[package - 135amd64-quarterly][biology/ncbi-cxx-toolkit] Failed for ncbi-cxx-toolkit-29.0.1 in build
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Date: Sun, 21 Sep 2025 07:06:56 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: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy14/data/135amd64-quarterly/4cc654b03590/logs/ncbi-cxx-toolkit-29.0.1.log
Build URL: https://pkg-status.freebsd.org/beefy14/build.html?mastername=135amd64-quarterly&build=4cc654b03590
Log:
=>> Building biology/ncbi-cxx-toolkit
build started at Sun Sep 21 05:27:38 -00 2025
port directory: /usr/ports/biology/ncbi-cxx-toolkit
package name: ncbi-cxx-toolkit-29.0.1
building for: FreeBSD 135amd64-quarterly-job-12 13.5-RELEASE-p3 FreeBSD 13.5-RELEASE-p3 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 1979 Jul 8 01:01 /usr/ports/biology/ncbi-cxx-toolkit/Makefile
Ports top last git commit: 4cc654b03
Ports top unclean checkout: no
Port dir last git commit: c4772dbff
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.3
Host OSVERSION: 1600000
Jail OSVERSION: 1305000
Job Id: 12
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--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
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#### ####
# 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*
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MAKE_JOBS_NUMBER=3
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GID=0
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kqueues (-k) unlimited
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--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License PD accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> ncbi-cxx-toolkit-29.0.1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.2.2.pkg
[135amd64-quarterly-job-12] Installing pkg-2.2.2...
[135amd64-quarterly-job-12] Extracting pkg-2.2.2: .......... done
===> ncbi-cxx-toolkit-29.0.1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of ncbi-cxx-toolkit-29.0.1
===========================================================================
=======================<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 PD accepted by the user
===> Fetching all distfiles required by ncbi-cxx-toolkit-29.0.1 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License PD accepted by the user
===> Fetching all distfiles required by ncbi-cxx-toolkit-29.0.1 for building
=> SHA256 Checksum OK for ncbi-ncbi-cxx-toolkit-public-release-29.0.1_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 PD accepted by the user
===> Fetching all distfiles required by ncbi-cxx-toolkit-29.0.1 for building
===> Extracting for ncbi-cxx-toolkit-29.0.1
=> SHA256 Checksum OK for ncbi-ncbi-cxx-toolkit-public-release-29.0.1_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 ncbi-cxx-toolkit-29.0.1
===> Applying FreeBSD patches for ncbi-cxx-toolkit-29.0.1 from /usr/ports/biology/ncbi-cxx-toolkit/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> ncbi-cxx-toolkit-29.0.1 depends on package: gmake>=4.4.1 - not found
===> Installing existing package /packages/All/gmake-4.4.1.pkg
[135amd64-quarterly-job-12] Installing gmake-4.4.1...
[135amd64-quarterly-job-12] `-- Installing gettext-runtime-0.23.1...
[135amd64-quarterly-job-12] | `-- Installing indexinfo-0.3.1_1...
[135amd64-quarterly-job-12] | `-- Extracting indexinfo-0.3.1_1: .... done
[135amd64-quarterly-job-12] `-- Extracting gettext-runtime-0.23.1: .......... done
[135amd64-quarterly-job-12] Extracting gmake-4.4.1: .......... done
===> ncbi-cxx-toolkit-29.0.1 depends on package: gmake>=4.4.1 - found
===> Returning to build of ncbi-cxx-toolkit-29.0.1
===> ncbi-cxx-toolkit-29.0.1 depends on file: /usr/local/bin/python3.11 - not found
===> Installing existing package /packages/All/python311-3.11.13.pkg
[135amd64-quarterly-job-12] Installing python311-3.11.13...
[135amd64-quarterly-job-12] `-- Installing libffi-3.5.1...
[135amd64-quarterly-job-12] `-- Extracting libffi-3.5.1: .......... done
[135amd64-quarterly-job-12] `-- Installing mpdecimal-4.0.1...
[135amd64-quarterly-job-12] `-- Extracting mpdecimal-4.0.1: .......... done
[135amd64-quarterly-job-12] `-- Installing readline-8.2.13_2...
[135amd64-quarterly-job-12] `-- Extracting readline-8.2.13_2: .......... done
[135amd64-quarterly-job-12] Extracting python311-3.11.13: .......... done
=====
Message from python311-3.11.13:
--
Note that some standard Python modules are provided as separate ports
as they require additional dependencies. They are available as:
<snip>
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/bin/datatool -oR /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1 \
-opm /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src -m gnomon.asn -M "" -oA \
-oc gnomon -or algo/gnomon -odi -od gnomon.def -oex '' \
-ocvs -pch 'ncbi_pch.hpp' -fd gnomon.dump \
datatool: 2.24.0
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon'
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon'
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon'
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon'
gmake[4]: Nothing to be done for 'export-headers'.
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon'
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon'
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon'
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon'
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon__.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon___.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_engine.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_objmgr.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/score.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_model.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/parse.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/hmm.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_seq.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/asn1.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/chainer.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/id_handler.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/annot.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/select_alignments_alt.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/aligncollapser.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/glb_align.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/variations.cpp.
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon__.cpp -o gnomon__.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon___.cpp -o gnomon___.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_engine.cpp -o gnomon_engine.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_objmgr.cpp -o gnomon_objmgr.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/score.cpp -o score.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_model.cpp -o gnomon_model.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/parse.cpp -o parse.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/hmm.cpp -o hmm.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/gnomon_seq.cpp -o gnomon_seq.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/asn1.cpp -o asn1.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/chainer.cpp -o chainer.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/id_handler.cpp -o id_handler.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/annot.cpp -o annot.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/select_alignments_alt.cpp -o select_alignments_alt.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/aligncollapser.cpp -o aligncollapser.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/glb_align.cpp -o glb_align.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/variations.cpp -o variations.o
/bin/rm -f libxalgognomon.so .libxalgognomon.so.stamp
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -shared -o libxalgognomon.so -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O -fPIC gnomon__.o gnomon___.o gnomon_engine.o gnomon_objmgr.o score.o gnomon_model.o parse.o hmm.o gnomon_seq.o asn1.o chainer.o id_handler.o annot.o select_alignments_alt.o aligncollapser.o glb_align.o variations.o -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/lib -lxalgoseq -lxobjutil -lxobjmgr -lgenome_collection -lseqedit -lseqsplit -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lm -pthread
/bin/sh /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/scripts/common/impl/if_diff.sh /bin/ln -f libxalgognomon.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/lib
/bin/ln -f libxalgognomon.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/lib/libxalgognomon.so
/bin/ln -f .xalgognomon.dep /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/status/.xalgognomon.dep
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon'
/usr/local/bin/gmake -C demo --jobserver-auth=fifo:/tmp/GMfifo18358 all_r || exit 5
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/demo'
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/demo'
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/demo'
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/demo'
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/demo/local_finder.cpp.
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_APP_BUILT_AS=localfinder -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/gnomon/demo/local_finder.cpp -o local_finder.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -Wl,-rpath,/usr/local/lib -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O local_finder.o -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/lib -lxalgognomon -lxalgoseq -lxalnmgr -lxobjread -lvariation -lsubmit -lxlogging -lxobjutil -ltaxon1 -ltables -lxregexp -lxconnect -lxobjmgr -lgenome_collection -lseqedit -lseqsplit -lsubmit -lseqset -lseq -lseqcode -lsequtil -lpub -lmedline -lbiblio -lgeneral -lxser -lxutil -lxncbi -L/usr/local/lib -lpcre -lz -lm -pthread -o localfinder
/bin/sh /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/scripts/common/impl/if_diff.sh /bin/ln -f localfinder /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/bin
/bin/ln -f localfinder /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/bin/localfinder
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/demo'
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/demo'
/usr/local/bin/gmake -C test --jobserver-auth=fifo:/tmp/GMfifo18358 all_r || exit 5
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/test'
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/test'
gmake[5]: *** No rule to make target '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/status/Boost.Test.Included.enabled', needed by 'requirements'. Stop.
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/test'
NOTE: skipping project "test_chainer" due to unmet requirements
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/test'
gmake[5]: *** No rule to make target '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/status/Boost.Test.Included.enabled', needed by 'requirements'. Stop.
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/test'
NOTE: skipping project "test_chainer" due to unmet requirements
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/gnomon/test'
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/usr/local/bin/gmake -C tree --jobserver-auth=fifo:/tmp/GMfifo18358 all_r || exit 5
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree'
/usr/local/bin/gmake -C test --jobserver-auth=fifo:/tmp/GMfifo18358 all_r || exit 5
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree/test'
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree/test'
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree/test'
gmake[5]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree/test'
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/tree/test/test_algo_tree.cpp.
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -DNCBI_APP_BUILT_AS=test_algo_tree -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/tree/test/test_algo_tree.cpp -o test_algo_tree.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -Wl,-rpath,/usr/local/lib -Wl,--enable-new-dtags -Wl,-export-dynamic -pthread -fstack-protector-strong -O test_algo_tree.o -L/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/lib -lxncbi -lm -pthread -o test_algo_tree
/bin/sh /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/scripts/common/impl/if_diff.sh /bin/ln -f test_algo_tree /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/bin
/bin/ln -f test_algo_tree /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/bin/test_algo_tree
gmake[5]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree/test'
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree/test'
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/tree'
/usr/local/bin/gmake -C phy_tree --jobserver-auth=fifo:/tmp/GMfifo18358 all_r || exit 5
gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree'
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree'
gmake[4]: Nothing to be done for 'export-headers'.
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree'
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree'
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree'
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/dist_methods.cpp:36:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbi_limits.hpp:61:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbistl.hpp:230:
In file included from /usr/include/c++/v1/atomic:626:
In file included from /usr/include/c++/v1/compare:147:
In file included from /usr/include/c++/v1/__compare/compare_partial_order_fallback.h:13:
In file included from /usr/include/c++/v1/__compare/partial_order.h:14:
In file included from /usr/include/c++/v1/__compare/weak_order.h:14:
/usr/include/c++/v1/__compare/strong_order.h:91:30: error: no member named 'bool_isnan' in namespace 'std::__math'; did you mean simply 'bool_isnan'?
91 | bool __t_is_nan = __math::isnan(__t);
| ^~~~~~~~
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbifloat.h:82:33: note: 'bool_isnan' declared here
82 | inline ISNAN_CONSTEXPR bool bool_isnan(float x) { return isnan(x); }
| ^
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/dist_methods.cpp:36:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbi_limits.hpp:61:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbistl.hpp:230:
In file included from /usr/include/c++/v1/atomic:626:
In file included from /usr/include/c++/v1/compare:147:
In file included from /usr/include/c++/v1/__compare/compare_partial_order_fallback.h:13:
In file included from /usr/include/c++/v1/__compare/partial_order.h:14:
In file included from /usr/include/c++/v1/__compare/weak_order.h:14:
/usr/include/c++/v1/__compare/strong_order.h:92:30: error: no member named 'bool_isnan' in namespace 'std::__math'; did you mean simply 'bool_isnan'?
92 | bool __u_is_nan = __math::isnan(__u);
| ^~~~~~~~
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbifloat.h:82:33: note: 'bool_isnan' declared here
82 | inline ISNAN_CONSTEXPR bool bool_isnan(float x) { return isnan(x); }
| ^
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/dist_methods.cpp:36:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbi_limits.hpp:61:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbistl.hpp:230:
In file included from /usr/include/c++/v1/atomic:626:
In file included from /usr/include/c++/v1/compare:147:
In file included from /usr/include/c++/v1/__compare/compare_partial_order_fallback.h:13:
In file included from /usr/include/c++/v1/__compare/partial_order.h:14:
/usr/include/c++/v1/__compare/weak_order.h:58:30: error: no member named 'bool_isnan' in namespace 'std::__math'; did you mean simply 'bool_isnan'?
58 | bool __t_is_nan = __math::isnan(__t);
| ^~~~~~~~
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbifloat.h:82:33: note: 'bool_isnan' declared here
82 | inline ISNAN_CONSTEXPR bool bool_isnan(float x) { return isnan(x); }
| ^
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/dist_methods.cpp:36:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbi_limits.hpp:61:
In file included from /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbistl.hpp:230:
In file included from /usr/include/c++/v1/atomic:626:
In file included from /usr/include/c++/v1/compare:147:
In file included from /usr/include/c++/v1/__compare/compare_partial_order_fallback.h:13:
In file included from /usr/include/c++/v1/__compare/partial_order.h:14:
/usr/include/c++/v1/__compare/weak_order.h:59:30: error: no member named 'bool_isnan' in namespace 'std::__math'; did you mean simply 'bool_isnan'?
59 | bool __u_is_nan = __math::isnan(__u);
| ^~~~~~~~
/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include/corelib/ncbifloat.h:82:33: note: 'bool_isnan' declared here
82 | inline ISNAN_CONSTEXPR bool bool_isnan(float x) { return isnan(x); }
| ^
4 errors generated.
gmake[4]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/Makefile.rules:103: dist_methods.o] Error 1
gmake[4]: *** Waiting for unfinished jobs....
lex.newick.cpp:1145:12: warning: function 'yyinput' is not needed and will not be emitted [-Wunneeded-internal-declaration]
1145 | static int yyinput()
| ^~~~~~~
1 warning generated.
newick.tab.cpp:1265:1: warning: unused label 'yyerrlab1' [-Wunused-label]
1265 | yyerrlab1:
| ^~~~~~~~~~
1 warning generated.
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree'
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/bio_tree.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/phy_node.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/dist_methods.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/lex.newick.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/newick.tab.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/tree_to_dist_mat.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/phytree_calc.cpp.
Updating dependency information for /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/bio_tree_format_label.cpp.
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree -D__C99FEATURES__ -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/bio_tree.cpp -o bio_tree.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree -D__C99FEATURES__ -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/phy_node.cpp -o phy_node.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree -D__C99FEATURES__ -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/dist_methods.cpp -o dist_methods.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree -D__C99FEATURES__ -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/lex.newick.cpp -o lex.newick.o
/usr/bin/c++ -stdlib=libc++ -std=gnu++20 -c -Wall -Wno-format-y2k -pthread -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -Wno-deprecated-register -fPIC -DNDEBUG -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_MT -D_REENTRANT -D_THREAD_SAFE -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/inc -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/include -I/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree -D__C99FEATURES__ -DNCBI_BUILD_SESSION_ID=809d4230-96ac-11f0-9aaa-0cc47ad9377e /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/algo/phy_tree/newick.tab.cpp -o newick.tab.o
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree'
FAILED: src/algo/phy_tree/Makefile.xalgophytree.lib
gmake[4]: Entering directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree'
/bin/rm -f libxalgophytree.so libxalgophytree.so .xalgophytree.dep .libxalgophytree.so.stamp
/bin/rm -f /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/lib/libxalgophytree.so /wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/status/.xalgophytree.dep
gmake[4]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree'
gmake[3]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/build-system/Makefile.meta_l:336: all.nonusr] Error 2
gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo/phy_tree'
gmake[2]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/build-system/Makefile.meta_r:41: all_r.real] Error 5
gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build/algo'
gmake[1]: *** [/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/src/build-system/Makefile.meta_r:41: all_r.real] Error 5
gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi-cxx-toolkit-public-release-29.0.1/Clang1917-ReleaseMTDLL64/build'
gmake: *** [Makefile:24: all] Error 2
===> Compilation failed unexpectedly.
Try to set MAKE_JOBS_UNSAFE=yes and rebuild before reporting the failure to
the maintainer.
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/ncbi-cxx-toolkit