From nobody Sun Feb 12 19:16:30 2023 X-Original-To: pkg-fallout@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4PFHJb33Zfz3qc0L for ; Sun, 12 Feb 2023 19:16:31 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4PFHJZ6ltbz3vw8; Sun, 12 Feb 2023 19:16:30 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1676229390; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:cc; bh=a+HcEfJ0LL7wRzQX4/287ltD1Hbx57Ps6JvDBHFIiiI=; b=sVlIqHlWkDz1RKG4/tXXhfP+wDQnAPLVuUaDNtXa5arwSgUTYAQOeJQefynU8ROt8zIj18 Eq1peWuxcoiwySYnxJqX9oITrubdZTBYyLP4al++NP0J5ds/IcLmYrGC9p7DoJUtkVGWkq wURpzYjpjE2ZNpjfNSWKetz2IWSWIqT7icgInv/+cLv2kj0NoRis3jXSTcwfn1lErSYsht nyQBc5SIJNTeLq3GyP/Ki8GeVbATxVnRafguBPJP3mf2AM9ynWULszKeS27CJGqg9IOVmW ZZvUZJrwJ/xOKSxs5tNgOn94XNj8DauxEBbxR8N9as86uTBB21lnru62/ULufg== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1676229390; a=rsa-sha256; cv=none; b=as04vUyEOvaF5VZnqt1MuDy+3O3kb9q8EmH678TjNST7IMeVC6ylF8ds45+DnYTyHQNfnN JMok4CCD6aSqevZn62qEv1blnbHJxrQHHUcwLHuqtZPs3TAp1hCbsP5aO8KmAzIcaJMSIL R7ctw8p0xtSpYoMusBI8DeNHkQ3qJoz04UuY/v5rfFFwZXPekz4M2yD8NKWsU4jJ/V8A2s ZAIna0QsxLJ+iHNpqJA1YYKYnI7Jmozg2dykXMLhAznVP/ji/1lnO5kM0Vf8i5KuPKD7xn ocnIGwGceU31yXR30XR8ngFKos9w5HqvN5jVZoL9R2XFD8i9kmmTRXR0HWsohA== Received: from beefy17.nyi.freebsd.org (beefy17.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:20]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4PFHJZ5t1Bzpyp; Sun, 12 Feb 2023 19:16:30 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy17.nyi.freebsd.org (localhost [127.0.0.1]) by beefy17.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 31CJGUh9094688; Sun, 12 Feb 2023 19:16:30 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy17.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 31CJGURB094670; Sun, 12 Feb 2023 19:16:30 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Sun, 12 Feb 2023 19:16:30 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202302121916.31CJGURB094670@beefy17.nyi.freebsd.org> To: jwb@FreeBSD.org Subject: [package - main-i386-default][biology/fastx-toolkit] Failed for fastx_toolkit-0.0.14 in build Cc: pkg-fallout@FreeBSD.org X-ThisMailContainsUnwantedMimeParts: N List-Id: Fallout logs from package building List-Archive: https://lists.freebsd.org/archives/freebsd-pkg-fallout List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-freebsd-pkg-fallout@freebsd.org You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: jwb@FreeBSD.org Log URL: https://pkg-status.freebsd.org/beefy17/data/main-i386-default/p909032bc6729_s7e44856e3a/logs/fastx_toolkit-0.0.14.log Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p909032bc6729_s7e44856e3a Log: =>> Building biology/fastx-toolkit build started at Sun Feb 12 19:16:06 UTC 2023 port directory: /usr/ports/biology/fastx-toolkit package name: fastx_toolkit-0.0.14 building for: FreeBSD main-i386-default-job-06 14.0-CURRENT FreeBSD 14.0-CURRENT 1400079 i386 maintained by: jwb@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400073 Jail OSVERSION: 1400079 Job Id: 06 !!! Jail is newer than host. (Jail: 1400079, Host: 1400073) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh UNAME_p=i386 UNAME_m=i386 OSVERSION=1400079 UNAME_v=FreeBSD 14.0-CURRENT 1400079 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-i386-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/main-i386-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=main-i386-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/main-i386-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-- jwb@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl PERL_USE_UNSAFE_INC=1 PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work/.cache HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fastx-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fastx-toolkit/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh DEFAULT_AUTOCONF=2.71 CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work/.cache HOME=/wrkdirs/usr/ports/biology/fastx-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/fastx-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/fastx-toolkit/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES DEFAULT_AUTOCONF=2.71 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="in stall -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-- 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/fastx_toolkit" EXAMPLESDIR="share/examples/fastx_toolkit" DATADIR="share/fastx_toolkit" WWWDIR="www/fastx_toolkit" ETCDIR="etc/fastx_toolkit" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/fastx_toolkit DOCSDIR=/usr/local/share/doc/fastx_toolkit EXAMPLESDIR=/usr/local/share/examples/fastx_toolkit WWWDIR=/usr/local/www/fastx_toolkit ETCDIR=/usr/local/etc/fastx_toolkit --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 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: i386-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: i386-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-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_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 15.0.7 (https://github.com/llvm/llvm-project.git llvmorg-15.0.7-0-g8dfdcc7b7bf6) Target: i386-unknown-freebsd14.0 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=i386 OPSYS=FreeBSD _OSRELEASE=14.0-CURRENT OSREL=14.0 OSVERSION=1400079 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) 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-- =================================================== ===> License AGPLv3+ accepted by the user =========================================================================== =================================================== ===> fastx_toolkit-0.0.14 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1.pkg [main-i386-default-job-06] Installing pkg-1.19.1... [main-i386-default-job-06] Extracting pkg-1.19.1: .......... done ===> fastx_toolkit-0.0.14 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of fastx_toolkit-0.0.14 =========================================================================== =================================================== =========================================================================== =================================================== ===> License AGPLv3+ accepted by the user ===> Fetching all distfiles required by fastx_toolkit-0.0.14 for building =========================================================================== =================================================== ===> License AGPLv3+ accepted by the user ===> Fetching all distfiles required by fastx_toolkit-0.0.14 for building => SHA256 Checksum OK for agordon-fastx_toolkit-0.0.14_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License AGPLv3+ accepted by the user ===> Fetching all distfiles required by fastx_toolkit-0.0.14 for building ===> Extracting for fastx_toolkit-0.0.14 => SHA256 Checksum OK for agordon-fastx_toolkit-0.0.14_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for fastx_toolkit-0.0.14 ===> Applying FreeBSD patches for fastx_toolkit-0.0.14 from /usr/ports/biology/fastx-toolkit/files =========================================================================== =================================================== checking how to convert i386-portbld-freebsd14.0 file names to toolchain format... func_convert_file_noop checking for /usr/bin/ld option to reload object files... -r checking for file... file checking for objdump... objdump checking how to recognize dependent libraries... pass_all checking for dlltool... no checking how to associate runtime and link libraries... printf %s\n checking for ar... ar checking for archiver @FILE support... no checking for strip... strip checking for ranlib... ranlib checking command to parse /usr/bin/nm output from cc object... ok checking for sysroot... no checking for a working dd... /bin/dd checking how to truncate binary pipes... /bin/dd bs=4096 count=1 checking for mt... mt checking if mt is a manifest tool... no checking for stdio.h... (cached) yes checking for stdlib.h... (cached) yes checking for string.h... (cached) yes checking for inttypes.h... (cached) yes checking for stdint.h... (cached) yes checking for strings.h... (cached) yes checking for sys/stat.h... (cached) yes checking for sys/types.h... (cached) yes checking for unistd.h... (cached) yes checking for dlfcn.h... (cached) yes checking for objdir... .libs checking if cc supports -fno-rtti -fno-exceptions... yes checking for cc option to produce PIC... -fPIC -DPIC checking if cc PIC flag -fPIC -DPIC works... yes checking if cc static flag -static works... yes checking if cc supports -c -o file.o... yes checking if cc supports -c -o file.o... (cached) yes checking whether the cc linker (/usr/bin/ld) supports shared libraries... yes checking whether -lc should be explicitly linked in... no checking dynamic linker characteristics... freebsd14.0 ld.so checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking if libtool supports shared libraries... yes checking whether to build shared libraries... yes checking whether to build static libraries... yes checking how to run the C++ preprocessor... c++ -E checking for ld used by c++... /usr/bin/ld checking if the linker (/usr/bin/ld) is GNU ld... yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking for c++ option to produce PIC... -fPIC -DPIC checking if c++ PIC flag -fPIC -DPIC works... yes checking if c++ static flag -static works... yes checking if c++ supports -c -o file.o... yes checking if c++ supports -c -o file.o... (cached) yes checking whether the c++ linker (/usr/bin/ld) supports shared libraries... yes checking dynamic linker characteristics... freebsd14.0 ld.so checking how to hardcode library paths into programs... immediate checking for long long int... yes checking for ISO C++ TR1 include files... no checking whether c++ supports C++11 features by default... yes checking pkg-config is at least version 0.9.0... yes checking for GTEXTUTILS... yes checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating Makefile config.status: creating doc/Makefile config.status: creating m4/Makefile config.status: creating src/Makefile config.status: creating src/libfastx/Makefile config.status: creating src/fastx_clipper/Makefile config.status: creating src/fastq_to_fasta/Makefile config.status: creating src/fastx_quality_stats/Makefile config.status: creating src/fastq_quality_converter/Makefile config.status: creating src/fastx_trimmer/Makefile config.status: creating src/fastq_quality_filter/Makefile config.status: creating src/fastq_quality_trimmer/Makefile config.status: creating src/fastx_artifacts_filter/Makefile config.status: creating src/fastx_reverse_complement/Makefile config.status: creating src/fastx_collapser/Makefile config.status: creating src/fastx_uncollapser/Makefile config.status: creating src/seqalign_test/Makefile config.status: creating src/fasta_formatter/Makefile config.status: creating src/fasta_nucleotide_changer/Makefile config.status: creating src/fastx_renamer/Makefile config.status: creating src/fastq_masker/Makefile config.status: creating galaxy/Makefile config.status: creating galaxy/tools/Makefile config.status: creating galaxy/tools/fastx_toolkit/Makefile config.status: creating galaxy/test-data/Makefile config.status: creating galaxy/static/Makefile config.status: creating galaxy/static/fastx_icons/Makefile config.status: creating galaxy/tool-data/Makefile config.status: creating scripts/Makefile config.status: creating build_scripts/Makefile config.status: creating config.h config.status: executing depfiles commands config.status: executing libtool commands =========================================================================== =================================================== ===> Building for fastx_toolkit-0.0.14 --- all --- /usr/bin/make all-recursive --- all-recursive --- Making all in m4 Making all in src --- all-recursive --- Making all in libfastx --- chomp.o --- --- fastx.o --- --- chomp.o --- cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT chomp.o -MD -MP -MF .deps/chomp.Tpo -c -o chomp.o chomp.c --- fastx.o --- cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx.o -MD -MP -MF .deps/fastx.Tpo -c -o fastx.o fastx.c --- chomp.o --- mv -f .deps/chomp.Tpo .deps/chomp.Po --- fastx_args.o --- cc -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_args.o -MD -MP -MF .deps/fastx_args.Tpo -c -o fastx_args.o fastx_args.c mv -f .deps/fastx_args.Tpo .deps/fastx_args.Po --- sequence_alignment.o --- c++ -DHAVE_CONFIG_H -I. -I../.. -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT sequence_alignment.o -MD -MP -MF .deps/sequence_alignment.Tpo -c -o sequence_alignment.o sequence_alignment.cpp --- fastx.o --- mv -f .deps/fastx.Tpo .deps/fastx.Po --- sequence_alignment.o --- mv -f .deps/sequence_alignment.Tpo .deps/sequence_alignment.Po --- libfastx.a --- rm -f libfastx.a ar cru libfastx.a chomp.o fastx.o fastx_args.o sequence_alignment.o ranlib libfastx.a Making all in fastx_clipper --- fastx_clipper.o --- c++ -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_clipper.o -MD -MP -MF .deps/fastx_clipper.Tpo -c -o fastx_clipper.o fastx_clipper.cpp mv -f .deps/fastx_clipper.Tpo .deps/fastx_clipper.Po --- fastx_clipper --- /bin/sh ../../libtool --tag=CXX --mode=link c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastx_clipper fastx_clipper.o ../libfastx/libfastx.a libtool: link: c++ -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastx_clipper fastx_clipper.o ../libfastx/libfastx.a Making all in fastx_trimmer --- fastx_trimmer.o --- cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_trimmer.o -MD -MP -MF .deps/fastx_trimmer.Tpo -c -o fastx_trimmer.o fastx_trimmer.c mv -f .deps/fastx_trimmer.Tpo .deps/fastx_trimmer.Po --- fastx_trimmer --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastx_trimmer fastx_trimmer.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastx_trimmer fastx_trimmer.o ../libfastx/libfastx.a Making all in fastx_quality_stats --- fastx_quality_stats.o --- cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_quality_stats.o -MD -MP -MF .deps/fastx_quality_stats.Tpo -c -o fastx_quality_stats.o fastx_quality_stats.c mv -f .deps/fastx_quality_stats.Tpo .deps/fastx_quality_stats.Po --- fastx_quality_stats --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastx_quality_stats fastx_quality_stats.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastx_quality_stats fastx_quality_stats.o ../libfastx/libfastx.a Making all in fastq_quality_converter --- fastq_quality_converter.o --- cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_quality_converter.o -MD -MP -MF .deps/fastq_quality_converter.Tpo -c -o fastq_quality_converter.o fastq_quality_converter.c mv -f .deps/fastq_quality_converter.Tpo .deps/fastq_quality_converter.Po --- fastq_quality_converter --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastq_quality_converter fastq_quality_converter.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastq_quality_converter fastq_quality_converter.o ../libfastx/libfastx.a Making all in fastq_to_fasta --- fastq_to_fasta.o --- cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_to_fasta.o -MD -MP -MF .deps/fastq_to_fasta.Tpo -c -o fastq_to_fasta.o fastq_to_fasta.c mv -f .deps/fastq_to_fasta.Tpo .deps/fastq_to_fasta.Po --- fastq_to_fasta --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastq_to_fasta fastq_to_fasta.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastq_to_fasta fastq_to_fasta.o ../libfastx/libfastx.a Making all in fastq_quality_filter --- fastq_quality_filter.o --- cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_quality_filter.o -MD -MP -MF .deps/fastq_quality_filter.Tpo -c -o fastq_quality_filter.o fastq_quality_filter.c mv -f .deps/fastq_quality_filter.Tpo .deps/fastq_quality_filter.Po --- fastq_quality_filter --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastq_quality_filter fastq_quality_filter.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastq_quality_filter fastq_quality_filter.o ../libfastx/libfastx.a Making all in fastq_quality_trimmer --- fastq_quality_trimmer.o --- cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastq_quality_trimmer.o -MD -MP -MF .deps/fastq_quality_trimmer.Tpo -c -o fastq_quality_trimmer.o fastq_quality_trimmer.c mv -f .deps/fastq_quality_trimmer.Tpo .deps/fastq_quality_trimmer.Po --- fastq_quality_trimmer --- /bin/sh ../../libtool --tag=CC --mode=link cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastq_quality_trimmer fastq_quality_trimmer.o ../libfastx/libfastx.a libtool: link: cc -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -fstack-protector-strong -o fastq_quality_trimmer fastq_quality_trimmer.o ../libfastx/libfastx.a Making all in fastx_artifacts_filter --- fastx_artifacts_filter.o --- cc -DHAVE_CONFIG_H -I. -I../.. -I../../src/libfastx -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wall -Wextra -Wformat-nonliteral -Wformat-security -Wswitch-default -Wswitch-enum -Wunused-parameter -Wfloat-equal -Werror -DDEBUG -g -O1 -MT fastx_artifacts_filter.o -MD -MP -MF .deps/fastx_artifacts_filter.Tpo -c -o fastx_artifacts_filter.o fastx_artifacts_filter.c fastx_artifacts_filter.c:58:6: error: variable 'n_count' set but not used [-Werror,-Wunused-but-set-variable] int n_count=0; ^ 1 error generated. *** [fastx_artifacts_filter.o] Error code 1 make[4]: stopped in /wrkdirs/usr/ports/biology/fastx-toolkit/work/fastx_toolkit-0.0.14/src/fastx_artifacts_filter 1 error make[4]: stopped in /wrkdirs/usr/ports/biology/fastx-toolkit/work/fastx_toolkit-0.0.14/src/fastx_artifacts_filter make[3]: stopped in /wrkdirs/usr/ports/biology/fastx-toolkit/work/fastx_toolkit-0.0.14/src make[2]: stopped in /wrkdirs/usr/ports/biology/fastx-toolkit/work/fastx_toolkit-0.0.14 make[1]: stopped in /wrkdirs/usr/ports/biology/fastx-toolkit/work/fastx_toolkit-0.0.14 ===> 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/fastx-toolkit