[package - main-armv7-default][biology/seqan-apps] Failed for seqan-apps-2.4.0_11 in build
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Date: Wed, 27 Nov 2024 08:20:04 UTC
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--
=======================<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-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
===========================================================================
=======================<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: 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-1.85.0.pkg
[main-armv7-default-job-04] Installing boost-libs-1.85.0...
<snip>
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<char, 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/bam_io/bam_sam_conversion.h:267:14: note: in instantiation of template class 'seqan::FunctorLowcase<char>' requested here
267 | char c = FunctorLowcase<char>()(typeC);
| ^
/usr/include/c++/v1/__functional/unary_function.h:23:29: note: 'unary_function<char, 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/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<seqan::FibreRecord, unsigned int, bool>' is deprecated [-Wdeprecated-declarations]
340 | struct FibreLess: public std::binary_function<FibreRecord, unsigned, bool>
| ^
/usr/include/c++/v1/__functional/binary_function.h:24:29: note: 'binary_function<seqan::FibreRecord, unsigned int, bool>' 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<const char *, 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/formatted_file.h:721:36: note: in implicit copy constructor for 'seqan::Segment<const char *, seqan::PrefixSegment>' first required 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/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<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<seqan::BufferedStream<std::istream, seqan::Tag<seqan::Input_>>, 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::BufferedStream<std::istream, seqan::Tag<seqan::Input_>>, 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<seqan::BufferedStream<std::istream, seqan::Tag<seqan::Input_>>, 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<seqan::BufferedStream<std::istream, seqan::Tag<seqan::Input_>>, 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, seqan::BufferedStream<std::istream, seqan::Tag<seqan::Input_>>, 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:568:20: note: in instantiation of function template specialization 'seqan::open<char, seqan::Tag<seqan::Input_>, std::char_traits<char>, seqan::BufferedStream<std::istream, seqan::Tag<seqan::Input_>>, seqan::TagSelector<seqan::TagList<seqan::Tag<seqan::BgzfFile_>, seqan::TagList<seqan::Tag<seqan::GZFile_>, seqan::TagList<seqan::Tag<seqan::Nothing_>>>>>>' 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<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: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<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/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<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/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<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))
| ^
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