-10] | `-- Installing indexinfo-0.3.1... <snip> src/Coord_Transform.cpp:89:7: error: use of undeclared identifier 'bind2nd' bind2nd(finding_intron_lesser_e<Genomic_Data::Intron>(), i)); ^ src/Coord_Transform.cpp:93:7: error: use of undeclared identifier 'bind2nd' bind2nd(finding_intron_lesser_s<Genomic_Data::Intron>(), i)); ^ 8 errors generated. make[3]: *** [Makefile:36: build/Coord_Transform.o] Error 1 make[3]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/utrrnaseq' gmake[2]: *** [Makefile:10: all] Error 2 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs' gmake[1]: *** [Makefile:16: auxprogs] Error 2 gmake[1]: *** Waiting for unfinished jobs.... c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o evaluation.o evaluation.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o motif.o motif.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneticcode.o geneticcode.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o hints.o hints.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o extrinsicinfo.o extrinsicinfo.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o projectio.o projectio.cc extrinsicinfo.cc:918:9: warning: variable 'grpcount' set but not used [-Wunused-but-set-variable] int grpcount = 0, hintcount=0; ^ extrinsicinfo.cc:918:23: warning: variable 'hintcount' set but not used [-Wunused-but-set-variable] int grpcount = 0, hintcount=0; ^ extrinsicinfo.cc:1079:9: warning: variable 'numIncompat' set but not used [-Wunused-but-set-variable] int numIncompat = 0, numWeakerThan = 0, numEqual = 0; ^ extrinsicinfo.cc:1079:26: warning: variable 'numWeakerThan' set but not used [-Wunused-but-set-variable] int numIncompat = 0, numWeakerThan = 0, numEqual = 0; ^ extrinsicinfo.cc:1079:45: warning: variable 'numEqual' set but not used [-Wunused-but-set-variable] int numIncompat = 0, numWeakerThan = 0, numEqual = 0; ^ extrinsicinfo.cc:1115:9: warning: variable 'numTrashy' set but not used [-Wunused-but-set-variable] int numTrashy=0; ^ c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o intronmodel.o intronmodel.cc 6 warnings generated. c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exonmodel.o exonmodel.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenicmodel.o igenicmodel.cc exonmodel.cc:1995:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] Double seqProb = 1; ^ exonmodel.cc:1986:5: note: previous statement is here if (!(right-left+1 == Constant::et_coding_len)) ^ c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrmodel.o utrmodel.cc 1 warning generated. c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o merkmal.o merkmal.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o vitmatrix.o vitmatrix.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o lldouble.o lldouble.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o mea.o mea.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o graph.o graph.cc mea.cc:326:29: warning: variable 'codlength' set but not used [-Wunused-but-set-variable] int transStart, transEnd, codlength = 0; ^ 1 warning generated. c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exoncand.o exoncand.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o randseqaccess.o randseqaccess.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o fasta.o fasta.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o ncmodel.o ncmodel.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o parser/parse.o parser/parse.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o scanner/lex.o scanner/lex.cc grammar:245:13: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] return elementPtr->d_action; ^ grammar:243:9: note: previous statement is here if (d_debug__) ^ parser/parse.cc:65:16: warning: unused variable 'author' [-Wunused-const-variable] char const author[] = "Frank B. Brokken (f.b.brokken@rug.nl)"; ^ 2 warnings generated. c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o genomicMSA.o genomicMSA.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o geneMSA.o geneMSA.cc In file included from genomicMSA.cc:10: In file included from ../include/genomicMSA.hh:11: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; ^~ ../include/alignment.hh:253:31: note: reference member declared here vector<Alignment*> const &a; ^ In file included from geneMSA.cc:11: In file included from ../include/genomicMSA.hh:11: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; ^~ ../include/alignment.hh:253:31: note: reference member declared here vector<Alignment*> const &a; ^ 1 warning generated. c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o contTimeMC.o contTimeMC.cc 1 warning generated. c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonevo.o codonevo.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o compgenepred.o compgenepred.cc In file included from codonevo.cc:10: In file included from ../include/geneMSA.hh:12: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; ^~ ../include/alignment.hh:253:31: note: reference member declared here vector<Alignment*> const &a; ^ In file included from compgenepred.cc:8: In file included from ../include/compgenepred.hh:15: In file included from ../include/geneMSA.hh:12: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; ^~ ../include/alignment.hh:253:31: note: reference member declared here vector<Alignment*> const &a; ^ 1 warning generated. c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o phylotree.o phylotree.cc In file included from phylotree.cc:12: ../include/phylotree.hh:54:10: warning: private field 'label' is not used [-Wunused-private-field] bool label; ^ 1 warning generated. c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc In file included from orthograph.cc:10: In file included from ../include/orthograph.hh:15: In file included from ../include/geneMSA.hh:12: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; ^~ ../include/alignment.hh:253:31: note: reference member declared here vector<Alignment*> const &a; ^ 1 warning generated. c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthoexon.o orthoexon.cc 1 warning generated. c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o alignment.o alignment.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o speciesgraph.o speciesgraph.cc In file included from alignment.cc:8: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; ^~ ../include/alignment.hh:253:31: note: reference member declared here vector<Alignment*> const &a; ^ 1 warning generated. c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonMSA.o codonMSA.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o train_logReg_param.o train_logReg_param.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o tokenizer.o tokenizer.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o sqliteDB.o sqliteDB.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o commontrain.o commontrain.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenictrain.o igenictrain.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o introntrain.o introntrain.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exontrain.o exontrain.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o utrtrain.o utrtrain.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o dummy.o dummy.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -o prepareAlign pp_prepare_align.cc c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_fastBlockSearcher.o pp_fastBlockSearcher.cc cp -f prepareAlign ../bin/ c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o pp_simScore pp_simscore.cc fasta.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2db load2db.cc fasta.o hints.o types.o properties.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 pp_simscore.cc:870:21: warning: unused variable 'count_miss' [-Wunused-variable] pair <int, int> count_miss; ^ load2db.cc:196:17: warning: result of comparison of constant -1 with expression of type 'FeatureType' is always true [-Wtautological-constant-out-of-range-compare] if(f.type != -1){ ~~~~~~ ^ ~~ 1 warning generated. cp -f load2db ../bin/ c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o getSeq getSeq.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o tr ain_logReg_param.o tokenizer.o sqliteDB.o dummy.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 1 warning generated. cp -f pp_simScore ../bin/ c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o load2sqlitedb load2sqlitedb.cc fasta.o hints.o types.o properties.o lldouble.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 cp -f load2sqlitedb ../bin/ echo "-Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE" > cxxflags c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o augustus augustus.cc genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylotree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA. o train_logReg_param.o tokenizer.o sqliteDB.o dummy.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 cp -f getSeq ../bin/ c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o etraining etraining.cc commontrain.o igenictrain.o introntrain.o exontrain.o utrtrain.o genbank.o properties.o pp_profile.o pp_hitseq.o pp_scoring.o statemodel.o namgene.o types.o gene.o evaluation.o motif.o geneticcode.o hints.o extrinsicinfo.o projectio.o intronmodel.o exonmodel.o igenicmodel.o utrmodel.o merkmal.o vitmatrix.o lldouble.o mea.o graph.o meaPath.o exoncand.o randseqaccess.o fasta.o ncmodel.o parser/parse.o scanner/lex.o genomicMSA.o geneMSA.o contTimeMC.o codonevo.o compgenepred.o phylot ree.o orthograph.o orthoexon.o alignment.o speciesgraph.o codonMSA.o train_logReg_param.o tokenizer.o sqliteDB.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 In file included from augustus.cc:21: In file included from ../include/compgenepred.hh:15: In file included from ../include/geneMSA.hh:12: ../include/alignment.hh:238:89: warning: binding reference member 'a' to stack allocated parameter 'a_' [-Wdangling-field] IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; ^~ ../include/alignment.hh:253:31: note: reference member declared here vector<Alignment*> const &a; ^ cp -f etraining ../bin/ c++ -isystem /usr/local/include -DZIPINPUT -DCOMPGENEPRED -DTESTING -DM_MYSQL -DM_SQLITE -Wall -Wno-sign-compare -pedantic -O3 -std=c++11 -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -I/usr/local/include/bamtools -I/usr/local/include/lpsolve -I/usr/local/include/mysql -isystem /usr/local/include -L/usr/local/lib/mysql -fstack-protector-strong -L/usr/local/lib -I../include -I/usr/include/lpsolve -I/usr/include/mysql -o fastBlockSearch fastBlockSearch.cc pp_fastBlockSearcher.o types.o properties.o geneticcode.o pp_profile.o lldouble.o -lboost_iostreams -lgsl -lgslcblas -llpsolve55 -lcolamd -ldl -lboost_serialization -lmysqlclient -lmysqlpp -lsqlite3 1 warning generated. cp -f augustus ../bin/ cp -f fastBlockSearch ../bin/ gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/src' gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0' ===> Compilation failed unexpectedly. Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to the maintainer. *** Error code 1 Stop. make: stopped in /usr/ports/biology/augustus