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Best regards QIANFAN INTL TEAM At 2026-04-13 10:15:40, [email protected] wrote: >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: [email protected] >Log URL: >https://pkg-status.freebsd.org/beefy22/data/143amd64-default/ec01825a2d0d/logs/seqan-apps-2.4.0_11.log >Build URL: >https://pkg-status.freebsd.org/beefy22/build.html?mastername=143amd64-default&build=ec01825a2d0d >Log: > >=>> Building biology/seqan-apps >build started at Mon Apr 13 01:54:57 UTC 2026 >port directory: /usr/ports/biology/seqan-apps >package name: seqan-apps-2.4.0_11 >building for: FreeBSD 143amd64-default-job-01 14.3-RELEASE-p10 FreeBSD >14.3-RELEASE-p10 amd64 >maintained by: [email protected] >Makefile datestamp: -rw-r--r-- 1 root wheel 1045 Feb 20 2025 >/usr/ports/biology/seqan-apps/Makefile >Ports top last git commit: ec01825a2d0d997f554b8fde4c49f6cdb7b2847a >Ports top unclean checkout: no >Port dir last git commit: 1bb147345dca7793cb9ad73a80d3610410ee2ceb >Port dir unclean checkout: no >Poudriere version: poudriere-git-3.4.6-4-g83739588 >Host OSVERSION: 1600014 >Jail OSVERSION: 1403000 >Job Id: 01 > >---Begin Environment--- >SHELL=/bin/sh >OSVERSION=1403000 >UNAME_v=FreeBSD 14.3-RELEASE-p10 >UNAME_r=14.3-RELEASE-p10 >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=3.4.6-4-g83739588 >MASTERMNT=/usr/local/poudriere/data/.m/143amd64-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/143amd64-default/01/.p >OUTPUT_REDIRECTED_STDOUT=3 >P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS >MASTERNAME=143amd64-default >SCRIPTPREFIX=/usr/local/share/poudriere >SCRIPTNAME=bulk.sh >OLDPWD=/usr/local/poudriere/data/.m/143amd64-default/ref/.p/pool >POUDRIERE_PKGNAME=poudriere-git-3.4.6-4-g83739588 >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-- >[email protected] >--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=" " LIBS="" CXX="c++" >CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing >-std=c++14 " CXXSTD=c++14 BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL >_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" >BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" >--End MAKE_ENV-- > >--PLIST_SUB-- > CMAKE_BUILD_TYPE="release" RM_I386="" OSREL=14.3 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--- >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 >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) 33554432 >stack size (kbytes, -s) 524288 >core file size (512-blocks, -c) unlimited >max memory size (kbytes, -m) unlimited >locked memory (kbytes, -l) unlimited >max user processes (-u) 89999 >open files (-n) 8192 >virtual mem size (kbytes, -v) unlimited >swap limit (kbytes, -w) unlimited >socket buffer size (bytes, -b) unlimited >pseudo-terminals (-p) unlimited >kqueues (-k) unlimited >umtx shared locks (-o) unlimited >pipebuf (-y) unlimited >--End resource limits-- >=======================<phase: check-sanity >============================ >===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 >===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user >=========================================================================== >=======================<phase: pkg-depends >============================ >===== 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-2.6.2_1.pkg >[143amd64-default-job-01] Installing pkg-2.6.2_1... >[143amd64-default-job-01] Extracting pkg-2.6.2_1: .......... 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 >=========================================================================== >=======================<phase: fetch-depends >============================ >===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 >=========================================================================== >=======================<phase: fetch >============================ >===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 >===> License BSD3CLAUSE LGPL3 GPLv3 accepted by the user >===> Fetching all distfiles required by seqan-apps-2.4.0_11 for building >=========================================================================== >=======================<phase: checksum >============================ >===== env: FETCH_REGET=0 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. >=========================================================================== >=======================<phase: extract-depends>============================ >===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 >=========================================================================== >=======================<phase: extract >============================ >===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 >===> License 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. >=========================================================================== >=======================<phase: patch-depends >============================ >===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0 >=========================================================================== >=======================<phase: patch >============================ >===== env: NO_DEPENDS=yes USER=root UID=0 GID=0 >===> Patching for seqan-apps-2.4.0_11 >=========================================================================== >=======================<phase: build-depends >============================ >===== 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-1.89.0_2.pkg >[143amd64-default-job-01] Installing boost-libs-1.89.0_2... >[143amd64-default-job-01] `-- Installing icu-76.1,1... >[143amd64-default-job-01] `-- Extracting icu-76.1,1: .......... done >[143amd64-default-job-01] `-- Installing zstd-1.5.7_1... >[143amd64-default-job-01] `-- Extracting zstd-1.5.7_1: .......... done >[143amd64-default-job-01] Extracting boost-libs-1.89.0_2: .......... done >===== >Message from boost-libs-1.89.0_2: > >-- >You have built the Boost library with thread support. > >Don't forget to add -pthread to your linker options when >linking your code. >===> seqan-apps-2.4.0_11 depends on package: boost-libs>0 - found >===> Returning to build of seqan-apps-2.4.0_11 >===> seqan-apps-2.4.0_11 depends on file: /usr/local/bin/cmake - not found ><snip> >/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/stream_base.h:209:58: > warning: 'sizeof (MagicHeader<TFormat>::VALUE)' will return the size of the >pointer, not the array itself [-Wsizeof-pointer-div] > 209 | for (i = 0; i != sizeof(MagicHeader<TFormat>::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<std::fstream, 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<std::fstream, >seqan::TagList<seqan::Tag<seqan::Nothing_>>>' requested here > 81 | return guessFormatFromStream(seq, static_cast<typename > TagSelector<TTagList>::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<std::fstream, >seqan::TagList<seqan::Tag<seqan::GZFile_>, >seqan::TagList<seqan::Tag<seqan::Nothing_>>>>' 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<std::fstream, >seqan::TagList<seqan::Tag<seqan::BgzfFile_>, >seqan::TagList<seqan::Tag<seqan::GZFile_>, >seqan::TagList<seqan::Tag<seqan::Nothing_>>>>>' 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<char, std::fstream, >seqan::TagSelector<seqan::TagList<seqan::Tag<seqan::BgzfFile_>, >seqan::TagList<seqan::Tag<seqan::GZFile_>, >seqan::TagList<seqan::Tag<seqan::Nothing_>>>>>>' 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<char, >seqan::Tag<seqan::Input_>, std::char_traits<char>, std::fstream, >seqan::TagSelector<seqan::TagList<seqan::Tag<seqan::BgzfFile_>, >seqan::TagList<seqan::Tag<seqan::GZFile_>, >seqan::TagList<seqan::Tag<seqan::Nothing_>>>>>>' 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<char, >seqan::Tag<seqan::Input_>, std::char_traits<char>>' 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<seqan::Bam_>, seqan::Tag<seqan::Input_>, 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<seqan::Bam_>, seqan::Tag<seqan::Input_>, 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<Nothing, T>::VALUE = NULL; > | ^ >In file included from >/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: >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<const char, const char>' is deprecated >[-Wdeprecated-declarations] > 113 | struct FunctorLowcase : public std::unary_function<InType, Result> > | ^ >/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<const char>' >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<seqan::FunctorLowcase<const char>>' 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<const char >*const, seqan::ModView<seqan::FunctorLowcase<const char>>>' 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<const char *, seqan::BgzfFile_>' 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<const char *, >seqan::TagList<seqan::Tag<seqan::BgzfFile_>, >seqan::TagList<seqan::Tag<seqan::GZFile_>, >seqan::TagList<seqan::Tag<seqan::Nothing_>>>>>' 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<char, >seqan::Tag<seqan::Input_>, std::char_traits<char>>' 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<seqan::Bam_>, seqan::Tag<seqan::Input_>, 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<seqan::Bam_>, seqan::Tag<seqan::Input_>, void>' >requested here > 699 | if (!open(bamFile, bamFilename)) > | ^ >/usr/include/c++/v1/__functional/unary_function.h:23:29: note: >'unary_function<const char, const char>' 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/roi_plot_thumbnails.cpp:41: >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<const char >*const, seqan::PrefixSegment>' 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<const char *const, >seqan::PrefixSegment>' 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<const char *, >seqan::TagList<seqan::Tag<seqan::BgzfFile_>, >seqan::TagList<seqan::Tag<seqan::GZFile_>, >seqan::TagList<seqan::Tag<seqan::Nothing_>>>>>' requested here > 721 | Prefix<const char *>::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<seqan::Bam_>, seqan::Tag<seqan::Input_>, 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<seqan::Bam_>, seqan::Tag<seqan::Input_>, 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/roi_plot_thumbnails.cpp:37: >In file included from /usr/include/c++/v1/fstream:193: >In file included from /usr/include/c++/v1/__locale:24: >/usr/include/c++/v1/string:2861:5: error: implicit instantiation of undefined >template 'std::char_traits<unsigned char>' > 2861 | traits_type::assign(std::__to_address(__p) + __sz, __n, __c); > | ^ >/usr/include/c++/v1/string:3302:5: note: in instantiation of member function >'std::basic_string<unsigned char>::append' requested here > 3302 | append(__n - __sz, __c); > | ^ >/usr/include/c++/v1/string:1303:84: note: in instantiation of member function >'std::basic_string<unsigned char>::resize' requested here > 1303 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 void > resize(size_type __n) { resize(__n, value_type()); } > | > ^ >/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/png_canvas.h:443:24: > note: in instantiation of member function 'std::basic_string<unsigned >char>::resize' requested here > 443 | idatChunk.data.resize(height + 4 * canvas.size()); // same as > input, should be enough > | ^ >/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here > 23 | struct _LIBCPP_TEMPLATE_VIS char_traits; > | ^ >In file included from >/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:37: >In file included from /usr/include/c++/v1/fstream:193: >In file included from /usr/include/c++/v1/__locale:24: >/usr/include/c++/v1/string:2864:5: error: implicit instantiation of undefined >template 'std::char_traits<unsigned char>' > 2864 | traits_type::assign(__p[__sz], value_type()); > | ^ >/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here > 23 | struct _LIBCPP_TEMPLATE_VIS char_traits; > | ^ >In file included from >/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:37: >In file included from /usr/include/c++/v1/fstream:193: >In file included from /usr/include/c++/v1/__locale:24: >/usr/include/c++/v1/string:2535:5: error: implicit instantiation of undefined >template 'std::char_traits<unsigned char>' > 2535 | traits_type::copy(std::__to_address(__p), > std::__to_address(__old_p), __n_copy); > | ^ >/usr/include/c++/v1/string:2556:3: note: in instantiation of member function >'std::basic_string<unsigned char>::__grow_by' requested here > 2556 | __grow_by(__old_cap, __delta_cap, __old_sz, __n_copy, __n_del, > __n_add); > | ^ >/usr/include/c++/v1/string:2858:7: note: in instantiation of member function >'std::basic_string<unsigned char>::__grow_by_without_replace' requested here > 2858 | __grow_by_without_replace(__cap, __sz + __n - __cap, __sz, __sz, > 0); > | ^ >/usr/include/c++/v1/string:3302:5: note: in instantiation of member function >'std::basic_string<unsigned char>::append' requested here > 3302 | append(__n - __sz, __c); > | ^ >/usr/include/c++/v1/string:1303:84: note: in instantiation of member function >'std::basic_string<unsigned char>::resize' requested here > 1303 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 void > resize(size_type __n) { resize(__n, value_type()); } > | > ^ >/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/png_canvas.h:443:24: > note: in instantiation of member function 'std::basic_string<unsigned >char>::resize' requested here > 443 | idatChunk.data.resize(height + 4 * canvas.size()); // same as > input, should be enough > | ^ >/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here > 23 | struct _LIBCPP_TEMPLATE_VIS char_traits; > | ^ >In file included from >/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:37: >In file included from /usr/include/c++/v1/fstream:193: >In file included from /usr/include/c++/v1/__locale:24: >/usr/include/c++/v1/string:2538:5: error: implicit instantiation of undefined >template 'std::char_traits<unsigned char>' > 2538 | traits_type::copy( > | ^ >/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here > 23 | struct _LIBCPP_TEMPLATE_VIS char_traits; > | ^ >In file included from >/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:37: >In file included from /usr/include/c++/v1/fstream:193: >In file included from /usr/include/c++/v1/__locale:24: >/usr/include/c++/v1/string:2221:5: error: implicit instantiation of undefined >template 'std::char_traits<unsigned char>' > 2221 | traits_type::assign(__p[__newsz], value_type()); > | ^ >/usr/include/c++/v1/string:2134:5: note: in instantiation of member function >'std::basic_string<unsigned char>::__null_terminate_at' requested here > 2134 | __null_terminate_at(std::__to_address(__get_pointer()), __pos); > | ^ >/usr/include/c++/v1/string:3304:5: note: in instantiation of member function >'std::basic_string<unsigned char>::__erase_to_end' requested here > 3304 | __erase_to_end(__n); > | ^ >/usr/include/c++/v1/string:1303:84: note: in instantiation of member function >'std::basic_string<unsigned char>::resize' requested here > 1303 | _LIBCPP_HIDE_FROM_ABI _LIBCPP_CONSTEXPR_SINCE_CXX20 void > resize(size_type __n) { resize(__n, value_type()); } > | > ^ >/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/png_canvas.h:443:24: > note: in instantiation of member function 'std::basic_string<unsigned >char>::resize' requested here > 443 | idatChunk.data.resize(height + 4 * canvas.size()); // same as > input, should be enough > | ^ >/usr/include/c++/v1/__fwd/string.h:23:29: note: template is declared here > 23 | struct _LIBCPP_TEMPLATE_VIS char_traits; > | ^ >In file included from >/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:41: >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<TFormat>::VALUE)' will return the size of the >pointer, not the array itself [-Wsizeof-pointer-div] > 209 | for (i = 0; i != sizeof(MagicHeader<TFormat>::VALUE) / > sizeof(char); ++i) > | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ^ >/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:565:12: > note: in instantiation of function template specialization >'seqan::guessFormatFromStream<seqan::VirtualStream<char, >seqan::Tag<seqan::Input_>>, seqan::Roi_>' requested here > 565 | return guessFormatFromStream(file.stream, file.format); > | ^ >/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/include/seqan/stream/formatted_file.h:712:14: > note: in instantiation of function template specialization >'seqan::guessFormat<seqan::Tag<seqan::Roi_>, void>' requested here > 712 | if (!guessFormat(file)) > | ^ >/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<seqan::Roi_>, seqan::Tag<seqan::Input_>, void, >seqan::False>' requested here > 739 | return _open(file, fileName, openMode, False()); > | ^ >/wrkdirs/usr/ports/biology/seqan-apps/work/seqan-seqan-v2.4.0/apps/ngs_roi/roi_plot_thumbnails.cpp:432:10: > note: in instantiation of function template specialization >'seqan::open<seqan::Tag<seqan::Roi_>, seqan::Tag<seqan::Input_>, void>' >requested here > 432 | if (!open(roiFileIn, toCString(options.inputFileName))) > | ^ >/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<Nothing, T>::VALUE = NULL; > | ^ >19 warnings and 7 errors generated. >ninja: build stopped: subcommand failed. >*** Error code 1 > >Stop. >make: stopped in /usr/ports/biology/seqan-apps
