From nobody Wed Nov 27 08:20:04 2024 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 4XysnJ5BpRz5dnyC for ; Wed, 27 Nov 2024 08:20:04 +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 "R10" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4XysnJ2tQCz4mxB for ; Wed, 27 Nov 2024 08:20:04 +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=1732695604; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc; bh=Wmxd5y7u1bBVRPZDkkL83O5mzDbc/scRZI5oE1aSjfU=; b=sPnqMEwaBMfVaS6xzbKKQThJxsdLl/3g90QoPqaH3tWOamv7kw0CcF7+yLXrEn22qlXuIl 7n6uwECGFmDZb5ZxAx7ONeOJXzsX4fqj8XkuMpe2KqcZnjPeq4U7VxeelG9SWYwo9v1EQJ BAs2qnx7NhGC3ksi4T4QgOXI3yxH1NNRoHaIrWKyOlS25cW8HHxU9Drawsr5QDZ1vW58OI RPjGuExrHcHT09XqHqSBcZp0/Mt2B6OH65ah4zSn15PrSUMwHJnz+BdGNKRJKy8+yVUAsN F8JNbphbS5Y8ps5FAWweyBuseCPE05+tiBKsKRFiHElK2o4VbVegoWZI3P2X9Q== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1732695604; a=rsa-sha256; cv=none; b=C6orD05tI60UgvVls5uLz4vsWgM5Vly8VBMLNLrKMYQzeVuZC0Gwf5MOh/xR+9glFZVvpM S58pqtkG5vPtXXCNbu6JBCiMVOT0mmbSwqY9JBEwTuO3qfPW+R02UpHloApWB/BnJzYzKv MFCbnROMkCiG5p0Jr3mioN0cDEb+VbYeGmcUihp/Nl+Qx8eZenGNW6ekbJBXXyWIgeLRbS YIYcmlWOoDBEAuKm/RVibBT3XPSsFoHkJ8mZdn0+Hj9DjNKIe/CubWc+w5lr3S/jwAxng0 5PiwryXHL/orWiUzy2lPBnAOw+V2xslz+rDsOfPWuwau/USvtY+e5dPVxErKpw== Received: from ampere2.nyi.freebsd.org (ampere2.nyi.freebsd.org [IPv6:2610:1c1:1:6080::16:24]) by mxrelay.nyi.freebsd.org (Postfix) with ESMTP id 4XysnJ2TsZz12Pp for ; Wed, 27 Nov 2024 08:20:04 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from root (uid 0) (envelope-from pkg-fallout@FreeBSD.org) id 36cd by ampere2.nyi.freebsd.org (DragonFly Mail Agent v0.13+ on ampere2.nyi.freebsd.org); Wed, 27 Nov 2024 08:20:04 +0000 To: pkg-fallout@FreeBSD.org Subject: [package - main-armv7-default][biology/seqan-apps] Failed for seqan-apps-2.4.0_11 in build Date: Wed, 27 Nov 2024 08:20:04 +0000 Message-Id: <6746d634.36cd.30057d9e@ampere2.nyi.freebsd.org> From: 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: https://pkg-status.freebsd.org/ampere2/data/main-armv7-default/p36c7e09f1f42_s21ca690b56/logs/seqan-apps-2.4.0_11.log Build URL: https://pkg-status.freebsd.org/ampere2/build.html?mastername=main-armv7-default&build=p36c7e09f1f42_s21ca690b56 Log: =>> Building biology/seqan-apps build started at Wed Nov 27 08:08:26 UTC 2024 port directory: /usr/ports/biology/seqan-apps package name: seqan-apps-2.4.0_11 building for: FreeBSD main-armv7-default-job-04 15.0-CURRENT FreeBSD 15.0-CURRENT 1500027 arm maintained by: h2+fbsdports@fsfe.org Makefile datestamp: -rw-r--r-- 1 root wheel 1045 Aug 12 2023 /usr/ports/biology/seqan-apps/Makefile Ports top last git commit: 36c7e09f1f4 Ports top unclean checkout: no Port dir last git commit: 6d558714dfd Port dir unclean checkout: no Poudriere version: poudriere-git-3.4.2 Host OSVERSION: 1500023 Jail OSVERSION: 1500027 Job Id: 04 !!! Jail is newer than host. (Jail: 1500027, Host: 1500023) !!! !!! This is not supported. !!! !!! Host kernel must be same or newer than jail. !!! !!! Expect build failures. !!! ---Begin Environment--- SHELL=/bin/sh OSVERSION=1500027 UNAME_v=FreeBSD 15.0-CURRENT 1500027 UNAME_r=15.0-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 MAKE_OBJDIR_CHECK_WRITABLE=0 LOCALBASE=/usr/local USER=root POUDRIERE_NAME=poudriere-git LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.4.2 MASTERMNT=/usr/local/poudriere/data/.m/main-armv7-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/main-armv7-default/04/.p OUTPUT_REDIRECTED_STDOUT=3 P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS MASTERNAME=main-armv7-default SCRIPTPREFIX=/usr/local/share/poudriere SCRIPTNAME=bulk.sh OLDPWD=/usr/local/poudriere/data/.m/main-armv7-default/ref/.p/pool POUDRIERE_PKGNAME=poudriere-git-3.4.2 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--- ===> The following configuration options are available for seqan-apps-2.4.0_11: ====> 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 PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig 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 PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/seqan-apps/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 DESTDIR=/wrkdirs/usr/ports/biology/seqan-apps/work/stage 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 -std=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-- CMAKE_BUILD_TYPE="release" RM_I386="@comment " OSREL=15.0 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--- # 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 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-- ulimit: can't get limit: Invalid argument 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) 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-- =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> seqan-apps-2.4.0_11 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.21.3.pkg [main-armv7-default-job-04] Installing pkg-1.21.3... [main-armv7-default-job-04] Extracting pkg-1.21.3: .......... done ===> seqan-apps-2.4.0_11 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of seqan-apps-2.4.0_11 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building => SHA256 Checksum OK for seqan-seqan-seqan-v2.4.0_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user ===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building ===> Extracting for seqan-apps-2.4.0_11 => SHA256 Checksum OK for seqan-seqan-seqan-v2.4.0_GH0.tar.gz. =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 =========================================================================== =================================================== ===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 ===> Patching for seqan-apps-2.4.0_11 =========================================================================== =================================================== ===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 ===> seqan-apps-2.4.0_11 depends on package: boost-libs>0 - not found ===> Installing existing package /packages/All/boost-libs-1.85.0.pkg [main-armv7-default-job-04] Installing boost-libs-1.85.0... In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 267 | char c = FunctorLowcase()(typeC); | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find.h:73: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/find/find_wild_shiftand.h:160:11: warning: variable 'len' set but not used [-Wunused-but-set-variable] 160 | TWord len = nl; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:47: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_builder.h:41: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/consensus.h:65: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/consensus/overlap_info_computation.h:38: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index.h:76: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/index/index_base.h:340:35: warning: 'binary_function' is deprecated [-Wdeprecated-declarations] 340 | struct FibreLess: public std::binary_function | ^ /usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function' has been explicitly marked deprecated here 24 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 binary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment' first required here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::Nothing_>' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>, seqan::TagList, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:568:20: note: in instantiation of function template specialization 'seqan::open, std::char_traits, seqan::BufferedStream>, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 568 | return open(stream, stream.bufferedStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:533:25: note: pointer 'VALUE' declared here 533 | static char const * VALUE; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:69: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: warning: 'sizeof (MagicHeader::VALUE)' will return the size of the pointer, not the array itself [-Wsizeof-pointer-div] 209 | for (i = 0; i != sizeof(MagicHeader::VALUE) / sizeof(char); ++i) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:75:13: note: in instantiation of function template specialization 'seqan::guessFormatFromStream' requested here 75 | if (guessFormatFromStream(seq, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream>>' requested here 81 | return guessFormatFromStream(seq, static_cast::Base &>(format)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:81:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList>>>' requested here /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:472:12: note: in instantiation of function template specialization 'seqan::guessFormatFromStream, seqan::TagList, seqan::TagList>>>>' requested here 472 | return guessFormatFromStream(fileStream, compressionType); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:575:10: note: in instantiation of function template specialization 'seqan::_guessFormat, seqan::TagList, seqan::TagList>>>>>' requested here 575 | if (!_guessFormat(stream, fileStream, compressionType)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:625:9: note: in instantiation of function template specialization 'seqan::open, std::char_traits, std::fstream, seqan::TagSelector, seqan::TagList, seqan::TagList>>>>>' requested here 625 | open(stream, stream.file, stream.format); // read from a pipe (without file extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/basic/basic_stream.h:537:39: note: pointer 'VALUE' declared here 537 | char const * MagicHeader::VALUE = NULL; | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:59: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier.h:74: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_functors.h:113:37: warning: 'unary_function' is deprecated [-Wdeprecated-declarations] 113 | struct FunctorLowcase : public std::unary_function | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:91:17: note: in instantiation of template class 'seqan::FunctorLowcase' requested here 91 | TFunctor func; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/modifier/modifier_view.h:140:13: note: in instantiation of template class 'seqan::ModViewCargo>' requested here 140 | TCargo_ _cargo; | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:159:14: note: in instantiation of template class 'seqan::ModifiedString>>' requested here 159 | TLowcase lowcaseFileName(fileName); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/guess_format.h:114:13: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename' requested here 114 | if (guessFormatFromFilename(fname, TFormat())) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:627:9: note: in instantiation of function template specialization 'seqan::guessFormatFromFilename, seqan::TagList, seqan::TagList>>>>' requested here 627 | guessFormatFromFilename(fileName, stream.format); // read/write from/to a file (with extension) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:704:10: note: in instantiation of function template specialization 'seqan::open, std::char_traits>' requested here 704 | if (!open(file.stream, fileName, openMode)) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ /usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function' has been explicitly marked deprecated here 23 | struct _LIBCPP_TEMPLATE_VIS _LIBCPP_DEPRECATED_IN_CXX11 unary_function { | ^ /usr/include/c++/v1/__config:736:41: note: expanded from macro '_LIBCPP_DEPRECATED_IN_CXX11' 736 | # define _LIBCPP_DEPRECATED_IN_CXX11 _LIBCPP_DEPRECATED | ^ /usr/include/c++/v1/__config:713:49: note: expanded from macro '_LIBCPP_DEPRECATED' 713 | # define _LIBCPP_DEPRECATED __attribute__((__deprecated__)) | ^ In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/bam2roi.cpp:40: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/arg_parse.h:46: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream.h:62: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/file.h:58: In file included from /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence.h:98: /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/sequence/segment_prefix.h:117:5: warning: definition of implicit copy constructor for 'Segment' is deprecated because it has a user-provided copy assignment operator [-Wdeprecated-copy-with-user-provided-copy] 117 | operator = (Segment const & source) | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/virtual_stream.h:527:16: note: in implicit copy constructor for 'seqan::Segment' first required here 527 | return _getUncompressedBasename(fname, TFormat()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:721:47: note: in instantiation of function template specialization 'seqan::_getUncompressedBasename, seqan::TagList, seqan::TagList>>>>' requested here 721 | Prefix::Type basename = _getUncompressedBasename(fileName, format(file.stream)); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:739:12: note: in instantiation of function template specialization 'seqan::_open, seqan::Tag, void, seqan::False>' requested here 739 | return _open(file, fileName, openMode, False()); | ^ /wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/bam_io/bam_index_bai.h:699:10: note: in instantiation of function template specialization 'seqan::open, seqan::Tag, void>' requested here 699 | if (!open(bamFile, bamFilename)) | ^ 20 warnings generated. ninja: build stopped: subcommand failed. ===> 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 making "build" in /usr/ports/biology/seqan-apps