[package - main-amd64-default][biology/py-pysam] Failed for py312-pysam-0.24.0 in stage

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From: <pkg-fallout_at_FreeBSD.org>
Date: Sat, 29 Aug 2026 02:17:54 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/beefy24/data/main-amd64-default/pc15851b5d6fc_s7dc4284615/logs/py312-pysam-0.24.0.log
Build URL:      https://pkg-status.freebsd.org/beefy24/build.html?mastername=main-amd64-default&build=pc15851b5d6fc_s7dc4284615
Log:

=>> Building biology/py-pysam
build started at Sat Aug 29 02:14:47 UTC 2026
port directory: /usr/ports/biology/py-pysam
package name: py312-pysam-0.24.0
building for: FreeBSD main-amd64-default-job-32 16.0-CURRENT FreeBSD 16.0-CURRENT 1600021 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r--  1 root wheel 1191 May  2 01:01 /usr/ports/biology/py-pysam/Makefile
Ports top last git commit: c15851b5d6fc3781f592602edc35589c21774938
Ports top unclean checkout: no
Port dir last git commit: 385ebc8cce3e671ab49a95c7b22486caa52050fa
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.8-2-g2e891d4a
Host OSVERSION: 1600019
Jail OSVERSION: 1600021
Job Id: 32




!!! Jail is newer than host. (Jail: 1600021, Host: 1600019) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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MAKE_ARGS= FLAVOR=py312
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--MAINTAINER--
yuri@FreeBSD.org
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MAKE=/usr/local/bin/gmake PYTHON="/usr/local/bin/python3.12" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py312  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py312  XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py312/.cache  HOME=/wrkdirs/usr/ports/biology/py-pysam/work-py312 TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/py-pysam/work-py312/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/py-pysam/work-py312/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
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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
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# try the next if the size is mismatched though.
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core file size      (512-blocks, -c)  unlimited
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umtx shared locks               (-o)  unlimited
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virtual machines                (-V)  unlimited
--End resource limits--
=======================<phase: check-sanity   >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  License MIT accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   py312-pysam-0.24.0 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-2.8.4.pkg
[main-amd64-default-job-32] Installing pkg-2.8.4...
[main-amd64-default-job-32] Extracting pkg-2.8.4: .......... done
===>   py312-pysam-0.24.0 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of py312-pysam-0.24.0
===========================================================================
=======================<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 MIT accepted by the user
===> Fetching all distfiles required by py312-pysam-0.24.0 for building
===========================================================================
=======================<phase: checksum       >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  License MIT accepted by the user
===> Fetching all distfiles required by py312-pysam-0.24.0 for building
=> SHA256 Checksum OK for pysam-developers-pysam-v0.24.0_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 MIT accepted by the user
===> Fetching all distfiles required by py312-pysam-0.24.0 for building
===>  Extracting for py312-pysam-0.24.0
=> SHA256 Checksum OK for pysam-developers-pysam-v0.24.0_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 py312-pysam-0.24.0
===========================================================================
=======================<phase: build-depends  >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   py312-pysam-0.24.0 depends on package: gmake>=4.4.1 - not found
===>   Installing existing package /packages/All/gmake-4.4.1.pkg
[main-amd64-default-job-32] Installing gmake-4.4.1...
[main-amd64-default-job-32] `-- Installing gettext-runtime-1.0_1...
[main-amd64-default-job-32] |   `-- Installing indexinfo-0.3.1_1...
[main-amd64-default-job-32] |   `-- Extracting indexinfo-0.3.1_1: .... done
[main-amd64-default-job-32] `-- Extracting gettext-runtime-1.0_1: .......... done
[main-amd64-default-job-32] Extracting gmake-4.4.1: .......... done
===>   py312-pysam-0.24.0 depends on package: gmake>=4.4.1 - found
===>   Returning to build of py312-pysam-0.24.0
===>   py312-pysam-0.24.0 depends on package: py312-cython>=3.2.4 - not found
===>   Installing existing package /packages/All/py312-cython-3.2.9.pkg
[main-amd64-default-job-32] Installing py312-cython-3.2.9...
[main-amd64-default-job-32] `-- Installing python312-3.12.14...
[main-amd64-default-job-32] |   `-- Installing expat-2.8.3...
<snip>
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/bam_stat.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_stat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/bamshuf.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bamshuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/bamtk.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bamtk.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
samtools/bamtk.c.pysam.c:317:9: warning: code will never be executed [-Wunreachable-code]
  317 |         print_error_errno(argv[1], "closing standard output failed");
      |         ^~~~~~~~~~~~~~~~~
samtools/bamtk.c.pysam.c:316:9: note: silence by adding parentheses to mark code as explicitly dead
  316 |     if (0) { //if (fclose(samtools_stdout) != 0 && errno != EBADF) {
      |         ^
      |         /* DISABLES CODE */ ( )
1 warning generated.
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/bedcov.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bedcov.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/bedidx.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bedidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/consensus_pileup.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/consensus_pileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/coverage.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/coverage.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/cram_size.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/cram_size.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/cut_target.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/cut_target.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/dict.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/dict.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/faidx.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/faidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/lz4/lz4.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/lz4/lz4.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/padding.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/padding.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/phase.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/phase.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/reference.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/reference.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/reset.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/reset.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/sam_opts.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/sam_opts.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/sam_utils.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/sam_utils.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/sam_view.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/sam_view.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/sample.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/samtools.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/samtools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/stats.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/stats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/stats_isize.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/stats_isize.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c samtools/tmp_file.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/tmp_file.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcsamtools.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/amplicon_stats.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam2depth.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_addrprg.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_ampliconclip.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_aux.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_cat.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_checksum.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_color.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_consensus.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/
samtools/bam_fastq.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_flags.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_import.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_index.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_lpileup.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_markdup.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_mate.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_md.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_plbuf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_plcmd.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_quickcheck.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_reheader.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_rmdup.c.pysam.o bui
ld/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_rmdupse.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_samples.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_sort.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_split.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bam_stat.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bamshuf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bamtk.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bedcov.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/bedidx.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/consensus_pileup.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/coverage.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/cram_size.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-31
2/samtools/cut_target.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/dict.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/faidx.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/lz4/lz4.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/padding.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/phase.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/reference.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/reset.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/sam_opts.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/sam_utils.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/sam_view.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/sample.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/samtools.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-
312/samtools/stats.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/stats_isize.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/samtools/tmp_file.c.pysam.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-312 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcsamtools.cpython-312.so -Wl,-rpath,$ORIGIN
Compiling pysam/libcbcftools.pyx because it changed.
[1/1] Cythonizing pysam/libcbcftools.pyx
building 'pysam.libcbcftools' extension
creating build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/HMM.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/HMM.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/abuf.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/abuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/bam2bcf.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bam2bcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/bam2bcf_edlib.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bam2bcf_edlib.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/bam2bcf_iaux.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/bam2bcf_indel.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/bam_sample.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bam_sample.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/bcftools.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bcftools.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/bin.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/ccall.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/ccall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/cols.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/cols.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/consensus.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/convert.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/convert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/convert.c.pysam.c:553:66: warning: code will never be executed [-Wunreachable-code]
  553 |         default: error("Unexpected type: %d\n", fmt->fmt->type); bcftools_exit(1); break;
      |                                                                  ^~~~~~~~~~~~~
1 warning generated.
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/csq.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/csq.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/dist.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/dist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/edlib.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/edlib.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/em.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/em.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/extsort.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/extsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/filter.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/filter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/filter.c.pysam.c:4152:12: warning: code will never be executed [-Wunreachable-code]
 4152 |     if (0) filter_debug_print(out, NULL, nout);
      |            ^~~~~~~~~~~~~~~~~~
bcftools/filter.c.pysam.c:4152:9: note: silence by adding parentheses to mark code as explicitly dead
 4152 |     if (0) filter_debug_print(out, NULL, nout);
      |         ^
      |         /* DISABLES CODE */ ( )
1 warning generated.
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/gff.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/gff.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/gvcf.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/gvcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/hclust.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/hclust.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/kmin.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/kmin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/main.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/main.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/mcall.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/mcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/mpileup.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/mpileup.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/ploidy.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/ploidy.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/prob1.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/prob1.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/read_consensus.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/read_consensus.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/regidx.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/regidx.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/reheader.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/reheader.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/smpl_ilist.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/smpl_ilist.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/str_finder.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/str_finder.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/tabix.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/tabix.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/tabix.c.pysam.c:58:22: warning: code will never be executed [-Wunreachable-code]
   58 |             detect = 0;
      |                      ^
1 warning generated.
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/tsv2vcf.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/tsv2vcf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfannotate.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfannotate.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfbuf.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfbuf.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfcall.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfcall.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfcnv.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfcnv.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfconcat.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfconcat.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfconvert.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfconvert.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcffilter.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcffilter.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfgtcheck.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfgtcheck.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
bcftools/vcfgtcheck.c.pysam.c:1427:39: warning: code will never be executed [-Wunreachable-code]
 1427 |                 args->min_inter_err = strtod(optarg,&tmp);
      |                                       ^~~~~~
1 warning generated.
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfhead.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfhead.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfindex.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfindex.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfisec.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfisec.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfmerge.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfmerge.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfnorm.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfnorm.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfplugin.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfplugin.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfquery.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfquery.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfroh.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfroh.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfsom.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfsom.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfsort.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfsort.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfstats.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfstats.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcfview.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfview.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/vcmp.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcmp.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c bcftools/version.c.pysam.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/version.c.pysam.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c pysam/libcbcftools.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcbcftools.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/HMM.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/abuf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bam2bcf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bam2bcf_edlib.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bam2bcf_iaux.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bam2bcf_indel.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bam_sample.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bcftools.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/bin.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/ccall.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/cols.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/consensus.c.p
ysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/convert.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/csq.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/dist.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/edlib.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/em.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/extsort.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/filter.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/gff.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/gvcf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/hclust.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/kmin.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/main.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/mcall.c.pysam.o build/temp.f
reebsd-16.0-CURRENT-amd64-cpython-312/bcftools/mpileup.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/ploidy.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/prob1.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/read_consensus.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/regidx.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/reheader.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/smpl_ilist.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/str_finder.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/tabix.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/tsv2vcf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfannotate.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfbuf.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfcall
.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfcnv.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfconcat.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfconvert.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcffilter.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfgtcheck.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfhead.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfindex.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfisec.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfmerge.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfnorm.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfplugin.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfquery.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cp
ython-312/bcftools/vcfroh.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfsom.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfsort.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfstats.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcfview.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/vcmp.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/bcftools/version.c.pysam.o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcbcftools.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-312 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcbcftools.cpython-312.so -Wl,-rpath,$ORIGIN
Compiling pysam/libcutils.pyx because it changed.
[1/1] Cythonizing pysam/libcutils.pyx
building 'pysam.libcutils' extension
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c pysam/libcutils.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcutils.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcutils.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-312 -lcsamtools.cpython-312 -lcbcftools.cpython-312 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcutils.cpython-312.so -Wl,-rpath,$ORIGIN
Compiling pysam/libcalignmentfile.pyx because it changed.
[1/1] Cythonizing pysam/libcalignmentfile.pyx
building 'pysam.libcalignmentfile' extension
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c pysam/libcalignmentfile.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcalignmentfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcalignmentfile.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-312 -lcutils.cpython-312 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcalignmentfile.cpython-312.so -Wl,-rpath,$ORIGIN
Compiling pysam/libcsamfile.pyx because it changed.
[1/1] Cythonizing pysam/libcsamfile.pyx
building 'pysam.libcsamfile' extension
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c pysam/libcsamfile.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcsamfile.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcsamfile.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-312 -lcutils.cpython-312 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcsamfile.cpython-312.so -Wl,-rpath,$ORIGIN
Compiling pysam/libcalignedsegment.pyx because it changed.
[1/1] Cythonizing pysam/libcalignedsegment.pyx
building 'pysam.libcalignedsegment' extension
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c pysam/libcalignedsegment.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcalignedsegment.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcalignedsegment.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-312 -lcutils.cpython-312 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcalignedsegment.cpython-312.so -Wl,-rpath,$ORIGIN
Compiling pysam/libctabix.pyx because it changed.
[1/1] Cythonizing pysam/libctabix.pyx
building 'pysam.libctabix' extension
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c pysam/libctabix.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libctabix.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libctabix.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-312 -lcutils.cpython-312 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libctabix.cpython-312.so -Wl,-rpath,$ORIGIN
Compiling pysam/libcfaidx.pyx because it changed.
[1/1] Cythonizing pysam/libcfaidx.pyx
building 'pysam.libcfaidx' extension
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c pysam/libcfaidx.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcfaidx.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcfaidx.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-312 -lcutils.cpython-312 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcfaidx.cpython-312.so -Wl,-rpath,$ORIGIN
Compiling pysam/libcbcf.pyx because it changed.
[1/1] Cythonizing pysam/libcbcf.pyx
building 'pysam.libcbcf' extension
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c pysam/libcbcf.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcbcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcbcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-312 -lcutils.cpython-312 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcbcf.cpython-312.so -Wl,-rpath,$ORIGIN
Compiling pysam/libcbgzf.pyx because it changed.
[1/1] Cythonizing pysam/libcbgzf.pyx
building 'pysam.libcbgzf' extension
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c pysam/libcbgzf.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcbgzf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcbgzf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-312 -lcutils.cpython-312 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcbgzf.cpytho
n-312.so -Wl,-rpath,$ORIGIN
Compiling pysam/libctabixproxies.pyx because it changed.
[1/1] Cythonizing pysam/libctabixproxies.pyx
building 'pysam.libctabixproxies' extension
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c pysam/libctabixproxies.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libctabixproxies.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libctabixproxies.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -L/usr/local/lib -lz -lhts -lchtslib.cpython-312 -lcutils.cpython-312 -o build
/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libctabixproxies.cpython-312.so -Wl,-rpath,$ORIGIN
warning: pysam/libcvcf.pyx:1084:27: Unreachable code
Compiling pysam/libcvcf.pyx because it changed.
[1/1] Cythonizing pysam/libcvcf.pyx
building 'pysam.libcvcf' extension
cc -fno-strict-overflow -Wsign-compare -Wunreachable-code -DNDEBUG -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -O2 -pipe -fstack-protector-strong -fno-strict-aliasing -fPIC -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -I/usr/local/include -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/samtools/lz4 -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/bcftools -I/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0 -I/usr/local/include/python3.12 -c pysam/libcvcf.c -o build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcvcf.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement
cc -shared -O2 -pipe -fstack-protector-strong -fno-strict-aliasing build/temp.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcvcf.o -L/wrkdirs/usr/ports/biology/py-pysam/work-py312/pysam-0.24.0/pysam -L/usr/local/lib -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -Lbuild/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam -L/usr/local/lib -lz -lhts -lc
htslib.cpython-312 -lcutils.cpython-312 -o build/lib.freebsd-16.0-CURRENT-amd64-cpython-312/pysam/libcvcf.cpython-312.so -Wl,-rpath,$ORIGIN
===========================================================================
=======================<phase: run-depends    >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===>   py312-pysam-0.24.0 depends on executable: bcftools - not found
===>   Installing existing package /packages/All/bcftools-1.24.pkg
[main-amd64-default-job-32] Installing bcftools-1.24...
[main-amd64-default-job-32] `-- Installing bash-5.3.15...
[main-amd64-default-job-32] `-- Extracting bash-5.3.15: .......... done
[main-amd64-default-job-32] `-- Installing gsl-2.8...
[main-amd64-default-job-32] `-- Extracting gsl-2.8: .......... done
[main-amd64-default-job-32] `-- Installing perl5-5.42.3...
[main-amd64-default-job-32] `-- Extracting perl5-5.42.3: .......... done
[main-amd64-default-job-32] Extracting bcftools-1.24: .......... done
===>   py312-pysam-0.24.0 depends on executable: bcftools - found
===>   Returning to build of py312-pysam-0.24.0
===>   py312-pysam-0.24.0 depends on executable: samtools - not found
===>   Installing existing package /packages/All/samtools-1.24.pkg
[main-amd64-default-job-32] Installing samtools-1.24...
[main-amd64-default-job-32] Extracting samtools-1.24: .......... done
===>   py312-pysam-0.24.0 depends on executable: samtools - found
===>   Returning to build of py312-pysam-0.24.0
===>   py312-pysam-0.24.0 depends on package: py312-cython>=3.2.4 - found
===>   py312-pysam-0.24.0 depends on file: /usr/local/bin/python3.12 - found
===========================================================================
=======================<phase: stage          >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===>  Staging for py312-pysam-0.24.0
===>   Generating temporary packing list
ld-elf.so.1: Shared object "libpython3.12.so.1.0" not found, required by "python3.12"
*** Error code 1

Stop.
make: stopped making "stage" in /usr/ports/biology/py-pysam