Date: Tue, 28 May 2019 16:04:34 GMT From: pkg-fallout@FreeBSD.org To: yuri@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - 112i386-default][biology/cufflinks] Failed for cufflinks-2.2.1.83 in build Message-ID: <201905281604.x4SG4Ygj035345@beefy10.nyi.freebsd.org>
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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 Last committer: yuri@FreeBSD.org Ident: $FreeBSD: head/biology/cufflinks/Makefile 502661 2019-05-25 22:28:12Z yuri $ Log URL: http://beefy10.nyi.freebsd.org/data/112i386-default/502843/logs/cufflinks-2.2.1.83.log Build URL: http://beefy10.nyi.freebsd.org/build.html?mastername=112i386-default&build=502843 Log: =>> Building biology/cufflinks build started at Tue May 28 15:57:13 UTC 2019 port directory: /usr/ports/biology/cufflinks package name: cufflinks-2.2.1.83 building for: FreeBSD 112i386-default-job-15 11.2-RELEASE-p10 FreeBSD 11.2-RELEASE-p10 i386 maintained by: yuri@FreeBSD.org Makefile ident: $FreeBSD: head/biology/cufflinks/Makefile 502661 2019-05-25 22:28:12Z yuri $ Poudriere version: 3.2.8-4-g701d8fe1 Host OSVERSION: 1300018 Jail OSVERSION: 1102000 Job Id: 15 ---Begin Environment--- SHELL=/bin/csh UNAME_p=i386 UNAME_m=i386 OSVERSION=1102000 UNAME_v=FreeBSD 11.2-RELEASE-p10 UNAME_r=11.2-RELEASE-p10 BLOCKSIZE=K MAIL=/var/mail/root 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=3.2.8-4-g701d8fe1 MASTERMNT=/usr/local/poudriere/data/.m/112i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/112i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=112i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/112i386-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-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake PYTHON="/usr/local/bin/python3.6" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cufflinks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=262144 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/cufflinks/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/cufflinks/work HOME=/wrkdirs/usr/ports/biology/cufflinks/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/cufflinks/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes 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 -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -I/usr/local/include/eigen3 " 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/python3.6m PYTHON_LIBDIR=lib/python3.6 PYTHON_PLATFORM=freebsd11 PYTHON_SITELIBDIR=lib/python3.6/site-packages PYTHON_SUFFIX=36 PYTHON_VER=3.6 PYTHON_VERSION=python3.6 PYTHON2="@comment " PYTHON3="" OSREL=11.2 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/cufflinks" EXAMPLESDIR="share/examples/cufflinks" DATADIR="share/cufflinks" WWWDIR="www/cufflinks" ETCDIR="etc/cufflinks" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/cufflinks DOCSDIR=/usr/local/share/doc/cufflinks EXAMPLESDIR=/usr/local/share/examples/cufflinks WWWDIR=/usr/local/www/cufflinks ETCDIR=/usr/local/etc/cufflinks --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 MACHINE=i386 MACHINE_ARCH=i386 ARCH=${MACHINE_ARCH} #### /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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: i386-unknown-freebsd11.2 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: i386-unknown-freebsd11.2 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-m" "elf_i386_fbsd" "-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_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 6.0.0 (tags/RELEASE_600/final 326565) (based on LLVM 6.0.0) Target: i386-unknown-freebsd11.2 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=11.2-RELEASE-p10 OSREL=11.2 OSVERSION=1102000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 524288 stack size (kbytes, -s) 65536 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 BSL accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> cufflinks-2.2.1.83 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_5.txz [112i386-default-job-15] Installing pkg-1.10.5_5... [112i386-default-job-15] Extracting pkg-1.10.5_5: .......... done ===> cufflinks-2.2.1.83 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of cufflinks-2.2.1.83 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License BSL accepted by the user => cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz doesn't seem to exist in /portdistfiles/. => Attempting to fetch https://codeload.github.com/cole-trapnell-lab/cufflinks/tar.gz/v2.2.1-83-gb4fa050?dummy=/cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz fetch: https://codeload.github.com/cole-trapnell-lab/cufflinks/tar.gz/v2.2.1-83-gb4fa050?dummy=/cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz: size unknown fetch: https://codeload.github.com/cole-trapnell-lab/cufflinks/tar.gz/v2.2.1-83-gb4fa050?dummy=/cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz: size of remote file is not known cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz 0 B 0 Bps ===> Fetching all distfiles required by cufflinks-2.2.1.83 for building =========================================================================== =======================<phase: checksum >============================ ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.83 for building => SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License BSL accepted by the user ===> Fetching all distfiles required by cufflinks-2.2.1.83 for building ===> Extracting for cufflinks-2.2.1.83 => SHA256 Checksum OK for cole-trapnell-lab-cufflinks-v2.2.1-83-gb4fa050_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for cufflinks-2.2.1.83 ===> Applying FreeBSD patches for cufflinks-2.2.1.83 =========================================================================== =======================<phase: build-depends >============================ ===> cufflinks-2.2.1.83 depends on package: autoconf>=2.69 - not found ===> Installing existing package /packages/All/autoconf-2.69_2.txz [112i386-default-job-15] Installing autoconf-2.69_2... [112i386-default-job-15] `-- Installing autoconf-wrapper-20131203... <snip> register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ 40 warnings generated. mv -f .deps/gff_utils.Tpo .deps/gff_utils.Po c++ -DHAVE_CONFIG_H -I. -I.. -I../src -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -MT gtf_tracking.o -MD -MP -MF .deps/gtf_tracking.Tpo -c -o gtf_tracking.o gtf_tracking.cpp In file included from gtf_tracking.cpp:10: In file included from ./gtf_tracking.h:12: In file included from ./gff.h:11: ./GHash.hh:90:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:168:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i,n,p,x,h; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:202:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:243:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:285:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,i,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:327:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:364:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:387:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int p,x,h,n; ^~~~~~~~~ ./GHash.hh:416:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:429:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:443:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCurrentEntry; ^~~~~~~~~ ./GHash.hh:461:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=0; ^~~~~~~~~ ./GHash.hh:469:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int pos=fCapacity-1; ^~~~~~~~~ ./GHash.hh:496:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ ./GHash.hh:553:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int i; ^~~~~~~~~ 40 warnings generated. mv -f .deps/gtf_tracking.Tpo .deps/gtf_tracking.Po rm -f libgc.a ar cru libgc.a codons.o GArgs.o GBase.o gdna.o GStr.o GFaSeqGet.o GFastaIndex.o gff.o gff_utils.o gtf_tracking.o ranlib libgc.a c++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -m64 -O3 -O2 -pipe -I/usr/local/include/eigen3 -fstack-protector-strong -fno-strict-aliasing -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -fstack-protector-strong -L/usr/lib -pthread -L/usr/local/lib -L/usr/local/lib -fstack-protector-strong -L/usr/lib -o cufflinks cufflinks.o libcufflinks.a libgc.a -lboost_thread -lboost_system -lboost_serialization -lboost_filesystem -lhts -lz cufflinks.o: file not recognized: File format not recognized c++: error: linker command failed with exit code 1 (use -v to see invocation) gmake[3]: *** [Makefile:802: cufflinks] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050/src' gmake[2]: *** [Makefile:400: all-recursive] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050' gmake[1]: *** [Makefile:341: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/cufflinks/work/cufflinks-2.2.1-83-gb4fa050' *** Error code 1 Stop. make: stopped in /usr/ports/biology/cufflinks
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