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Maintainer: [email protected] Log URL: https://pkg-status.freebsd.org/beefy16/data/135amd64-default/774fe8f3f054/logs/augustus-gene-prediction-3.5.0_15.log Build URL: https://pkg-status.freebsd.org/beefy16/build.html?mastername=135amd64-default&build=774fe8f3f054 Log: =>> Building biology/augustus build started at Tue Oct 21 00:47:07 -00 2025 port directory: /usr/ports/biology/augustus package name: augustus-gene-prediction-3.5.0_15 building for: FreeBSD 135amd64-default-job-08 13.5-RELEASE-p5 FreeBSD 13.5-RELEASE-p5 amd64 maintained by: [email protected] Makefile datestamp: -rw-r--r-- 1 root wheel 1209 Aug 3 01:02 /usr/ports/biology/augustus/Makefile Ports top last git commit: 774fe8f3f05 Ports top unclean checkout: no Port dir last git commit: 935de0247ea Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.3-12-g245259ce Host OSVERSION: 1600000 Jail OSVERSION: 1305000 Job Id: 08 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1305000 UNAME_v=FreeBSD 13.5-RELEASE-p5 UNAME_r=13.5-RELEASE-p5 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=3.4.3-12-g245259ce MASTERMNT=/usr/local/poudriere/data/.m/135amd64-default/ref LC_COLLATE=C POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= OUTPUT_REDIRECTED_STDERR=4 OUTPUT_REDIRECTED=1 PWD=/usr/local/poudriere/data/.m/135amd64-default/08/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=135amd64-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/135amd64-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.3-12-g245259ce 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--- ---End OPTIONS List--- --MAINTAINER-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- 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 PYTHON="/usr/local/bin/python3.11" 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 -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 -std=c++14 " CXXSTD=c++14 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/python3.11 PYTHON_LIBDIR=lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 PYTHON2="@comment " PYTHON3="" OSREL=13.5 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/augustus" EXAMPLESDIR="share/examples/augustus" DATADIR="share/augustus" WWWDIR="www/augustus" ETCDIR="etc/augustus" --End PLIST_SUB-- --SUB_LIST-- PYTHON_INCLUDEDIR=/usr/local/include/python3.11 PYTHON_LIBDIR=/usr/local/lib/python3.11 PYTHON_PLATFORM=freebsd13 PYTHON_SITELIBDIR=/usr/local/lib/python3.11/site-packages PYTHON_SUFFIX=311 PYTHON_BASESUFFIX=311 PYTHON_TAG=.cpython-311 PYTHON_SOABI=.cpython-311 PYTHON_VER=3.11 PYTHON_BASEVER=3.11 PYTHON_VERSION=python3.11 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 #### #### # 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 3 jobs MAKE_JOBS_NUMBER=3 #### Misc Poudriere #### .include "/etc/make.conf.ports_env" GID=0 UID=0 ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 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 --End resource limits-- =======================<phase: check-sanity >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> augustus-gene-prediction-3.5.0_15 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-2.3.1.pkg [135amd64-default-job-08] Installing pkg-2.3.1... [135amd64-default-job-08] Extracting pkg-2.3.1: .......... done ===> augustus-gene-prediction-3.5.0_15 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of augustus-gene-prediction-3.5.0_15 =========================================================================== =======================<phase: fetch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: fetch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by augustus-gene-prediction-3.5.0_15 for building =========================================================================== =======================<phase: checksum >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by augustus-gene-prediction-3.5.0_15 for building => SHA256 Checksum OK for Gaius-Augustus-Augustus-v3.5.0_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: extract >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by augustus-gene-prediction-3.5.0_15 for building ===> Extracting for augustus-gene-prediction-3.5.0_15 => SHA256 Checksum OK for Gaius-Augustus-Augustus-v3.5.0_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =======================<phase: patch >============================ ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for augustus-gene-prediction-3.5.0_15 ===> Applying FreeBSD patches for augustus-gene-prediction-3.5.0_15 from /usr/ports/biology/augustus/files =========================================================================== =======================<phase: build-depends >============================ ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> augustus-gene-prediction-3.5.0_15 depends on package: gmake>=4.4.1 - not found ===> Installing existing package /packages/All/gmake-4.4.1.pkg [135amd64-default-job-08] Installing gmake-4.4.1... [135amd64-default-job-08] `-- Installing gettext-runtime-0.23.1... [135amd64-default-job-08] | `-- Installing indexinfo-0.3.1_1... [135amd64-default-job-08] | `-- Extracting indexinfo-0.3.1_1: .... done [135amd64-default-job-08] `-- Extracting gettext-runtime-0.23.1: .......... done [135amd64-default-job-08] Extracting gmake-4.4.1: .......... done ===> augustus-gene-prediction-3.5.0_15 depends on package: gmake>=4.4.1 - found ===> Returning to build of augustus-gene-prediction-3.5.0_15 ===> augustus-gene-prediction-3.5.0_15 depends on file: /usr/local/bin/python3.11 - not found ===> Installing existing package /packages/All/python311-3.11.14.pkg [135amd64-default-job-08] Installing python311-3.11.14... [135amd64-default-job-08] `-- Installing libffi-3.5.1... [135amd64-default-job-08] `-- Extracting libffi-3.5.1: .......... done [135amd64-default-job-08] `-- Installing mpdecimal-4.0.1... [135amd64-default-job-08] `-- Extracting mpdecimal-4.0.1: .......... done [135amd64-default-job-08] `-- Installing readline-8.2.13_2... [135amd64-default-job-08] `-- Extracting readline-8.2.13_2: .......... done [135amd64-default-job-08] Extracting python311-3.11.14: .......... done ===== Message from python311-3.11.14: -- Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: <snip> Finished building: src/Coord_Transform.cpp make[2]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs/utrrnaseq' gmake[1]: *** [Makefile:10: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/auxprogs' gmake: *** [Makefile:16: auxprogs] Error 2 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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o intronmodel.o intronmodel.cc gmake: *** 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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exonmodel.o exonmodel.cc extrinsicinfo.cc:918:9: warning: variable 'grpcount' set but not used [-Wunused-but-set-variable] 918 | int grpcount = 0, hintcount=0; | ^ extrinsicinfo.cc:918:23: warning: variable 'hintcount' set but not used [-Wunused-but-set-variable] 918 | int grpcount = 0, hintcount=0; | ^ extrinsicinfo.cc:1079:9: warning: variable 'numIncompat' set but not used [-Wunused-but-set-variable] 1079 | int numIncompat = 0, numWeakerThan = 0, numEqual = 0; | ^ extrinsicinfo.cc:1079:26: warning: variable 'numWeakerThan' set but not used [-Wunused-but-set-variable] 1079 | int numIncompat = 0, numWeakerThan = 0, numEqual = 0; | ^ extrinsicinfo.cc:1079:45: warning: variable 'numEqual' set but not used [-Wunused-but-set-variable] 1079 | int numIncompat = 0, numWeakerThan = 0, numEqual = 0; | ^ extrinsicinfo.cc:1115:9: warning: variable 'numTrashy' set but not used [-Wunused-but-set-variable] 1115 | int numTrashy=0; | ^ exonmodel.cc:1995:2: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 1995 | Double seqProb = 1; | ^ exonmodel.cc:1986:5: note: previous statement is here 1986 | 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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o igenicmodel.o igenicmodel.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 -std=c++14 -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 -std=c++14 -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 -std=c++14 -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 -std=c++14 -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 -std=c++14 -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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o graph.o graph.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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o meaPath.o meaPath.cc mea.cc:326:29: warning: variable 'codlength' set but not used [-Wunused-but-set-variable] 326 | int transStart, transEnd, codlength = 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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o exoncand.o exoncand.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 -std=c++14 -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 -std=c++14 -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 -std=c++14 -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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o parser/parse.o parser/parse.cc grammar:245:13: warning: misleading indentation; statement is not part of the previous 'if' [-Wmisleading-indentation] 245 | return elementPtr->d_action; | ^ grammar:243:9: note: previous statement is here 243 | if (d_debug__) | ^ parser/parse.cc:65:16: warning: unused variable 'author' [-Wunused-const-variable] 65 | char const author[] = "Frank B. Brokken ([email protected])"; | ^~~~~~ 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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o scanner/lex.o scanner/lex.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 -std=c++14 -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 -std=c++14 -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] 238 | IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | 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] 238 | IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | vector<Alignment*> const &a; | ^ 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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o contTimeMC.o contTimeMC.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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonevo.o codonevo.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] 238 | IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | 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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o compgenepred.o compgenepred.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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o phylotree.o phylotree.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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o orthograph.o orthograph.cc 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] 238 | IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | vector<Alignment*> const &a; | ^ In file included from phylotree.cc:12: ../include/phylotree.hh:54:10: warning: private field 'label' is not used [-Wunused-private-field] 54 | bool label; | ^ 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] 238 | IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | 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 -std=c++14 -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 -std=c++14 -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 -std=c++14 -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] 238 | IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | 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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o codonMSA.o codonMSA.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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o train_logReg_param.o train_logReg_param.cc train_logReg_param.cc:490:3: warning: 'random_shuffle<std::__wrap_iter<std::pair<int, std::vector<double>> *>>' is deprecated [-Wdeprecated-declarations] 490 | random_shuffle ( samples->begin(), samples->end() ); | ^ /usr/include/c++/v1/__algorithm/shuffle.h:95:23: note: 'random_shuffle<std::__wrap_iter<std::pair<int, std::vector<double>> *>>' has been explicitly marked deprecated here 95 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_DEPRECATED_IN_CXX14 void | ^ /usr/include/c++/v1/__config:742:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX14' 742 | # define _LIBCPP_DEPRECATED_IN_CXX14 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ 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 -std=c++14 -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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o sqliteDB.o sqliteDB.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 -std=c++14 -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 -std=c++14 -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 -std=c++14 -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 -std=c++14 -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 -std=c++14 -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 -std=c++14 -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 -std=c++14 -L/usr/local/lib/mysql -L/usr/local/lib -o prepareAlign pp_prepare_align.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 -std=c++14 -I../include -I/usr/include/lpsolve -I/usr/include/mysql -c -o pp_fastBlockSearcher.o pp_fastBlockSearcher.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 -std=c++14 -L/usr/local/lib/mysql -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 -std=c++14 -L/usr/local/lib/mysql -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 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 -std=c++14 -L/usr/local/lib/mysql -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 train_logReg_par am.o tokenizer.o sqliteDB.o dummy.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] 870 | 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] 196 | 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 -std=c++14 -L/usr/local/lib/mysql -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 1 warning generated. cp -f pp_simScore ../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 -std=c++14 -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 -std=c++14 -L/usr/local/lib/mysql -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 load2sqlitedb ../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 -std=c++14 -L/usr/local/lib/mysql -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 phylotree.o orthogra ph.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 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 -std=c++14 -L/usr/local/lib/mysql -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 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] 238 | IdxSortCriterion(vector<Alignment*> const a_, size_t speciesIdx) : s(speciesIdx), a(a_) {}; | ^~ ../include/alignment.hh:253:31: note: reference member declared here 253 | vector<Alignment*> const &a; | ^ cp -f etraining ../bin/ cp -f fastBlockSearch ../bin/ 1 warning generated. cp -f augustus ../bin/ gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/augustus/work/Augustus-3.5.0/src' ===> 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
