From nobody Thu Feb 17 14:58:01 2022 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 3562119C1823 for ; Thu, 17 Feb 2022 14:58:02 +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 4JzycT6pQjz3nnp for ; Thu, 17 Feb 2022 14:58:01 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy7.nyi.freebsd.org (beefy7.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:16]) (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 CA0553BFD for ; Thu, 17 Feb 2022 14:58:01 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from beefy7.nyi.freebsd.org (localhost [127.0.0.1]) by beefy7.nyi.freebsd.org (8.16.1/8.16.1) with ESMTP id 21HEw1VW082112 for ; Thu, 17 Feb 2022 14:58:01 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by beefy7.nyi.freebsd.org (8.16.1/8.16.1/Submit) id 21HEw1aH082110; Thu, 17 Feb 2022 14:58:01 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Thu, 17 Feb 2022 14:58:01 GMT From: pkg-fallout@FreeBSD.org Message-Id: <202202171458.21HEw1aH082110@beefy7.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 130releng-riscv64-quarterly][biology/seqan-apps] Failed for seqan-apps-2.4.0_10 in package ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1645109882; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=c5v+Y/4QmZNs5jwe/DGOZb5b8+SPPaZEN2Xy9aI9Yxc=; b=ZuJDJz1ZB6gNLCFvflojOJpPU6Xw8vAg7muXZOTblxhaMEktbtvyiVVvJE6kUjABP13LaX pRwq9hAJvmngfBFaeytxrdEkxSXilwhBezhjgXoSDJ9G/NgX4z6pN+yWS6fFnvlQseHpIk j5erZppvUM4r3vVeYWvU8Hl/9FMkwwcgiXQmbO2ZaxDP6fiD38d8FV/4dcJsiRbfMJjy0e APVLjyI/7k6VbcL+Gs1unJ3jvlVKZ/gUapkeznOXo1WMBqy3dxh4XYT02HqS4cNHI/pIhU QLVB/nCS9LPBzAgLYo5P1xe56Mn+xLs90/iHLnAEHnSC45r68ZKm0OCvO98V3A== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1645109882; a=rsa-sha256; cv=none; b=yHnXUS7QLZdFDS82qPTaHxtliXjRo1OR1qCNxA39EU0BD7pVRxIfJ87afbw6Hg+3lzlS+z R5B2yaw7Ysta8GAfZktVpA4Eyf+YB8XjfGUc1dgFp0p45bS/yGmhjMAfH3zVgw6zlDZE9b w4/CnJSm8ap2MAh6hj9LzeTA7z9pledONkd9RFe4AXu6XWnOpTRC39m5jVX/eql0ok5KJB 7Y6U6VwKQB/3TKq/inpt5AZv2tQkWHmiUYnBC7fRPwEFL/3GOkAI5sBeVYvji2rhTEDrZI nz0N9d1yGH2jZLAZB4Xyd4reLmI3x0gN6El+LXUTopDM4ZBc392yZrYWNVQi0g== ARC-Authentication-Results: i=1; mx1.freebsd.org; none 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: h2+fbsdports@fsfe.org Log URL: http://beefy7.nyi.freebsd.org/data/130releng-riscv64-quarterly/08ea50a33146/logs/seqan-apps-2.4.0_10.log Build URL: http://beefy7.nyi.freebsd.org/build.html?mastername=130releng-riscv64-quarterly&build=08ea50a33146 Log: =>> Building biology/seqan-apps build started at Thu Feb 17 14:03:25 UTC 2022 port directory: /usr/ports/biology/seqan-apps package name: seqan-apps-2.4.0_10 building for: FreeBSD 130releng-riscv64-quarterly-job-13 13.0-RELEASE-p7 FreeBSD 13.0-RELEASE-p7 1300139 riscv maintained by: h2+fbsdports@fsfe.org Makefile ident: Poudriere version: 3.2.8-21-g883afb07 Host OSVERSION: 1400050 Jail OSVERSION: 1300139 Job Id: 13 ---Begin Environment--- SHELL=/bin/csh UNAME_p=riscv64 UNAME_m=riscv ABI_FILE=/usr/lib/crt1.o OSVERSION=1300139 UNAME_v=FreeBSD 13.0-RELEASE-p7 1300139 UNAME_r=13.0-RELEASE-p7 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 QEMU_EMULATING=1 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-21-g883afb07 MASTERMNT=/usr/local/poudriere/data/.m/130releng-riscv64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/130releng-riscv64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=130releng-riscv64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/130releng-riscv64-quarterly/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--- ===> The following configuration options are available for seqan-apps-2.4.0_10: ====> Options available for the radio ARCH: you can only select none or one of them SSE4=off: Use SSE4 and POPCNT instructions AVX2=off: Use SSE4, AVX2 and POPCNT instructions NATIVE=off: Use all available instruction sets (-march=native) ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- h2+fbsdports@fsfe.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work/.cache HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqan-apps/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- NINJA_STATUS="[%p %s/%t] " XDG_DATA_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/seqan-apps/work/.cache HOME=/wrkdirs/usr/ports/biology/seqan-apps/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/seqan-apps/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 DESTDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/stage PREFIX=/usr/local LOCALBASE=/usr/local CC="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -fno-strict-aliasing " 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-- CMAKE_BUILD_TYPE="release" RM_I386="" OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/seqan-apps" EXAMPLESDIR="share/examples/seqan-apps" DATADIR="share/seqan-apps" WWWDIR="www/seqan-apps" ETCDIR="etc/seqan-apps" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/seqan-apps DOCSDIR=/usr/local/share/doc/seqan-apps EXAMPLESDIR=/usr/local/share/examples/seqan-apps WWWDIR=/usr/local/www/seqan-apps ETCDIR=/usr/local/etc/seqan-apps --End SUB_LIST-- ---Begin make.conf--- .sinclude "/etc/make.nxb.conf" USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes MACHINE=riscv MACHINE_ARCH=riscv64 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_9d218390=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: riscv64-unknown-freebsd13.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin _ALTCCVERSION_9d218390=none _CXXINTERNAL_9c45a5b1=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: riscv64-unknown-freebsd13.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--enable-new-dtags" "-m" "elf64lriscv" "-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_9d218390_58173849=yes CC_OUTPUT_9d218390_9bdba57c=yes CC_OUTPUT_9d218390_6a4fe7f5=yes CC_OUTPUT_9d218390_6bcac02b=yes CC_OUTPUT_9d218390_67d20829=yes CC_OUTPUT_9d218390_bfa62e83=yes CC_OUTPUT_9d218390_f0b4d593=yes CC_OUTPUT_9d218390_308abb44=yes CC_OUTPUT_9d218390_f00456e5=yes CC_OUTPUT_9d218390_65ad290d=yes CC_OUTPUT_9d218390_f2776b26=yes CC_OUTPUT_9d218390_b2657cc3=yes CC_OUTPUT_9d218390_380987f7=yes CC_OUTPUT_9d218390_160933ec=yes CC_OUTPUT_9d218390_fb62803b=yes _OBJC_CCVERSION_9d218390=FreeBSD clang version 11.0.1 (git@github.com:llvm/llvm-project.git llvmorg-11.0.1-0-g43ff75f2c3fe) Target: riscv64-unknown-freebsd13.0 Thread model: posix InstalledDir: /nxb-bin/usr/bin _OBJC_ALTCCVERSION_9d218390=none ARCH=riscv64 OPSYS=FreeBSD _OSRELEASE=13.0-RELEASE-p7 OSREL=13.0 OSVERSION=1300139 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- ---Begin make.nxb.conf--- CC=/nxb-bin/usr/bin/cc CPP=/nxb-bin/usr/bin/cpp CXX=/nxb-bin/usr/bin/c++ NM=/nxb-bin/usr/bin/nm LD=/nxb-bin/usr/bin/ld OBJCOPY=/nxb-bin/usr/bin/objcopy SIZE=/nxb-bin/usr/bin/size STRIPBIN=/nxb-bin/usr/bin/strip SED=/nxb-bin/usr/bin/sed RANLIB=/nxb-bin/usr/bin/ranlib YACC=/nxb-bin/usr/bin/yacc MAKE=/nxb-bin/usr/bin/make STRINGS=/nxb-bin/usr/bin/strings AWK=/nxb-bin/usr/bin/awk FLEX=/nxb-bin/usr/bin/flex ---End make.nxb.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) 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 BSD3CLAUSE LGPL3 GPLv3 accepted by the user =========================================================================== =================================================== ===> seqan-apps-2.4.0_10 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.17.5.pkg [130releng-riscv64-quarterly-job-13] Installing pkg-1.17.5... [130releng-riscv64-quarterly-job-13] Extracting pkg-1.17.5: .......... done ===> seqan-apps-2.4.0_10 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqan-apps-2.4.0_10 =========================================================================== =================================================== =========================================================================== =================================================== ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.4.0_10 for building =========================================================================== =================================================== ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.4.0_10 for building => SHA256 Checksum OK for seqan-seqan-seqan-v2.4.0_GH0.tar.gz. =========================================================================== =================================================== =========================================================================== _splitAtXDrops(localAlign, scoreMatrix, scoreDropOff, minScore, seedAlignments); ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/stellar/stellar.h:705:3: note: in instantiation of function template specialization 'verifySwiftHit>, seqan::InfixSegment>, double, int, unsigned int, double, unsigned int, seqan::String>, seqan::String>, seqan::Tag>' requested here verifySwiftHit(finderSegment, patternSegment, epsilon, minLength, xDrop, ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:56:9: note: in instantiation of function template specialization 'stellar>, seqan::Dependent>, seqan::IndexQGram, seqan::Tag>, int, double, unsigned int, bool, seqan::String>, seqan::String>, seqan::Tag>' requested here stellar(swiftFinder, swiftPattern, options.epsilon, options.minLength, options.xDrop, ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:174:18: note: in instantiation of function template specialization '_stellarOnOne>, seqan::String>, seqan::Pattern>, seqan::Dependent>>, seqan::IndexQGram, seqan::Tag>>, seqan::Swift>, seqan::StringSet>, seqan::String>>>, seqan::Owner>>>' requested here if (!_stellarOnOne(databases[i], databaseIDs[i], swiftPattern, true, matches, options)) ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:655:10: note: in instantiation of function template specialization '_stellarOnAll>, seqan::String>>' requested here if (!_stellarOnAll(databases, databaseIDs, queries, queryIDs, options)) ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/stellar/stellar.cpp:695:9: note: in instantiation of function template specialization 'mainWithOptions' requested here mainWithOptions(options, String()); ^ 19 warnings generated. [100% 135/135] : && /nxb-bin/usr/bin/c++ -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -fno-strict-aliasing -W -Wall -pedantic -O2 -pipe -march=rv64imafdc -mabi=lp64d -fstack-protector-strong -fno-strict-aliasing -fstack-protector-strong -s -Wl,--whole-archive -lpthread -Wl,--no-whole-archive apps/stellar/CMakeFiles/stellar.dir/stellar.cpp.o -o bin/stellar -lexecinfo -lelf && : =========================================================================== =================================================== =========================================================================== =================================================== ===> Staging for seqan-apps-2.4.0_10 ===> Generating temporary packing list [ 0% 1/1] cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build && /usr/local/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake -- Install configuration: "Release" -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/alf -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/alf/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/alf/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/alf/example/small.fasta -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/bisar -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/casbar -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/four2three -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/bs_tools/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/bs_tools/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/dfi -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/example/fasta1.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/dfi/example/fasta2.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/fx_bam_coverage -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fx_tools/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fx_tools/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/gustaf -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/gustaf_mate_joining -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/adeno.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/adeno_modified.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/adeno_modified_reads.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/gustaf/example/stellar.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/insegt -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/annoOutput.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/annotations.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/readOutput.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/insegt/example/tupleOutput.gff -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_frag_sequencing -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_genome -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_materializer -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_methylation -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_simulator -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_splicing -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/mason_variator -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_frag_sequencing -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_genome -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_materializer -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_methylation -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_simulator -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_splicing -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/README.mason_variator -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/mason2/example/adeno_virus.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/micro_razers -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/example/genome.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/example/reads.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/micro_razers/example/reads.fa.result -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/bam2roi -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_feature_projection -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_plot_thumbnails -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/bed_sort.sh -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/gff_sort.sh -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_sort.sh -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/roi_plot_9.sh -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/plot.awk -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/ps2pswLinks.gawk -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/example/dmel.bed -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/example/dmel.gtf -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/example/example.bam -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/R/ngsroi_0.1.tar.gz -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/ngs_roi/R/ngsroi_0.1.zip -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/pair_align -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/pair_align/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/pair_align/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/param_chooser -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/param_chooser/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/param_chooser/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_prepare_sam -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_build_gold_standard -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_evaluate -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_prepare_sam -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_build_gold_standard -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rabema_evaluate -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rabema/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rabema/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/razers -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/example/genome.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/example/reads.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers/example/reads2.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/razers3 -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/example/genome.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/example/reads.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/razers3/example/reads2.fa -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/rep_sep -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rep_sep/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/rep_sep/README [ 50% 2/2] cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak && /wrkdirs/usr/ports/biology/seqan-apps/work/.build/bin/sak --export-help=man > sak.1 [100% 2/2] cd /wrkdirs/usr/ports/biology/seqan-apps/work/.build/apps/sak && /wrkdirs/usr/ports/biology/seqan-apps/work/.build/bin/sak --export-help=txt > README.sak.txt -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/sak -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sak/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/sak/README -- Installing: 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/wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/tree_recon -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/tree_recon/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/tree_recon/README -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/tree_recon/example/example.dist -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/yara_indexer -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/yara_mapper -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/yara/LICENSE -- Installing: /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/yara/README.rst ====> Compressing man pages (compress-man) =========================================================================== =================================================== ===> Building package for seqan-apps-2.4.0_10 pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/compute_gain:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/bin/fiona:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fiona/LICENSE:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fiona/README:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/seqan-apps/work/stage/usr/local/share/doc/fiona/example/reads.fa:No such file or directory *** Error code 1 Stop. make: stopped in /usr/ports/biology/seqan-apps